Abstract
The completion of the Arabidopsis Genome Initiative project in the year 2000 and decoding the whole genome sequence of many plant species thereafter lead to generation of mountains of sequence information. But the function of most of these sequences remains elusive. This grand challenge of defining the function of all the sequence information and genes has been the scope of functional genomics. Functional genomics deals with the function of gene at transcription, at translation and at regulation level. Numerous techniques including microarray, serial analysis of gene expression (SAGE), gene knockout, RNA interference (RNAi), virus-induced gene silencing (VIGS), insertional mutagenesis, Targeting Induced Local Lesions in Genomes (TILLING), EcoTILLING and next-generation sequencing (NGS) technologies have been developed as component of functional genomics to elucidate the function of genes/sequences and can assist in understanding the genetic mechanism of growth, development and physiological responses of plant. Therefore, functional genomics can aid in discovery of alleles/QTLs, development of high-throughput markers, development of high-density linkage map and ultimately assigning the function of genes/QTLs related with yield and associated traits and biotic and abiotic stress tolerance to develop high yielding genotypes to mitigate the challenges of global food security.
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Aarts MG, Dirkse WG, Stiekema WJ, Pereira A (1993) Transposon tagging of a male sterility gene in Arabidopsis. Nature 363:715–717
Abe A, Kosugi S, Yoshida K et al (2012) Genome sequencing reveals agronomically-important loci in rice from mutant populations. Nat Biotechnol 30:174–178
Adams MD, Kerlavage AR, Fleischmann RD, Fuldner RA, Bult CJ, Lee NH, Kirkness EF, Weinstock KG, Gocayne JD, White O et al (1995) Initial assessment of human gene discovery and expression patterns based upon 83-million nucleotides of cDNA sequence. Nature 377:3–7
Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS, Parida SK, Garg R, Tyagi AK, Jain M (2012) Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS One 7:e52443
Aharoni A, Vorst O (2001) DNA microarrays for functional plant genomics. Plant Mol Biol 48:99–118
Aharoni A, Keizer LC, Bouwmeester HJ, Sun Z, Alvarez-Huerta M, Verhoeven HA, Blaas J, van Houwelingen AM, De Vos RC, van der Voet H, Jansen RC, Guis M, Mol J, Davis RW, Schena M, van Tunen AJ, O’Connell AP (2000) Identification of the SAAT gene involved in strawberry flavor biogenesis by using DNA microarrays. Plant Cell 12:647–662
Ahmad R, Parfitt DE, Fass J, Ogundiwin E, Dhingra A, Gradziel TM, Lin D, Joshi NA, Martinez-Garcia PJ, Crisosto CH (2011) Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. BMC Genomics 12:569
Ahmed NU, Park JI, Seo MS, Kumar TS, Lee IH, Park BS, Nou IS (2012) Identification and expression analysis of chitinase genes related to biotic stress resistance in Brassica. Mol Biol Rep 39:3649–3657
Allen AM, Barker GL, Wilkinson P, Burridge A, Winfield M, Coghill J, Uauy C, Griffiths S, Jack P, Berry S, Werner P, Melichar JP, McDougall J, Gwilliam R, Robinson P, Edwards KJ (2013) Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.). Plant Biotechnol J 11:279–295
Alonso JM, Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet 7:524–536
Altshul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Ansorge WJ (2009) Next- generation DNA sequencing techniques. New Biotechnol 25:195–203
Antollin-Llovere M, Parniske M (2007) TILLING: examples of utilization in plant breeding. Lotus Newsl 37:103–104
Asamizu E, Shimoda Y, Kouchi H, Tabata S, Sato S (2008) A positive regulatory role for LjERF1 in the nodulation process is revealed by systematic analysis of nodule-associated transcription factors of Lotus japonicas. Plant Physiol 147:2030–2040
Ashelford K, Eriksson ME, Allen CM, D’Amore R, Johansson M, Gould P, Kay S, Miller AJ, Hall N, Hall A (2011) Full genome resequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biol 12:R28
Asmussen MA, Gilliland LU, Meagher RB (1998) Detection of deleterious genotypes in multigenerational studies. II. Theoretical and experimental dynamics with selfing and selection. Genetics 149:727–737
Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627–631
Auer C, Frederick R (2009) Crop improvement using small RNAs: applications and predictive ecological risk assessments. Trends Biotechnol 27:644–651
Austin RS, Vidaurre D, Stamatiou G, Breit R, Provart NJ, Bonetta D, Zhang J, Fung P, Gong Y, Wang PW, McCourt P, Guttman DS (2011) Next-generation mapping of Arabidopsis genes. Plant J 67:715–725
Axtell MJ, Jan C, Rajagopalan R, Bartel DP (2006) A two hit trigger for siRNA biogenesis in plants. Cell 127:565–577
Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JD, Varshney RK (2012) Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. Am J Bot 99:186–192
Azpiroz-Leehan R, Feldmann KA (1997) T-DNA insertion mutagenesis in A. thaliana: going back and forth. Trends Genet 13:146–152
Babiyachuk E, Fuanghthong M, Montagu MV, Inze D, Kushnir S (1997) Efficient gene tagging in Arabidopsis thaliana using a gene trap approach. Proc Natl Acad Sci U S A 94:12722–12727
Bachlava E, Taylor CA, Tang S, Bowers JE, Mandel JR, Burke JM, Knapp SJ (2012) SNP discovery and development of a high-density genotyping array for sunflower. PLoS One 7:e29814
Bade J, Van Grinsven E, Custers J, Hoekstra S, Ponstein A (2003) T-DNA tagging in Brassica napus as an efficient tool for the isolation of new promoters for selectable marker genes. Plant Mol Biol 52:53–68
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376
Bao JY, Lee S, Chen C, Zhang XO, Zhang Y, Liu S, Clark T, Wang J, Cao ML, Yang HM, Wang SM, Yu J (2005) Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars. Plant Physiol 138:1216–1231
Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 12:304
Barchi L, Lanteri S, Portis E, Valè G, Volante A, Pulcini L, Ciriaci T, Acciarri N, Barbierato V, Toppino L, Rotino GL (2012) A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation. PLoS One 7:e43740
Barkley NA, Wang ML, Gillaspie AG, Dean RE, Pederson GA, Jenkins TM (2008) Discovering and verifying DNA polymorphisms in a mung bean [V. radiata (L.) R. Wilczek] collection by EcoTILLING and sequencing. BMC Res Notes 1:28
Bashir K, Ishimaru Y, Nishizawa NK (2011) Identification and characterization of the major mitochondrial Fe transporter in rice. Plant Signal Behav 6:1591–1593
Bauer P, Lubkowitz M, Tyers R, Nemoto K, Meeley RB, Goff SA, Freeling M (2004) Regulation and a conserved intron sequence of liguleless3/4 knox class-I homeobox genes in grasses. Planta 219:359–368
Baulcombe DC (1999) Fast forward genetics based on virus induced gene silencing. Curr Opin Plant Biol 2:109–113
Baulcombe D (2002) RNA silencing. Curr Biol 12:82–84
Baulcombe D (2004) RNA silencing in plants. Nature 431:356–363
Baum JA, Bogaert T, Clinton W, Heck RG, Feldman P, Ilagan O, Johnson S, PlaetincK G, Munyikwa T, Pleau M, Vaughn T, Robert J (2007) Control of coleopteran insect pests through RNA interference. Nat Biotechnol 25:1322–1326
Beadle GW, Tatum EL (1941) Genetic control of biochemical reactions in Neurospora. Proc Natl Acad Sci U S A 27:499–506
Becker KG (2001) The sharing of cDNA microarray data. Nat Rev Neurosci 2:438–440
Becker A, Lange M (2010) VIGS: genomics goes functional. Trends Plant Sci 15:1–4
Beer SC, Siripoonwiwat W, Donoughue LSO, Souza E, Matthews D, Sorrels ME (1997) Associations between molecular markers and quantitative traits in an oat germplasm pool: can we infer linkages? J Agric Genomics 3:1997
Benlloch R, d’ErfurthI I, Ferrandiz C, Cosson V, Beltron JP, Canas AL, Kondorosi A, Aduen F, Ratet P (2006) Isolation of mtpim proves Tnt1 a useful reverse genetics tool in Medicago truncatula and uncovers new aspects of AP1-like functions in legumes. Plant Physiol 142:972–983
Berger GL, Liu S, Hall MD, Brooks WS, Chao S, Muehlbauer GJ, Baik BK, Steffenson B, Griffey CA (2013) Marker-trait associations in Virginia Tech winter barley identified using genome-wide mapping. Theor Appl Genet 126:693–710
Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363–366
Bertolini E, Verelst W, Horner DS, Gianfranceschi L, Piccolo V, Inzé D, Pè ME, Mica E (2013) Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon. Mol Plant 6:423–443
Bi YP, Liu W, Xia H, Su L, Zhao CZ, Wan SB, Wang XJ (2010) EST sequencing and gene expression profiling of cultivated peanut (Arachis hypogaea L.). Genome 53:832–839
Bird A (2007) Perceptions of epigenetics. Nature 447:396–398
Blanca J, Esteras C, Ziarsolo P, Pérez D, Fernã Ndez-Pedrosa V, Collado C, Rodrã Guez de Pablos R, Ballester A, Roig C, Cañizares J, Picó B (2012) Transcriptome sequencing for SNP discovery across Cucumis melo. BMC Genomics 13:280
Blanco FA, Meschini EP, Zanetti ME, Aguilar OM (2009) A small GTPase of the Rab family is required for root hair formation and preinfection stages of the common bean-Rhizobium symbiotic association. Plant Cell 21:2797–2810
Bonfim K, Faria JC, Nogueira EO, Mendes EA, Aragão FJ (2007) RNAi-mediated resistance to Bean golden mosaic virus in genetically engineered common bean (Phaseolus vulgaris). Mol Plant Microbe Interact 20:717–726
Bouché N, Bouchez D (2001) Arabidopsis gene knockout: phenotypes wanted. Curr Opin Plant Biol 4:111–117
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365–371
Brenchley R, Spannagl M, Pfeifer M, Barker GL, D’Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491:705–710
Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18:630–634
Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177
Brueggeman R, Druka A, Nirmala J, Cavileer T, Drader T, Rostoks N, Mirlohi A, Bennypaul H, Gill U, Kudrna D, Whitelaw C, Kilian A, Han F, Sun Y, Gill K, Steffenson B, Kleinhofs A (2008) The stem rust resistance gene Rpg5 encodes a protein with nucleotide-binding-site, leucine-rich, and protein kinase domains. Proc Natl Acad Sci U S A 105:14970–14975
Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Sanchez Villeda H, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD (2009) The genetic architecture of maize flowering time. Science 325:714–718
Buckler ES, Warburton ML, Rocheford T (2010) Rare genetic variation at Zea mays crtRB1 increases beta-carotene in maize grain. Nat Genet 42:322–327
Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, Aitken KS, Henry RJ (2009) Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol J 7:347–354
Burch-Smith TM, Anderson JC, Martin GB, Dinesh-Kumar SP (2004) Applications and advantages of virus- induced gene silencing for gene function studies in plants. Plant J 39:734–746
Burch-Smith TM, Schiff M, Liu Y, Dinesh-Kumar SP (2006) Efficient virus-induced gene silencing in Arabidopsis. Plant Physiol 142:21–27
Bus A, Hecht J, Huettel B, Reinhardt R, Stich B (2012) High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genomics 13:281
Butrón A, Chen YC, Rottinghaus GE, McMullen MD (2010) Genetic variation at bx1 controls DIMBOA content in maize. Theor Appl Genet 120:721–734
Byzova M, Verduyn C, De Brouwer D, De Block M (2004) Transforming petals into sepaloid organs in Arabidopsis and oilseed rape: implementation of the hairpin RNA-mediated gene silencing technology in an organ-specific manner. Planta 218:379–387
Caldwell DG, McCallum N, Shaw P, Muehlbauer GJ, Marshall DF, Waugh R (2004) A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). Plant J 40:143–150
Campisi L, Yang Y, Yi Y, Heilig E, Herman B, Cassista AJ, Allen DW, Xiang H, Jack T (1999) Generation of enhancer trap lines in Arabidopsis and characterization of expression patterns in the inflorescence. Plant J 17:699–707
Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43:956–963
Chai YM, Jia HF, Li CL, Dong QH, Shen YY (2011) FaPYR1 is involved in strawberry fruit ripening. J Exp Bot 62:5079–5089
Chang Y, Long T, Wu C (2012) Effort and contribution of T-DNA Insertion mutant library for rice functional genomics research in China: review and perspective. J Integr Plant Biol 54:953–966
Chawade A, Sikora P, Brautigam M, Larsson M, Vivekanand V, Nakash AM, Chen T, Olsson O (2010) Development and characterization of an oat TILLING- population and identification of mutations in lignin and beta-glucan biosynthesis genes. BMC Plant Biol 10:86
Chen J, Sun M, Lee S, Zhou G, Rowley JD, Wang SM (2002) Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci U S A 99:12257–12262
Chen J, Zhang D, Yao Q, Zhang J, Dong X, Tian H, Chen J, Zhang W (2011) Feeding-based RNA interference of a trehalose phosphate synthase gene in the brown planthopper, Nilaparvata lugens. Insect Mol Biol 19:777–786
Chen ZC, Yamaji N, Motoyama R, Nagamura Y, Ma JF (2012) Up-regulation of a magnesium transporter gene OsMGT1 is required for conferring aluminum tolerance in rice. Plant Physiol 159:1624–1633
Choi YE, Goodwin SB (2011) Gene encoding a c-type cyclin in Mycosphaerella graminicola is involved in aerial mycelium formation, filamentous growth, hyphal swelling, melanin biosynthesis, stress response, and pathogenicity. Mol Plant Microbe Interact 24:469–477
Chu Y, Corey DR (2012) RNA sequencing: platform selection, experimental design, and data interpretation. Nucleic Acid Ther 22:271–274
Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistue L, Corey A, Filichkina T, Johnson EA, Hayes PM (2011) Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics 12:4
Cockram J, White J, Zuluaga DL, Smith D, Comadran J, Macaulay M, Luo Z, Kearsey MJ, Werner P, Harrap D, Tapsell C, Liu H, Hedley PE, Stein N, Schulte D, Steuernagel B, Marshall DF, Thomas WT, Ramsay L, Mackay I, Balding DJ, AGOUEB Consortium, Waugh R, O’Sullivan DM (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc Natl Acad Sci U S A 107:21611–21616
Cokus SJ, Feng SH, Zhang XY, Chen ZG, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobson SE (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215–219
Colbert T, Till BJ, Tompa R, Reynolds S, Steine MN, Yueng AT, McCullum CM, Comai L, Henikoff S (2001) High throughput screening for induced point mutations. Plant Physiol 126:480–484
Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc B 363:557–572
Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196
Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Henikoff S (2004) Efficient discovery of DNA polymorphisms in natural populations by ecotilling. Plant J 37:778–786
Constantin GD, Krath BN, MacFarlane SA, Nicolaisen M, Johansen IE, Lund OS (2004) Virus-induced gene silencing as a tool for functional genomics in legume species. Plant J 40:622–631
Cook JP, McMullen MD, Holland JB, Tian F, Bradbury P, Ross-Ibarra J, Buckler ES, Flint-Garcia SA (2012) Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiol 158:824–834
Cooper JL, Till BJ, Laport RG, Darlow MC, Jamai A, Kleffner JM, El- Mellouki T, Liu S, Ritchie R, Nielsen N (2008) TILLING to detect induced mutations in soybean. BMC Plant Biol 8:9
Costello JF, Krzywinski M, Marra MA (2009) A first look at entire human methylomes. Nat Biotechnol 27:1130–1132
Courtial B, Feuerbach F, Eberhard S, Rohmer L, Chiapello H, Camilleri C, Lucas H (2001) Tnt1 transposition events are induced by in vitro transformation of Arabidopsis thaliana and transposed copies integrate into genes. Mol Genet Genomics 265:32–42
Cuperus JT, Montgomery TA, Fahlgren N, Burke RT, Townsend T, Sullivan CM, Carrington JC (2010) Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proc Natl Acad Sci U S A 107:466–471
Dahmani-Mardas F, Troadec C, Boualem A, Lévêque S, Alsadon AA, Aldoss AA, Dogimont C, Bendahmane A (2010) Engineering melon plants with improved fruit shelf life using the TILLING approach. PLoS One 5:e15776
Dalmais M, Schmidt J, Le Signor C, Moussy F, Burstin J, Savois V, Aubert G, Brunaud V, Oliviera YD, Guichard C, Thompson R, Bendahmane A (2008) UTILLdb, a Pisum sativum in silico forward and reverse genetics tool. Genome Biol 9:R43
Dalmais M, Antelme S, Ho-Yue-Kuang S, Wang Y, Darracq O, d’Yvoire MB, Cézard L, Légée F, Blondet E, Oria N, Troadec C, Brunaud V, Jouanin L, Höfte H, Bendahmane A, Lapierre C, Sibout R (2013) A TILLING platform for functional genomics in Brachypodium distachyon. PLoS One 8:e65503
Davey JW, Blaxter ML (2011) RADSeq: next generation population genetics. Brief Funct Genomics 9:416–423
Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510
Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML (2012) Special features of RAD Sequencing data: implications for genotyping. Mol Ecol. doi:10.1111/mec.12084
Delteil A, Blein M, Faivre-Rampant O, Guellim A, Estevan J, Hirsch J, Bevitori R, Michel C, Morel JB (2012) Building a mutant resource for the study of disease resistance in rice reveals the pivotal role of several genes involved in defence. Mol Plant Pathol 13:72–82
Deschamps S, Llaca V, May GD (2012a) Genotyping-by-sequencing in plants. Biology 1:460–483
Deschamps S, Nannapaneni K, Zhang Y, Hayes K (2012b) Local assemblies of paired-end reduced representation libraries sequenced with the illumina genome analyzer in maize. Int J Plant Genomics 2012:360598
Distelfeld A, Pearce SP, Avni R, Scherer B, Uauy C, Piston F, Slade A, Zhao R, Dubcovsky J (2012) Divergent functions of orthologous NAC transcription factors in wheat and rice. Plant Mol Biol 78:515–524
Dodig D, Zoric M, Kobiljski B, Savic J, Kandic V, Quarrie S, Barnes J (2012) Genetic and association mapping study of wheat agronomic traits under contrasting water regimes. Int J Mol Sci 13:6167–6188
Dong X, Kim WK, Lim YP, Kim YK, Hur Y (2013) Ogura-CMS in Chinese cabbage (Brassica rapa ssp. pekinensis) causes delayed expression of many nuclear genes. Plant Sci 199–200:7–17
Draffehn AM, Meller S, Li L, Gebhardt C (2010) Natural diversity of potato (Solanum tuberosum) invertases. BMC Plant Biol 10:271
Du HY, Shen YZ, Huang ZJ (2013a) Function of the wheat TaSIP gene in enhancing drought and salt tolerance in transgenic Arabidopsis and rice. Plant Mol Biol 81:417–429
Du J, Tian Z, Liu J, Vleeshouwers VG, Shi X, Xie C (2013b) Functional analysis of potato genes involved in quantitative resistance to Phytophthora infestans. Mol Biol Rep 40:957–967
Duan J, Xia C, Zhao G, Jia J, Kong X (2012) Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. BMC Genomics 13:392
Dugas DV, Monaco MK, Olsen A, Klein RR, Kumari S, Ware D, Klein PE (2011) Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. BMC Genomics 12:514
Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM (1999) Expression profiling using cDNA microarrays. Nat Genet 21:10–14
Dunoyer P, Voinnet O (2008) Mixing and matching: the essence of plant systemic silencing? Trends Genet 24:151–154
Eamens A, Wang MB, Smith NA, Waterhouse PM (2008) RNA silencing in plants: yesterday, today, and tomorrow. Plant Physiol 147:456–468
Eckardt NA (2009) Deep sequencing maps the maize epigenomic landscape. Plant Cell 21:1024–1026
Eckert AJ, Pande B, Ersoz ES, Wright MH, Rashbrook VK, Nicolet CM, Neale DB (2009) High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genet Genomes 5:225–234
Edwards D, Batley J, Snowdon RJ (2013) Accessing complex crop genomes with next-generation sequencing. Theor Appl Genet 126:1–11
Egan AN, Schlueter J, Spooner DM (2012) Applications of next-generation sequencing in plant biology. Am J Bot 99:175–185
Elling AA, Deng XW (2009) Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize. Plant Signal Behav 4:760–762
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379
Escobar MA, Civerolo EL, Summerfelt KR, Dandeker AM (2001) RNAi-mediated oncogene silencing confers resistance to crown gall tumorigenesis. Proc Natl Acad Sci U S A 98:13437–13442
Esfandiari E, Jin Z, Abdeen A, Griffiths JS, Western TL, Haughn GW (2013) Identification and analysis of an outer-seed-coat-specific promoter from Arabidopsis thaliana. Plant Mol Biol 81:93–104
Falcone Ferreyra ML, Pezza A, Biarc J, Burlingame AL, Casati P (2010) Plant L10 ribosomal proteins have different roles during development and translation under ultraviolet-B stress. Plant Physiol 153:1878–1894
Fekih R, Takagi H, Tamiru M, Abe A, Natsume S, Yaegashi H, Sharma S, Sharma S, Kanzaki H, Matsumura H, Saitoh H, Mitsuoka C, Utsushi H, Uemura A, Kanzaki E, Kosugi S, Yoshida K, Cano L, Kamoun S, Terauchi R (2013) MutMap+: genetic mapping and mutant identification without crossing in rice. PLoS One 8(7):e68529
Feldmann KA (1991) T-DNA insertion mutagenesis in Arabidopsis: mutational spectrum. Plant J 1:71–82
Feng H, Fan X, Fan X, Liu X, Miller AJ, Xu G (2011) Multiple roles of nitrate transport accessory protein NAR2 in plants. Plant Signal Behav 6:1286–1289
Fernandez-Moreno JP, Orzaez D, Granell A (2013) VIGS: a tool to study fruit development in Solanum lycopersicum. Methods Mol Biol 975:183–196
Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of posttranscriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9:102–114
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811
Friebe B, Zhang P, Nasuda S, Gill BS (2003) Characterization of a knock-out mutation at the Gc2 locus in wheat. Chromosoma 111:509–517
Fu SX, Cheng H, Qi C (2009) Microarray analysis of gene expression in seeds of Brassica napus planted in Nanjing (altitude: 8.9 m), Xining (altitude: 2261.2 m) and Lhasa (altitude: 3658 m) with different oil content. Mol Biol Rep 36:2375–2386
Fuchs U, Damm-Welk C, Borkhardt A (2004) Silencing of disease-related genes by small interfering RNAs. Curr Mol Med 4:507–517
Fukuoka H, Yamaguchi H, Nunome T, Negoro S, Miyatake K, Ohyama A (2010) Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant (Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato. Gene 450:76–84
Fusari CM, Di Rienzo JA, Troglia C, Nishinakamasu V, Moreno MV, Maringolo C, Quiroz F, Alvarez D, Escande A, Hopp E, Heinz R, Lia VV, Paniego NB (2012) Association mapping in sunflower for sclerotinia head rot resistance. BMC Plant Biol 12:93
Galvão VC, Nordström KJ, Lanz C, Sulz P, Mathieu J, Posé D, Schmid M, Weigel D, Schneeberger K (2012) Synteny-based mapping-by-sequencing enabled by targeted enrichment. Plant J 71:517–526
Gao X, Shan L (2013) Functional genomic analysis of cotton genes with agrobacterium-mediated virus-induced gene silencing. Methods Mol Biol 975:157–165
Gao X, Starr J, Göbel C, Engelberth J, Feussner I, Tumlinson J, Kolomiets M (2008) Maize 9-lipoxygenase ZmLOX3 controls development, root-specific expression of defense genes, and resistance to root-knot nematodes. Mol Plant Microbe Interact 21:98–109
Gao X, Wheeler T, Li Z, Kenerley CM, He P, Shan L (2011) Silencing GhNDR1 and GhMKK2 compromises cotton resistance to Verticillium wilt. Plant J 66:293–305
Gao Q, Yue G, Li W, Wang J, Xu J, Yin Y (2012) Recent progress using high-through put sequencing technologies in plant molecular breeding. J Integr Plant Biol 54:215–227
Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E, Câmara F, Cozzuto L, Lowy E, Alioto T, Capella-Gutiérrez S, Blanca J, Cañizares J, Ziarsolo P, Gonzalez-Ibeas D, Rodríguez-Moreno L, Droege M, Du L, Alvarez-Tejado M, Lorente-Galdos B, Melé M, Yang L, Weng Y, Navarro A, Marques-Bonet T, Aranda MA, Nuez F, Picó B, Gabaldón T, Roma G, Guigó R, Casacuberta JM, Arús P, Puigdomènech P (2012) The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A 109:11872–11877
Gaur R, Azam S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S (2012) High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res 19:357–373
Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I, Jones SJ, Cronk QC, Douglas CJ (2011) SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour 1:81–92
Gheysen G, Vanholme B (2007) RNAi from plants to nematodes. Trends Biotechnol 25:89–92
Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94–108
Gibson G, Muse SV (2009) A primer of genome science, 3rd edn. Sinauer Associates, Sunderland. ISBN ISBN-13: 978-0878932368
Gierl A, Saedler H (1992) Plant transposable elements and gene tagging. Plant Mol Biol 19:39–49
Gilchrist JE, Haughn WG (2005) TILLING without a plough: a new method with applications for reverse genetics. Curr Opin Plant Biol 8:211–215
Gilchrist E, Haughn G (2010) Reverse genetics techniques: engineering loss and gain of gene function in plants. Brief Funct Genomics 9:103–110
Gilchrist EJ, Haughn GW, Ying CC, Otto SP, Zhuang J, Cheung D, Hamberger B, Aboutorabi F, Kalynyak T, Johnson L, Bohlmann J, Ellis BE, Douglas CJ, Cronk QC (2006) Use of EcoTILLING as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol Ecol 15:1367–1378
Gilliland LU, McKinney EC, Asmussen MA, Meagher RB (1998) Detection of deleterious genotypes in multigenerational studies. I. Disruptions in individual Arabidopsis actin genes. Genetics 149:717–725
Goddard ME, Hayes BJ (2007) Genomic selection. J Anim Breed Genet 124:323–330
Golas TM, van de Geest H, Gros J, Sikkema A, D’Agostino N, Nap JP, Mariani C, Allefs JJ, Rieu I (2013) Comparative next-generation mapping of the Phytophthora infestans resistance gene Rpi-dlc2 in a European accession of Solanum dulcamara. Theor Appl Genet 126:59–68
Gore MA, Chia J-M, Elshire RJ, Sun Q, Ersoz ES et al (2009) A first-generation haplotype map of maize. Science 326:1115–1117
Gottwald S, Bauer P, Komatsuda T, Lundqvist U, Stein N (2009) TILLING in the two-rowed barley cultivar ‘Barke’ reveals preferred sites of functional diversity in the gene HvHox1. BMC Res Notes 2:258
Gowda M, Jantasuriyarat C, Dean R, Wang G-L (2004) Robust-LongSAGE (RL-SAGE) for both gene discovery and transcriptome analysis. Plant Physiol 134:890–897
Gowda M, Venu RC, Jia Y, Stahlberg E, Pampanwar V, Soderlund C, Wang GL (2007) Use of robust-long serial analysis of gene expression to identify novel fungal and plant genes involved in host-pathogen interactions. Methods Mol Biol 354:131–144
Greco R, Ouwerkerk PBF, Sallaud C, Kohli A, Colombo L, Puigdomènech P, Guiderdoni E, Christou P, Hoge JHC, Pereira A (2001) Transposon insertional mutagenesis in rice. Plant Physiol 125:1175–1177
Green RM, Tobin EM (1999) Loss of the circadian clock-associated protein 1 in Arabidopsis results in altered clock-regulated gene expression. Proc Natl Acad Sci U S A 96:4176–4179
Groover A, Fontan RJ, Dupper GMAC, Martienssen R, Strauss S, Milan R (2004) Gene and enhancer trap tagging of vascular- expressed genes in poplar trees. Plant Physiol 134:1742–1751
Guan JC, Koch KE, Suzuki M, Wu S, Latshaw S, Petruff T, Goulet C, Klee HJ, McCarty DR (2012a) Diverse roles of strigolactone signaling in maize architecture and the uncoupling of a branching-specific subnetwork. Plant Physiol 160:1303–1317
Guan M, Li X, Guan C (2012b) Microarray analysis of differentially expressed genes between Brassica napus strains with high- and low-oleic acid contents. Plant Cell Rep 31:929–943
Hackenberg M, Huang PJ, Huang CY, Shi BJ, Gustafson P, Langridge P (2013) A comprehensive expression profile of MicroRNAs and other classes of non-coding small RNAs in Barley under phosphorus-deficient and -sufficient conditions. DNA Res 20:109–125
Hamer L, DeZwaan TM, Montenegro-Chamorro MV, Frank SA, Hamer JE (2001) Recent advances in large-scale transposon mutagenesis. Curr Opin Chem Biol 5:67–73
Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, Van Deynze A, De Jong WS, Douches DS, Buell CR (2011) Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics 12:302
Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293–296
Han B, Huang X (2013) Sequencing-based genome-wide association study in rice. Curr Opin Plant Biol 16:133–138
Han Y, Kang Y, Torres-Jerez I, Cheung F, Town CD, Zhao PX, Udvardi MK, Monteros MJ (2011) Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis. BMC Genomics 12:1–11
Hannon GJ (2002) RNA interference. Nature 418:244–251
Hannoufa A, Negruk V, Eisner G, Lemieux B (1996) The CER3 gene of Arabidopsis thaliana is expressed in leaves, stems, roots, flowers and apical meristems. Plant J 10:459–467
Harmer SL, Kay SA (2000) Microarrays: determining the balance of cellular transcription. Plant Cell 12:613–615
Harmer SL, Hogenesch LB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290:2110–2113
Hayes F (2003) Transposon- based strategies for microbial functional genomics and proteomics. Annu Rev Genet 37:1–7
Hayward A, Vighnesh G, Delay C, Samian MR, Manoli S, Stiller J, McKenzie M, Edwards D, Batley J (2012) Second-generation sequencing for gene discovery in the Brassicaceae. Plant Biotechnol J 10:750–759
Hazen SP, Pathan MS, Sanchez A, Baxter I, Dunn M, Estes B, Chang HS, Zhu T, Kreps JA, Nguyen HT (2005) Expression profiling of rice segregating for drought tolerance QTLs using rice genome array. Funct Integr Genomics 5:104–116
He Z, Zhai W, Wen H, Tang T, Wang Y, Lu X, Greenberg AJ, Hudson RR, Wu CI, Shi S (2011) Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet 7:e1002100
Hebert CG, James JV, Bentley WE (2008) Beyond silencing – engineering applications of RNA interference and antisense technology for altering cellular phenotypes. Curr Opin Biotechnol 19:500–505
Hegarty M, Yadav R, Lee M, Armstead I, Sanderson R, Scollan N, Powell W, Skøt L (2013) Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne (L.)). Plant Biotechnol J 11:572–581
Hein I, Barciszewska-Pacak M, Hrubikova K, Williamson S, Dinesen M, Soenderby IE, Sundar S, Jarmolowski A, Shirasu K, Lacomme C (2005) Virus-induced gene silencing-based functional characterization of genes associated with powdery mildew resistance in barley. Plant Physiol 138:2155–2164
Henikoff S, Comai L (2003) Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol 54:375–401
Hieter P, Boguski M (1997) Functional genomics: it’s all how you read it. Science 278:601–602
Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, Bhanuprakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L, Gaur PM, Kavikishor PB, Shah T, Srinivasan R, Lohse M, Xiao Y, Town CD, Cook DR, May GD, Varshney RK (2011) Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol J 9:922–931
Hofer J, Turner L, Moreau C, Ambrose M, Isaac P, Butcher S, Weller J, Dupin A, Dalmais M, Le Signor C, Bendahmane A, Ellis N (2009) Tendril-less regulates tendril formation in pea leaves. Plant Cell 21:420–428
Holzberg S, Brosio P, Gross C, Pogue GP (2002) Barley stripe mosaic virus-induced gene silencing in a monocot plant. Plant J 30:315–327
Hou H, Li J, Gao M, Singer SD, Wang H, Mao L, Fei Z, Wang X (2013) Genomic organization, phylogenetic comparison and differential expression of the SBP-box family genes in grape. PLoS One 8:e59358
Howarth JR, Parmar S, Barraclough PB, Hawkesford MJ (2009) A sulphur deficiency-induced gene, sdi1, involved in the utilization of stored sulphate pools under sulphur-limiting conditions has potential as a diagnostic indicator of sulphur nutritional status. Plant Biotechnol J 7:200–209
Hribova E, Neumann P, Macas J, Dolezel J (2009) Analysis of genome structure and organization in banana (Musa acuminata) using 454 sequencing. Plant and Animal Genomes XVII, San Diego, CA
Hsing YI, Chern CG, Fan MJ, Lu PC, Chen KT, Lo SF, Sun PK, Ho SL, Lee KW, Wang YC, Huang WL, Ko SS, Chen S, Chen JL, Chung CI, Lin YC, Hour AL, Wang YW, Chang YC, Tsai MW, Lin YS, Chen YC, Yen HM, Li CP, Wey CK, Tseng CS, Lai MH, Huang SC, Chen LJ, Yu SM (2007) A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol Biol 63:351–364
Hu Z, Hua W, Huang S, Yang H, Zhan G, Wang X, Liu G, Wang H (2012) Discovery of pod shatter-resistant associated SNPs by deep sequencing of a representative library followed by bulk segregant analysis in rapeseed. PLoS One 7:e34253
Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19(6):1068–1076
Huang CF, Yamaji N, Chen Z, Ma JF (2012a) A tonoplast-localized half-size ABC transporter is required for internal detoxification of aluminum in rice. Plant J 69:857–867
Huang CF, Yamaji N, Ono K, Ma JF (2012b) A leucine-rich repeat receptor-like kinase gene is involved in the specification of outer cell layers in rice roots. Plant J 69:565–576
Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B (2012c) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497
Huang X, Lu T, Han B (2013a) Resequencing rice genomes: an emerging new era of rice genomics. Trends Genet 29:225–232
Huang D, Koh C, Feurtado JA, Tsang EW, Cutler AJ (2013b) MicroRNAs and their putative targets in Brassica napus seed maturation. BMC Genomics 14:140
Huang J, Zhang J, Li W, Hu W, Duan L, Feng Y, Qiu F, Yue B (2013c) Genome wide analysis of ten chilling tolerance indices at the germination and seedling stages in maize. J Integr Plant Biol. doi:10.1111/jipb.12051
Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44:808–811
Hyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor-Corrales M, Cregan PB (2010a) High-throughput SNP discovery and assay development in common bean. BMC Genomics 11:475
Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB (2010b) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11:38
Iantcheva A, Vassileva V, Ugrinova M, Vlahova M (2009) Development of functional genomic platform for model legumes Medicago truncatula in Bulgaria. Biotechnol Biotechnol. Eq 23:1440–1443
Igarashi K, Kazama T, Motomura K, Toriyama K (2013) Whole genomic sequencing of RT98 mitochondria derived from Oryza rufipogon and northern blot analysis to uncover a cytoplasmic male sterility-associated gene. Plant Cell Physiol 54:237–243
Iida S, Terada R (2004) A tale of two integrations, transgene and T-DNA: gene targeting by homologous recombination in rice. Curr Opin Biotechnol 15:132–138
Impey S, McCorkle SR, Cha-Molstad H, Dwyer JM, Yochum GS, Boss JM, McWeeney S, Dunn JJ, Mandel G, Goodman RH (2004) Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell 119:1041–1054
Ingvarsson PK, Street NR (2011) Association genetics of complex traits in plants. New Phytol 189:909–922
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800
Irian S, Xu P, Dai X, Zhao PX, Roossinck MJ (2007) Regulation of a virus-induced lethal disease in tomato revealed by LongSAGE analysis. Mol Plant Microbe Interact 20:1477–1488
Ishii M, Hashimoto S, Tsutsumi S, Wada Y, Matsushima K, Kodama T, Aburatani H (2000) Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis. Genomics 68:136–143
Ito T, Seki M, Hayashida N, Shibata D, Shinozaki K (1999) Regional insertional mutagenesis of genes on Arabidopsis thaliana chromosome V using the Ac/Ds transposon in combination with a cDNA scanning method. Plant J 17:433–444
Jacquier A (2009) The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 10:833–844
Jain M, Misra G, Patel RK, Priya P, Jhanwar S, Khan AW, Shah N, Singh VK, Garg R, Jeena G, Yadav M, Kant C, Sharma P, Yadav G, Bhatia S, Tyagi AK, Chattopadhyay D (2013) A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J. doi:10.1111/tpj.12173
Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177
Jeon JS, Lee S, Jung KH, Jun SH, Jeong DH, Lee J, Kim C, Jang S, Yang K, Nam J, An J, Han MJ, Sung RJ, Choi HS, Yu JH, Choi JH, Cho SY, Cha SS, Kim SL, An G (2000) T-DNA insertional mutagenesis for functional genomics in rice. Plant J 22:561–570
Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK, Jain M (2012) Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol J 10:690–702
Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X, Jing R, Zhang C, Ma Y, Gao L, Gao C, Spannagl M, Mayer KF, Li D, Pan S, Zheng F, Hu Q, Xia X, Li J, Liang Q, Chen J, Wicker T, Gou C, Kuang H, He G, Luo Y, Keller B, Xia Q, Lu P, Wang J, Zou H, Zhang R, Xu J, Gao J, Middleton C, Quan Z, Liu G, Wang J, International Wheat Genome Sequencing Consortium, Yang H, Liu X, He Z, Mao L, Wang J (2013a) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95
Jia G, Huang X, Zhi H, Zhao Y, Zhao Q, Li W, Chai Y, Yang L, Liu K, Lu H, Zhu C, Lu Y, Zhou C, Fan D, Weng Q, Guo Y, Huang T, Zhang L, Lu T, Feng Q, Hao H, Liu H, Lu P, Zhang N, Li Y, Guo E, Wang S, Wang S, Liu J, Zhang W, Chen G, Zhang B, Li W, Wang Y, Li H, Zhao B, Li J, Diao X, Han B (2013b) A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet. doi:10.1038/ng.2673
Jiang Y, Deyholos MK (2010) Transcriptome analysis of secondary-wall-enriched seed coat tissues of canola (Brassica napus L.). Plant Cell Rep 29:327–342
Jiang J, Jiang J, Qiu L, Miao Y, Yao L, Cao J (2013) Identification of gene expression profile during fertilization in Brassica campestris subsp. chinensis. Genome 56:39–48
Jiménez-López S, Mancera-Martínez E, Donayre-Torres A, Rangel C, Uribe L, March S, Jiménez-Sánchez G, Sánchez de Jiménez E (2011) Expression profile of maize (Zea mays L.) embryonic axes during germination: translational regulation of ribosomal protein mRNAs. Plant Cell Physiol 52:1719–1733
Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ (2006) Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res 16:1505–1516
Jorgensen R, Snyder C, Jones JG (1987) T-DNA is organized predominantly in inverted repeat structures in plants transformed with Agrobacterium tumefaciens C58 derivatives. Mol Gen Genet 3:1263–1275
Jun TH, Michel AP, Mian MA (2011) Development of soybean aphid genomic SSR markers using next generation sequencing. Genome 54:360–367
Kadaru SB, Yadav AS, Fjellstrom RG, Oard JH (2006) Alternative EcoTILLING protocol for rapid, cost-effective single-nucleotide polymorphism discovery and genotyping in rice (Oryza sativa L.). Plant Mol Biol Rep 24:3–22
Kamath RS, Martinez CM, Zipperlen P, Fraser AG, Ahringer J (2001) Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans. Genome Biol 21:2.1–2.10
Kantar M, Akpınar BA, Valárik M, Lucas SJ, Doležel J, Hernández P, Budak H (2012) Subgenomic analysis of microRNAs in polyploid wheat. Funct Integr Genomics 12:465–479
Kaur S, Cogan NO, Pembleton LW, Shinozuka M, Savin KW, Materne M, Forster JW (2011) Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics 12:265
Kaur S, Pembleton LW, Cogan NO, Savin KW, Leonforte T, Paull J, Materne M, Forster JW (2012) Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 13:104
Kawaura K, Mochida K, Yamazaki Y, Ogihara Y (2006) Transcriptome analysis of salinity stress responses in common wheat using 22k oligo-DNA microarray. Funct Integr Genomics 6:132–142
Kim SI, Tai TH (2013) Identification of SNPs in closely related Temperate Japonica rice cultivars using restriction enzyme-phased sequencing. PLoS One 8:e60176
Kim MY, Lee S, Van K, Kim TH, Jeong SC, Choi IY, Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim KD, Liu WX, Chaisan T, Kang YJ, Lee YH, Kim KH, Moon JK, Schmutz J, Jackson SA, Bhak J, Lee SH (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. And Zucc.) genome. Proc Natl Acad Sci U S A 107:22032–22037
Kocábek T, Repková J, Dudová M, Hoyerová K, Vrba L (2006) Isolation and characterization of a novel semi-lethal Arabidopsis thaliana mutant of gene for pentatricopeptide (PPR) repeat-containing protein. Genetica 128:395–407
Koncz C, Mayerhofer R, Koncz-Kalman Z, Nawrath C, Reiss B, Redei GP, Schell J (1990) Isolation of a gene encoding a novel chloroplast protein by T-DNA tagging in Arabidopsis thaliana. EMBO J 9:1337–1346
Kong X, Lv W, Zhang D, Jiang S, Zhang S, Li D (2013) Genome-wide identification and analysis of expression profiles of maize mitogen-activated protein kinase kinase kinase. PLoS One 8:e57714
Koornneef M, Dellbaert LW, van der Veen JH (1982) EMS- and radiation-induced mutation frequencies at individual loci in Arabidopsis thaliana (L) Heynh. Mutat Res 93:109–123
Kou Y, Chang Y, Li X, Xiao J, Wang S (2012) The rice RAD51C gene is required for the meiosis of both female and male gametocytes and the DNA repair of somatic cells. J Exp Bot 63:5323–5335
Kraakman AT, Niks RE, Van den Berg PM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446
Krusell L, Sato N, Fukuhara I, Koch BE, Grossmann C, Okamoto S, Oka-Kira E, Otsubo Y, Aubert G, Nakagawa T, Sato S, Tabata S, Duc G, Parniske M, Wang TL, Kawaguchi M, Stougaard J (2011) The Clavata2 genes of pea and Lotus japonicus affect autoregulation of nodulation. Plant J 65:861–871
Krysan PJ, Young JC, Sussman MR (1999) T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11:2283–2290
Kulwal P, Ishikawa G, Benscher D, Feng Z, Yu LX, Jadhav A, Mehetre S, Sorrells ME (2012) Association mapping for pre-harvest sprouting resistance in white winter wheat. Theor Appl Genet 125:793–805
Kumagai MH, Donson J, Della-Cioppa G, Harvey D, Hanley K, Grill LK (1995) Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc Natl Acad Sci U S A 92:1679–1683
Kumar S, Banks TW, Cloutier S (2012) SNP discovery through next-generation sequencing and its applications. Int J Plant Genomics 2012:831460
Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, Oropeza-Rosas MA, Zwonitzer JC, Kresovich S, McMullen MD, Ware D, Balint-Kurti PJ, Holland JB (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43:163–168
Kusaba M (2004) RNA interference in plants. Curr Opin Biotechnol 15:139–143
La H, Ding B, Mishra GP, Zhou B, Yang H, BellizziMdel R, Chen S, Meyers BC, Peng Z, Zhu JK, Wang GL (2011) A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice. Proc Natl Acad Sci U S A 108:15498–15503
Lababidi S, Mejlhede N, Rasmussen SK, Backes G, Al-Said W, Bau M, Jahoor A (2009) Identification of barley mutants in the cultivar ‘Lux’ at the Dhn loci through TILLING. Plant Breed 128:332–336
Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS, Wang J (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1030
Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden MJ, Forrest KL, Fleury D, Baumann U, Zander M, Mason AS, Batley J, Edwards D (2012) Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnol J 10:743–749
Laird PW (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11:191–203
Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42:1053–1059
Larsson SJ, Lipka AE, Buckler ES (2013) Lessons from Dwarf8 on the strengths and weaknesses of structured association mapping. PLoS Genet 9:e1003246
Le Gouis J, Bordes J, Ravel C, Heumez E, Faure S, Praud S, Galic N, Remoué C, Balfourier F, Allard V, Rousset M (2012) Genome-wide association analysis to identify chromosomal regions determining components of earliness in wheat. Theor Appl Genet 124:597–611
Le Signor C, Dalamis M, Brunaud V, Thompson R, Bendahmane A (2009) High throughput identification of Pisum sativum mutant lines by TILLING: a tool for crop improvement using either forward or reverse genetic approaches. Grain Legumes 52:18–19
Ledger SE, Janssen BJ, Karunairetnam S, Wang T, Snowden KC (2010) Modified CAROTENOID CLEAVAGE DIOXYGENASE8 expression correlates with altered branching in kiwifruit (Actinidia chinensis). New Phytol 188:803–813
Lee JY, Lee DH (2003) Use of serial analysis of gene expression technology to reveal changes in gene expression in Arabidopsis pollen undergoing cold stress. Plant Physiol 132:517–529
Lee S, Kim J, Son SJ, Nam J, Jeong HD, Lee K, Jang S, Yoo J, Lee J, Lee YD, Kang GH, An G (2003) Systemic reverse genetics screening of T- DNA tagged genes in rice for functional genomics analyses: MADS- box genes as a test case. Plant Cell Physiol 12:1403–1411
Lee S, Jung KH, An G, Chung YY (2004) Isolation and characterization of a rice cysteine protease gene, OsCP1, using T-DNA gene-trap system. Plant Mol Biol 54:755–765
Lee SC, Lim MH, Yu JG, Park BS, Yang TJ (2012) Genome-wide characterization of the CBF/DREB1 gene family in Brassica rapa. Plant Physiol Biochem 61:142–152
Letta T, Maccaferri M, Badebo A, Ammar K, Ricci A, Crossa J, Tuberosa R (2013) Searching for novel sources of field resistance to Ug99 and Ethiopian stem rust races in durum wheat via association mapping. Theor Appl Genet 126:1237–1256
Lewin B (2004) Genes VII. Pearson Prentice Hall, Upper Saddle River
Li X, Lassner M, Zhang Y (2002) Deleteagene: a fast neutron deletion mutagenesis-based gene knockout system for plants. Comp Funct Genomics 3:158–160
Li L, Paulo MJ, Strahwald J, Lübeck J, Hofferbert HR, Tacke E, Junghans H, Wunder J, Draffehn A, van Eeuwijk F, Gebhardt C (2008) Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield. Theor Appl Genet 116:1167–1181
Li L, Zhu B, Fu D, Luo Y (2011a) RIN transcription factor plays an important role in ethylene biosynthesis of tomato fruit ripening. J Sci Food Agric 91:2308–2314
Li W, Zhang J, Mou Y, Geng J, McVetty PB, Hu S, Li G (2011b) Integration of Solexa sequences on an ultradense genetic map in Brassica rapa L. BMC Genomics 12:249
Li W, Xu YP, Zhang ZX, Cao WY, Li F, Zhou X, Chen GY, Cai XZ (2012a) Identification of genes required for nonhost resistance to Xanthomonas oryzae pv. oryzae reveals novel signaling components. PLoS One 7:e42796
Li D, Deng Z, Qin B, Liu X, Men Z (2012b) De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13:192
Li L, Tacke E, Hofferbert HR, Lübeck J, Strahwald J, Draffehn AM, Walkemeier B, Gebhardt C (2013) Validation of candidate gene markers for marker-assisted selection of potato cultivars with improved tuber quality. Theor Appl Genet 126:1039–1052
Lian X, Wang S, Zhang J, Feng Q, Zhang L, Fan D, Li X, Yuan D, Han B, Zhang Q (2006) Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray. Plant Mol Biol 60:617–631
Liang S, Lu Y, Jelinek J, Estecio M, Li H, Issa JP (2009) Analysis of epigenetic modifications by next generation sequencing. Conf Proc IEEE Eng Med Biol Soc 2009:6730
Limpens E, Ramos J, Franken C, Raz V, Compaan B, Franssen H, Besseling T, Geurts R (2004) RNA interference in Agrobacterium rhizogenes transformed roots of Arabidopsis and Medicago truncatula. J Exp Bot 55:983–992
Limpens E, Mirabella R, Fedorova E, Franken C, Franssen H, Bisseling T, Geurts R (2005) Formation of organelle-like N2-fixing symbiosomes in legume root nodules is controlled by DMI2. Proc Natl Acad Sci U S A 104:10375–10380
Lindbo JA, Fitzmaurice WP, della-Cioppa G (2001) Virus mediated reprogramming of gene expression in plants. Curr Opin Plant Biol 4:181–185
Lindesy K, Wei W, Clarke MC, Mcardle HF, Rooke LM, Topping JF (1993) Tagging genomic sequences that direct transgene expression by activation of a promoter trap in plants. Transgenic Res 2:33–47
Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y, Gao C, Wu H, Li Y, Cui Y, Guo X, Zheng S, Wang B, Yu K, Liang Q, Yang W, Lou X, Chen J, Feng M, Jian J, Zhang X, Luo G, Jiang Y, Liu J, Wang Z, Sha Y, Zhang B, Wu H, Tang D, Shen Q, Xue P, Zou S, Wang X, Liu X, Wang F, Yang Y, An X, Dong Z, Zhang K, Zhang X, Luo MC, Dvorak J, Tong Y, Wang J, Yang H, Li Z, Wang D, Zhang A, Wang J (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87–90
Lister R, Ecker JR (2009) Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res 19:959–966
Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536
Liu Y, Schiff M, Dinesh-Kumar SP (2002a) Virus-induced gene silencing in tomato. Plant J 31:777–786
Liu Y, Schiff M, Marathe R, Dinesh-Kumar SP (2002b) Tobacco Rar1, EDS1 and NPR1/NIM1 like genes are required for N-mediated resistance to tobacco mosaic virus. Plant J 30:415–429
Liu S, Chen HD, Makarevitch I, Shirmer R, Emrich SJ, Dietrich CR, Barbazuk WB, Springer NM, Schnable PS (2010) High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing. Genetics 184:19–26
Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:1–12
Liu H, Fu D, Zhu B, Yan H, Shen X, Zuo J, Zhu Y, Luo Y (2013) Virus-induced gene silencing in eggplant (Solanum melongena). J Integr Plant Biol 54:422–429
Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjálmsson BJ, Korte A, Nizhynska V, Voronin V, Korte P, Sedman L, Mandáková T, Lysak MA, Seren U, Hellmann I, Nordborg M (2013) Massive genomic variation and strong selection in Arabidopsis thaliana from Sweden. Nat Genet. doi:10.1038/ng.2678
Lu R, Martin-Hernandez AM, Peart JR, Malcuit I, Baulcombe DC (2003a) Virus- Induced gene silencing in plants. Methods 30:296–303
Lu R, Malcuit I, Moffett P, Ruiz MT, Peart J, Wu AJ, Rathjen JP, Bendahmane A, Day L, Baulcombe DC (2003b) High throughput virus-induced gene silencing implicates heat shock protein 90 in plant disease resistance. EMBO J 22:5690–5699
Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ (2005) Elucidation of the small RNA component of the transcriptome. Science 309:1567–1569
Lu SJ, Yang ZT, Sun L, Sun L, Song ZT, Liu JX (2012) Conservation of IRE1-regulated bZIP74 mRNA unconventional splicing in rice (Oryza sativa L.) involved in ER stress responses. Mol Plant 5:504–514
Lv MZ, Chao DY, Shan JX, Zhu MZ, Shi M, Gao JP, Lin HX (2012) Rice carotenoid β-ring hydroxylase CYP97A4 is involved in lutein biosynthesis. Plant Cell Physiol 53:987–1002
Ma M, Yan Y, Huang L, Chen M, Zhao H (2012) Virus-induced gene-silencing in wheat spikes and grains and its application in functional analysis of HMW-GS-encoding genes. BMC Plant Biol 12:141
Mace ES, Hunt CH, Jordan DR (2013) Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time. Theor Appl Genet 126:1377–1395
Maguire TL, Grimmond S, Forrest A, Iturbe-Ormaetxe I, Meksem K, Gresshoff P (2002) Tissue-specific gene expression in soybean (Glycine max) detected by cDNA microarray analysis. J Plant Physiol 159:1361–1374
Malatrasi M, Corradi M, Svensson JT, Close TJ, Gulli M, Marmiroli N (2006) A branched-chain amino acid aminotransferase gene isolated from Hordeum vulgare is differentially regulated by drought stress. Theor Appl Genet 113:965–976
Maleck K, Levine A, Eulgem T, Morgan A, Schmid J, Lawton KA, Dangl JL, Dietrich RA (2000) The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat Genet 26:403–410
Malonae JH, Oliver B (2011) Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol 9:34
Mandel MA, Feldmann KA, Herrera-Estrella L, Rocha-Sosa M, León P (1996) CLA1, a novel gene required for chloroplast development, is highly conserved in evolution. Plant J 9:649–658
Manmathan H, Shaner D, Snelling J, Tisserat N, Lapitan N (2013) Virus-induced gene silencing of Arabidopsis thaliana gene homologues in wheat identifies genes conferring improved drought tolerance. J Exp Bot 64:1381–1392
Martin A, Lee J, Kichey T, Gerentes D, Zivy M, Tatout C, Dubois F, Balliau T, Valot B, Davanture M, Tercé-Laforgue T, Quilleré I, Coque M, Gallais A, Gonzalez-Moro MB, Bethencourt L, Habash DZ, Lea PJ, Charcosset A, Perez P, Murigneux A, Sakakibara H, Edwards KJ, Hirel B (2006) Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain production. Plant Cell 18:3252–3274
Martin B, Ramiro M, Martinez ZJM, Alanso BC (2009) A high- density collection of EMS-induced mutations for TILLING in Landsberg erecta genetic background of Arabidopsis. BMC Plant Biol 9:147
Matsumura H, Nirasawa S, Kiba A, Urasaki N, Saitoh H, Ito M, Kawai-Yamada M, Uchimiya H, Terauchi R (2003) Overexpression of Bax inhibitor suppresses the fungal elicitor-induced cell death in rice (Oryza sativa L) cells. Plant J 33:425–434
Matsumura H, Nasir KHB, Yoshida K, Ito A, Kahl G, Kruger DH, Terauchi R (2006) SuperSAGE array: the direct use of 26 base-pair transcript tags in oligonucleotide arrays. Nat Methods 3:469–474
Mattiello L, da Silva FR, Menossi M (2012) Linking microarray data to QTLs highlights new genes related to Al tolerance in maize. Plant Sci 191–192:8–15
Matzke MA, Matzke AJ, Pruss GJ, Vance VB (2001) RNA-based silencing strategy in plants. Curr Opin Genet Dev 11:221–227
Maughan PJ, Yourstone SM, Byers RL, Smith SM, Udall JA (2010) Single-nucleotide polymorphism genotyping in mapping populations via genomic reduction and next-generation sequencing: proof of concept. Plant Genome 3:166–178
McCallum CM, Comai L, Greene EA, Henikoff S (2000a) Target screening for induced mutations. Nat Biotechnol 18:455–457
McCallum CM, Comai L, Greene EA, Henikoff S (2000b) Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiol 123:439–442
McIntosh S, Watson L, Bundock P, Crawford A, White J, Cordeiro G, Barbary D, Rooke L, Henry R (2007) SAGE of the developing wheat caryopsis. Plant Biotechnol J 5:69–83
McKinney EC, Ali N, Traut A, Feldmann KA, Belostotsky DA, McDowell JM, Meagher RB (1995) Sequence-based identification of T-DNA insertion mutations in Arabidopsis: actin mutants act2-1 and act4-1. Plant J 8:613–622
McKusick VA (1997) Genomics: structural and functional studies of genomes. Genomics 45:244–249
Meaburn E, Schulz R (2011) Next generation sequencing in epigenetics: insights and challenges. Semin Cell Dev Biol. doi:10.1016/j.semcdb.2011.10.010
Meissner R, Chague V, Zhu Q, Emmanuel E, Elkind Y, Levy A (2000) A high throughput system for transposon tagging and promoter trapping in tomato. Plant J 22:265–274
Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431:343–349
Mejlhede N, Kyjovska Z, Backes G, Burhenne K, Rasmussen SK, Jahoor A (2006) EcoTILLING for the identification of allelic variation in the powdery mildew resistance genes mlo and Mla of barley. Plant Breed 125:461–467
Menda N, Semel Y, Peled D, Eshed Y, Zamir D (2004) In silico screening of a saturated mutation library of tomato. Plant J 38:861–872
Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11:31–46
Meyers BC, Galbraith DW, Nelson T, Agrawal V (2004) Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiol 135:637–652
Michael T, Jackson M (2013) The first 50 plant genomes. Plant Genome 6:1–7
Mikkelsen TS, Ku MC, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560
Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248
Min K, Kang J, Lee J (2010) A modified feeding RNAi method for simultaneous knock-down of more than one gene in Caenorhabditis elegans. BioTechniques 48:229–232
Minoia S, Petrozza A, Onofrio DO, Piron F, Mosca G, Giovanni S (2010) A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Res Notes 3:69
Mitchell-Olds T (2010) Complex-trait analysis in plants. Genome Biol 11:113
Miyashita Y, Dolferus R, Ismond KP, Good AG (2007) Alanine aminotransferase catalyses the breakdown of alanine after hypoxia in Arabidopsis thaliana. Plant J 49:1108–1121
Mohorianu I, Schwach F, Jing R, Lopez-Gomollon S, Moxon S, Szittya G, Sorefan K, Moulton V, Dalmay T (2011) Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. Plant J 67:232–246
Molina C, Rotter B, Horres R, Udupa SM, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, Winter P (2008) SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9:553
Monson-Miller J, Sanchez-Mendez DC, Fass J, Henry IM, Tai TH, Comai L (2012) Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. BMC Genomics 13:72
Montiel J, Nava N, Cárdenas L, Sánchez-López R, Arthikala MK, Santana O, Sánchez F, Quinto C (2012) A Phaseolus vulgaris NADPH oxidase gene is required for root infection by Rhizobia. Plant Cell Physiol 53:1751–1767
Moritoh S, Miki D, Akiyama M, Kawahara M, Izawa T, Maki H, Shimamoto K (2005) RNAi- mediated silencing of OsGEN-L (OsGEN-like), a new member of the RAD2/XPG nuclease family, causes male sterility by defect of microspore development in rice. Plant Cell Physiol 46:699–715
Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255–264
Muller HJ (1930) Types of visible variations induced by X-rays in Drosophila. J Genet 22:299–334
Mutasa-Göttgens ES, Joshi A, Holmes HF, Hedden P, Göttgens B (2012) A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses. BMC Genomics 13:99
Myles S, Chia JM, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D (2010) Rapid genomic characterization of the genus vitis. PLoS One 5:e8219
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349
Nagamatsu A, Masuta C, Senda M, Matsuura H, Kasai A, Hong JS, Kitamura K, Abe J, Kanazawa A (2007) Functional analysis of soybean genes involved in flavonoid biosynthesis by virus-induced gene silencing. Plant Biotechnol J 5:778–790
Nagamatsu A, Masuta C, Matsuura H, Kitamura K, Abe J, Kanazawa A (2009) Down-regulation of flavonoid 3′-hydroxylase gene expression by virus-induced gene silencing in soybean reveals the presence of a threshold mRNA level associated with pigmentation in pubescence. J Plant Physiol 166:32–39
Newell MA, Asoro FG, Scott MP, White PJ, Beavis WD, Jannink JL (2012) Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin. Theor Appl Genet 125:1687–1696
Ng PC, Henikoff S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31:3812–3814
Nicolaï M, Pisani C, Bouchet JP, Vuylsteke M, Palloix A (2012) Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum). Genet Mol Res 11:2295–2300
Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo M, Weining S (2012) Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. Am J Bot 99:e369–e371
Nishizawa T, Tamaoki M, Kaneko Y, Aono M, Kubo A, Saji H, Nakajima N (2012) High-throughput capture of nucleotide sequence polymorphisms in three Brassica species (Brassicaceae) using DNA microarrays. Am J Bot 99:e94–e96
Nordborg M, Tavare S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18:83–90
Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9:312
Oikawa A, Rahman A, Yamashita T, Taira H, Kidou S (2007) Virus-induced gene silencing of P23k in barley leaf reveals morphological changes involved in secondary wall formation. J Exp Bot 58:2617–2625
Okabe Y, Asamizu E, Saito T, Matsukura C, Ariizumi T, Bres C, Rothan C, Mizoguchi T, Ezura H (2011) Tomato TILLING technology: development of a reverse genetics tool for the efficient isolation of mutants from Micro-Tom mutant libraries. Plant Cell Physiol 52:1994–2005
Okabe Y, Ariizumi T, Ezura H (2013) Updating the Micro-Tom TILLING platform. Breed Sci 63:42–48
Okamoto H, Hirochika H (2000) Efficient insertion mutagenesis of Arabidopsis by tissue culture- induced activation of the tobacco retrotransposon Tto1. Plant J 23:291–304
Oliver RE, Lazo GR, Lutz JD, Rubenfield MJ, Tinker NA, Anderson JM, Wisniewski Morehead NH, Adhikary D, Jellen EN, Maughan PJ, Brown Guedira GL, Chao S, Beattie AD, Carson ML, Rines HW, Obert DE, Bonman JM, Jackson EW (2011) Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. BMC Genomics 12:77
O’Neil ST, Emrich SJ (2013) Assessing De Novo transcriptome assembly metrics for consistency and utility. BMC Genomics 14:465
Oono Y, Kobayashi F, Kawahara Y, Yazawa T, Handa H, Itoh T, Matsumoto T (2013) Characterisation of the wheat (Triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat. BMC Genomics 14:77
Ortiz-Morea FA, Vicentini R, Silva GF, Silva EM, Carrer H, Rodrigues AP, Nogueira FT (2013) Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth. J Exp Bot 64:2307–2320
Pacak A, Geisler K, Jørgensen B, Barciszewska-Pacak M, Nilsson L, Nielsen TH, Johansen E, Grønlund M, Jakobsen I, Albrechtsen M (2010) Investigations of barley stripe mosaic virus as a gene silencing vector in barley roots and in Brachypodium distachyon and oat. Plant Methods 6:26
Padmanabhan M, Dinesh-Kumar PS (2009) Virus-induced gene silencing as a tool for delivery of dsRNA into plants. Cold Spring Harb Protoc 4:1–4
Palauqui J, Vaucheret H (1998) Transgenes are dispensable for the RNA degradation step of cosuppression. Proc Natl Acad Sci U S A 95:9675–9680
Papi M, Sabatini S, Bouchez D, Camilleri C, Costantino P, Vittorioso P (2000) Identification and disruption of an Arabidopsis zinc finger gene controlling seed germination. Genes Dev 14:28–33
Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180
Park MY, Chung MS, Koh HS, Lee DJ, Ahn SJ, Kim CS (2009) Isolation and functional characterization of the Arabidopsis salt-tolerance 32 (AtSAT32) gene associated with salt tolerance and ABA signaling. Physiol Plant 135:426–435
Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A (2012) Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol 12:16
Pavlidis P, Noble WS (2001) Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol 2:1–15
Peart JR, Cook G, Feys BJ, Parker JE, Baulcombe DC (2002a) An EDS1 orthologue is required for N-mediated resistance against tobacco mosaic virus. Plant J 29:569–579
Peart JR, Lu R, Sadanandom A, Malcuit I, Moffett P, Brice DC, Schauser L, Jaggard DA, Xiao S, Coleman MJ, Dow M, Jones JD, Shirasu K, Baulcombe DC (2002b) Ubiquitin -associated protein SGT1 is required for host and non –host disease resistance in plants. Proc Natl Acad Sci U S A 99:10865–10869
Peng FY, Weselake RJ (2013) Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants. Theor Appl Genet 126:1305–1319
Peng JH, Bai Y, Haley SD, Lapitan NL (2009) Microsatellite-based molecular diversity of bread wheat germplasm and association mapping of wheat resistance to the Russian wheat aphid. Genetica 135:95–122
Pérez-de-Castro AM, Vilanova S, Cañizares J, Pascual L, Blanca JM, Díez MJ, Prohens J, Picó B (2012) Application of genomic tools in plant breeding. Curr Genomics 13:179–195
Perry JA, Wang TL, Welham TJ, Gardner S, Pike JM, Yoshida S, Parniske M (2003) A TILLING reverse genetics tool and a Web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol 131:866–871
Perry J, Brachmann A, Welham T, Binder A, Charpentier M, Groth M, Haage K, Markmann K, Wang TL, Parniske M (2009) TILLING in Lotus japonicus identified large allelic series for symbiosis genes and revealed a bias in functionally defective ethyl methanesulfonate alleles toward glycine replacements. Plant Physiol 151:1281–1291
Pevsner J (2009) Bioinformatics and functional genomics, 2nd edn. Wiley-Blackwell, Hoboken
Pfender WF, Saha MC, Johnson EA, Slabaugh MB (2011) Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet 122:1467–1480
Piferrer F (2013) Epigenetics of sex determination and gonadogenesis. Dev Dyn 242:360–370
Piron F, Nicolai M, Minoi S, Piednoir E, Moretti A, Salgues A, Zamir D, Caranta C, Bendahmane A (2010) An induced mutation in tomato eIF4E leads to immunity to two potyviruses. PLoS One 5:e11313
Poland JA, Bradbury PJ, Buckler ES, Nelson RJ (2011) Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci U S A 108:6893–6898
Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253
Poole RL, Barker GL, Werner K, Biggi GF, Coghill J, Gibbings JG, Berry S, Dunwell JM, Edwards KJ (2008) Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription. BMC Genomics 9:475
Porch TG, Blair MW, Lariguet P, Galeano C, Pankhurst CE, Broughton WJ (2008) Generation of a mutant population for TILLING common bean genotype BAT 93. J Am Soc Hort Sci 134:348–355
Poroyko V, Calugaru V, Fredricksen M, Bohnert HJ (2004) Virtual-SAGE: a new approach to EST data analysis. DNA Res 11:145–152
Primerose SB, Twyman RM (2006) Principles of gene manipulation and genomics, 7th edn. Blackwell Publishing, Oxford
Puzio PS, Lausen J, Almeida-Engler J, Cai D, Gheysen G, Grundler FM (1999) Isolation of a gene from Arabidopsis thaliana related to nematode feeding structures. Gene 239:163–172
Qiu S, Adema CM, Lane T (2005) A computational study of off-target effects of RNA interference. Nucleic Acids Res 33:1834–1847
Qu J, Ye J, Geng YF, Sun YW, Gao SQ, Zhang BP, Chen W, Chua NH (2012) Dissecting functions of KATANIN and WRINKLED1 in cotton fiber development by virus-induced gene silencing. Plant Physiol 160:738–748
Radhamony RN, Prasad AM, Srinivasan R (2005) T-DNA insertional mutagenesis in Arabidopsis: a tool for functional genomics. Electron J Biotechnol 1:82–106
Ramachandran S, Sundersan V (2001) Transposon as tools for functional genomics. Plant Physiol Biochem 39:243–252
Raman H, Stodart B, Ryan PR, Delhaize E, Emebiri L, Raman R, Coombes N, Milgate A (2010) Genome-wide association analyses of common wheat (Triticum aestivum L.) germplasm identifies multiple loci for aluminium resistance. Genome 53:957–966
Ramos ML, Huntley JJ, Maleki SJ, Ozias-Akins P (2009) Identification and characterization of a hypoallergenic ortholog of Ara h 2.01. Plant Mol Biol 69:325–335
Rawat N, Sehgal SK, Joshi A, Rothe N, Wilson DL, McGraw N, Vadlani PV, Li W, Gill BS (2012) BMC Plant Biol 12:205
Reif JC, Gowda M, Maurer HP, Longin CF, Korzun V, Ebmeyer E, Bothe R, Pietsch C, Würschum T (2011) Association mapping for quality traits in soft winter wheat. Theor Appl Genet 122:961–970
Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci U S A 98:11479–11484
Ren Y, Hong Z, Kou Q, Jiang J, Guo S, Zhang H, Hou W, Zou X, Sun H, Gong G, Levi A, Xu Y (2012) A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome. PLoS One 7:e29453
Riascos JJ, Weissinger AK, Weissinger SM, Burks AW (2010) Hypoallergenic legume crops and food allergy: factors affecting feasibility and risk. J Agric Food Chem 58:20–27
Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516–1517
Rival A, Beule T, Bertossi FA, Tregear J, Jaligot E (2010) Plant epigenetics: from genomes to epigenomes. Not Bot Hort Agrobot Cluj 38:09–15
Robertson D (2004) VIGS vectors for gene silencing; many targets, many tools. Annu Rev Plant Biol 55:495–519
Rogers C, Wen J, Chen R, Oldroyd G (2009) Deletion- based reverse genetics in Medicago truncatula. Plant Physiol 151:1077–1086
Ronaghi M (2001) Pyrosequencing sheds light on DNA sequencing. Genome Res 11:3–11
Rousset M, Bonnin I, Remoué C, Falque M, Rhoné B, Veyrieras JB, Madur D, Murigneux A, Balfourier F, Le Gouis J, Santoni S, Goldringer I (2011) Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.). Theor Appl Genet 123:907–926
Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ (2010) Association mapping of spot blotch resistance in wild barley. Mol Breed 26:243–256
Ruan Y, Gilmore J, Conner T (1998) Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J 15:821–833
Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE (2002) Using the transcriptome to annotate the genome. Nat Biotechnol 20:508–512
Sallaud C, Gay C, Larmande P, Be M, Piffanelli P, Piegu B, Droc G, Bourgeois E, Meynard D, Perin C, Sabau X, Ghesquiere A, Glaszmann JC, Delseny M, Guiderdoni E (2004) High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics. Plant J 39:450–464
Salvio S, Tuberosa R (2007) Cloning QTLS in plants. Development and applications. In: Varshney RK, Tuberosa R (eds) Genomic-assisted crop improvement: vol. 1. Genomics approaches and platforms. Springer, Netherlands, pp 207–225
Sanger F, Coulson AR (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94:441–448
Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S (2012) RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genomics 13:3
Schaefer DG, Zryd JP (1997) Efficient gene targeting in the moss Physcomitrella patens. Plant J 11:1195–1206
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470
Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, Nielsen KL, Jørgensen JE, Weigel D, Andersen SU (2009) SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat Methods 6:550–551
Schneider A, Kirch T, Gigolashvili T, Mock HP, Sonnewald U, Simon R, Flügge UI, Werr W (2005) A transposon-based activation-tagging population in Arabidopsis thaliana (TAMARA) and its application in the identification of dominant developmental and metabolic mutations. FEBS Lett 579:4622–4628
Schuster SC (2008) Next generation DNA sequencing transforms today’s biology. Nat Methods 5:16–18
Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199–208
Scofield SR, Brandt AS (2012) Virus-induced gene silencing in hexaploid wheat using barley stripe mosaic virus vectors. Methods Mol Biol 894:93–112
Scofield SR, Huang L, Brandt AS, Gill BS (2005) Development of a virus-induced gene-silencing system for hexaploid wheat and its use in functional analysis of the Lr21-mediated leaf rust resistance pathway. Plant Physiol 138:2165–2173
Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi- Shinozaki K, Carninci P, Hayashizaki Y, Shinozaki K (2001) Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13:61–72
Senthil Kumar M, Udayakumar M (2006) High-throughput virus-induced gene-silencing approach to assess the functional relevance of a moisture stress-induced cDNA homologous to lea4. J Exp Bot 57:2291–2302
Senthil Kumar M, RameGowda HV, Hema R, Mysore KS, UdayaKumar M (2008) Virus- induced gene silencing and its application in characterizing gene involved in water-deficit stress tolerance. J Plant Physiol 165:1404–1421
Seo JS, Koo YJ, Jung C, Yeu SY, Song JT, Kim JK, Choi Y, Lee JS, Do Choi Y (2013) Identification of a novel jasmonate-responsive element in the AtJMT promoter and its binding protein for AtJMT repression. PLoS One 8:e55482
Settles AM, Holding DR, Tan BC, Latshaw SP, Liu J, Suzuki M, Li L, O’Brien BA, Fajardo DS, Wroclawska E, Tseung CW, Lai J, Hunter CT, Avigne WT, Baier J, Messing J, Hannah LC, Koch KE, Becraft PW, Larkins BA, McCarty DR (2007) Sequence-indexed mutations in maize using the Uniform Mu transposon-tagging population. BMC Genomics 8:116
Seymour DK, Filiault DL, Henry IM, Monson-Miller J, Ravi M, Pang A, Comai L, Chan SW, Maloof JN (2012) Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping. Proc Natl Acad Sci U S A 109:4227–4232
Sharpe AG, Ramsay L, Sanderson LA, Fedoruk MJ, Clarke WE, Li R, Kagale S, Vijayan P, Vandenberg A, Bett KE (2013) Ancient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil. BMC Genomics 14:192
Shendure J, Ji H (2008) Next-generation sequencing. Nat Biotechnol 26:1135–1145
Shi C, Navabi A, Yu K (2011) Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations. BMC Plant Biol 11:52
Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109–116
Sim SC, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S, Francis DM (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One 7:e40563
Simko I, Costanzo S, Haynes KG, Christ BJ, Jones RW (2004) Linkage disequilibrium mapping of a Verticillium dahliae resistance quantitative trait locus in tetraploid potato (Solanum tuberosum) through a candidate gene approach. Theor Appl Genet 108:217–224
Simon SA, Meyers BC (2011) Small RNA-mediated epigenetic modifications in plants. Curr Opin Plant Biol 14:148–155
Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D (2005) A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 23:75–81
Small I (2007) RNAi for revealing and engineering plant gene functions. Curr Opin Biotechnol 18:148–153
Song S, Qu H, Chen C, Hu S, Yu J (2007) Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data. BMC Plant Biol 7:49
Song GS, Zhai HL, Peng YG, Zhang L, Wei G, Chen XY, Xiao YG, Wang L, Chen YJ, Wu B, Chen B, Zhang Y, Chen H, Feng XJ, Gong WK, Liu Y, Yin ZJ, Wang F, Liu GZ, Xu HL, Wei XL, Zhao XL, Ouwerkerk PB, Hankemeier T, Reijmers T, van der Heijden R, Lu CM, Wang M, van der Greef J, Zhu Z (2010) Comparative transcriptional profiling and preliminary study on heterosis mechanism of super-hybrid rice. Mol Plant 3:1012–1025
Soyka S, Heyer AG (1999) Arabidopsis knockout mutation of ADC2 gene reveals inducibility by osmotic stress. FEBS Lett 458:219–223
Spiegelman JI, Mindrinos MN, Fankhauser C, Richards D, Lutes J, Chory J, Oefner PJ (2000) Cloning of the arabidopsis RSF1 gene by using a mapping strategy based on high-density DNA arrays and denaturing high-performance liquid chromatography. Plant Cell 12:2485–2498
Srivastava AK, Ramaswamy NK, Suprasanna P, D’Souza SF (2010) Genome-wide analysis of thiourea-modulated salinity stress-responsive transcripts in seeds of Brassica juncea: identification of signalling and effector components of stress tolerance. Ann Bot 106:663–674
Srivastava A, Ohm RA, Oxiles L, Brooks F, Lawrence CB, Grigoriev IV, Cho Y (2012) A zinc-finger-family transcription factor, AbVf19, is required for the induction of a gene subset important for virulence in Alternaria brassicicola. Mol Plant Microbe Interact 25:443–452
Stemple DL (2004) TILLING- a high-throughput harvest for functional genomics. Nat Rev Genet 5:145–150
Stephenson P, Baker D, Girin T, Perez A, Amoah S, King GJ, Ostergaard L (2010) A rich TILLING resource for studying gene function in Brassica rapa. BMC Plant Biol 10:62
Stracke S, Haseneyer G, Veyrieras JB, Geiger HH, Sauer S, Graner A, Piepho HP (2009) Association mapping reveals gene action and interactions in the determination of flowering time in barley. Theor Appl Genet 118:259–273
Straton M (2008) Genome resequencing and genetic variation. Nat Biotechnol 26:65–66
Sunilkumar G, Campbell ML, Puckhaber L, Stipanovic DR, Rathore SK (2006) Engineering cottonseed for use in human nutrition by tissue-specific reduction of toxic gossypol. Proc Natl Acad Sci U S A 103:18054–18059
Swanson-Wagner R, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM (2012) Reshaping of the maize transcriptome by domestication. Proc Natl Acad Sci U S A 109:11878–11883
Tabara H, Grishok A, Mello CC (1998) RNAi in C. elegans: soaking in the genome sequence. Science 282:430–431
Tadege M, Wang TL, Wen J, Ratet P, Mysore KS (2009) Mutagenesis and beyond! Tools for understanding legume biology. Plant Physiol 151:978–984
Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183
Tang Y, Wang F, Zhoa J, Xie K, Hong Y, Liu Y (2010) Virus-Based MicroRNA expression for gene functional analysis in plants. Plant Physiol 153:632–641
Taylor NE, Greene EA (2003) PARSESNP: a tool for the analysis of nucleotide polymorphisms. Nucleic Acids Res 31:3808–3811
Tenllado F, Gracia MB, Vargas M, Ruiz RDJ (2003) Crude extracts of bacterially expressed dsRNA can be used to protect plants against virus infections. BMC Biotechnol 3:3–14
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
Thorneycroft D, Sherson SM, Smith SM (2001) Using gene knockouts to investigate plant metabolism. J Exp Bot 52:1593–1601
Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289
Thudi M, Li Y, Jackson SA, May GD, Varshney RK (2012) Current state-of-art of sequencing technologies for plant genomics research. Brief Funct Genomics 11:3–11
Tian F, Bradbury PJ, Brown PJ et al (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43:159–162
Tierney MB, Lamour KH (2005) An introduction to reverse genetic tools for investigating gene function. The Plant Health Instructor. doi:10.1094/PHI-A-2005-1025-01
Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE, Henikoff JG, Comai L, Henikoff S (2003) Large- scale discovery of induced point mutations with high- throughput TILLING. Genome Res 13:524–530
Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR et al (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:12
Till BJ, Cooper J, Tai T, Colowit P, Greene E, Henikoff S, Comai L (2007a) Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol 7:19
Till BJ, Comai L, Henikoff AS (2007b) TILLING and ECOTILLING for crop improvement. In: Varshney RK, Tuberosa R (eds) Genomics- assisted crop improvement: genomic approaches and platforms. Springer, Dordrecht, pp 333–349
Till BJ, Jankowicz-Cieslak J, Sági L, Huynh OA, Utushi H, Swennen R, Terauchi R, Mba C (2010) Discovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling. Theor Appl Genet 121:1381–1389
Tissier AF, Marillonnet S, Klimyuk V, Patel K, Torres MA, Murphy G, Jones JD (1999) Multiple independent defective suppressor–mutator transposon insertions in Arabidopsis: a tool for functional genomics. Plant Cell 11:1841–1852
Todd AT, Liu E, Polvi SL, Pammett RT, Page JE (2010) A functional genomics screen identifies diverse transcription factors that regulate alkaloid biosynthesis in Nicotiana benthamiana. Plant J 62:589–600
Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, Lee JR, Lorenc MT, Manoli S, Stiller J, Raman R, Raman H, Edwards D, Batley J (2012) Identification and characterization of candidate Rlm4 blackleg resistance genes in Brassica napus using next-generation sequencing. Plant Biotechnol J 10:709–715
Travella S, Klimm TE, Keller B (2006) RNA interference-based gene silencing as an efficient tool for functional genomics in hexaploid bread wheat. Plant Physiol 142:16–20
Trebbi D, Maccaferri M, de Heer P, Sørensen A, Giuliani S, Salvi S, Sanguineti MC, Massi A, van der Vossen EA, Tuberosa R (2011) High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theor Appl Genet 123:555–569
Trichine L, Bourcy M, Ratet P (2009) Insertion mutant collections as genetic tools in model legumes. Grain Legumes 53:14
Trick M, Long Y, Meng J, Bancroft I (2009) Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol J 4:334–346
Trieu AT, Burleigh SH, Kardailsky IV, Maldonado-Mendoza IE, Versaw WK, Blaylock LA, Shin H, Chiou TJ, Katagi H, Cewbre GR, Weigel D, Harrison MJ (2000) Transformation of Medicago truncatula via infiltration of seedlings or flowering plants with Agrobacterium. Plant J 22:531–541
Tsaballa A, Pasentsis K, Darzentas N, Tsaftaris AS (2011) Multiple evidence for the role of an Ovate-like gene in determining fruit shape in pepper. BMC Plant Biol 11:46
Uauy C, Paraiso F, Colasuonno P, Tran RK, Tasi H, Berardi S, Comai L, Dubcovsky J (2009) A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat. BMC Plant Biol 9:115
Udvardi MK, Tabata S, Parniske M, Stougaard J (2005) Lotus japonicus: legume research in the fast lane. Trends Plant Sci 10:222–228
Uehara T, Sugiyama S, Masuta C (2007) Comparative serial analysis of gene expression of transcript profiles of tomato roots infected with cyst nematode. Plant Mol Biol 63:185–194
Van Eck L, Schultz T, Leach JE, Scofield SR, Peairs FB, Botha AM, Lapitan NL (2010) Virus-induced gene silencing of WRKY53 and an inducible phenylalanine ammonia-lyase in wheat reduces aphid resistance. Plant Biotechnol J 8:1023–1032
van Kammen A (1997) Virus-induced gene silencing in infected and transgenic plants. Trends Plant Sci 2:409–411
Varala K, Swaminathan K, Li Y, Hudson ME (2011) Rapid genotyping of soybean cultivars using high throughput sequencing. PLoS One 6:e24811
Várallyay E, Giczey G, Burgyán J (2012) Virus-induced gene silencing of Mlo genes induces powdery mildew resistance in Triticum aestivum. Arch Virol 157:1345–1350
Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530
Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MT, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang SP, Shah T, Saxena KB, Michael T, McCombie WR, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, Jackson SA (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30:83–89
Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar’an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo MC, Thudi M, Gowda CL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J, Cook DR (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246
Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20:759–771
Vaucheret H (2008) Plant ARGONAUTES. Trends Plant Sci 13:350–358
Vazquez F (2006) Arabidopsis endogenous small RNAs: highways and byways. Trends Plant Sci 11:460–468
Vazquez F, Legrand S, Windels D (2010) The biosynthetic pathways and biological scopes of plant small RNAs. Trends Plant Sci 15:337–345
Vega-Sánchez ME, Verhertbruggen Y, Christensen U, Chen X, Sharma V, Varanasi P, Jobling SA, Talbot M, White RG, Joo M, Singh S, Auer M, Scheller HV, Ronald PC (2012) Loss of Cellulose synthase-like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties, and defense responses in vegetative tissues of rice. Plant Physiol 159:56–69
Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One 2:e1326
Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484–487
Venu RC, Jia Y, Gowda M, Jia MH, Jantasuriyarat C, Stahlberg E, Li H, Rhineheart A, Boddhireddy P, Singh P, Rutger N, Kudrna D, Wing R, Nelson JC, Wang GL (2007) RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection. Mol Genet Genomics 278:421–431
Virk PS, Ford-Lloyd BV, Jackson MT, Pooni HS, Clemeno TP, Newbury HJ (1996) Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76:296–304
Vitulo N, Albiero A, Forcato C, Campagna D, Dal Pero F, Bagnaresi P, Colaiacovo M, Faccioli P, Lamontanara A, Šimková H, Kubaláková M, Perrotta G, Facella P, Lopez L, Pietrella M, Gianese G, Doležel J, Giuliano G, Cattivelli L, Valle G, Stanca AM (2011) First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One 6:e26421
Vodkin LO, Khanna A, Shealy R, Clough SJ, Gonzalez DO, Philip R, Zabala G, Thibaud-Nissen F, Sidarous M, Stromvik M et al (2004) Microarrays for global expression constructed with a low redundancy set of 27500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC Genomics 5:73
Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687
Walbot V (2000) Saturation mutagenesis using maize transposons. Curr Opin Plant Biol 3:103–107
Walden R (2002) T-DNA tagging in genomics era. Crit Rev Plant Sci 21:143–165
Wang WY, Barratt BJ, Clayton DG, Todd JA (2005) Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 6:109–118
Wang DK, Sun ZX, Tao YZ (2006) Application of TILLING in plant improvement. Acta Genet Sin 33:957–964
Wang J, Sun JZ, Liu DC, Yang WL, Wang DW, Tong YP, Zhang AM (2008) Analysis of Pina and Pinb alleles in the microcore collections of Chinese wheat germplasm by EcoTILLING and identification of a novel Pinb allele. J Cereal Sci 48:836–842
Wang X, Cao A, Yu C, Wang D, Wang X, Chen P (2010) Establishment of an effective virus induced gene silencing system with BSMV in Haynaldia villosa. Mol Biol Rep 37:967–972
Wang YH, Poudel DD, Hasenstein KH (2011a) Identification of SSR markers associated with saccharification yield using pool-based genome-wide association mapping in sorghum. Genome 54:883–889
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y et al (2011b) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039
Wang Y, Sun S, Liu B, Wang H, Deng J, Liao Y, Wang Q, Cheng F, Wang X, Wu J (2011c) A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly. BMC Genomics 12:239
Wang Y, Zeng X, Iyer NJ, Bryant DW, Mockler TC, Mahalingam R (2012a) Exploring the switchgrass transcriptome using second-generation sequencing technology. PLoS One 7:e34225
Wang S, Wang X, He Q, Liu X, Xu W, Li L, Gao J, Wang F (2012b) Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep 31:1437–1447
Wang H, Walla JA, Zhong S, Huang D, Dai W (2012c) Development and cross-species/genera transferability of microsatellite markers discovered using 454 genome sequencing in chokecherry (Prunus virginiana L.). Plant Cell Rep 31:2047–2055
Wang W, Huang S, Liu Y, Fang Z, Yang L, Hua W, Yuan S, Liu S, Sun J, Zhuang M, Zhang Y, Zeng A (2012d) Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata). BMC Genomics 13:523
Wang N, Fang L, Xin H, Wang L, Li S (2012e) Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing. BMC Plant Biol 12:148
Wang S, Meyer E, McKay JK, Matz MV (2012f) 2b-RAD: a simple and flexible method for genome-wide genotyping. Nat Methods 9:808–810
Wang X, Zhang C, Li L, Fritsche S, Endrigkeit J, Zhang W, Long Y, Jung C, Meng J (2012g) Unraveling the genetic basis of seed tocopherol content and composition in rapeseed (Brassica napus L.). PLoS One 7:e50038
Wang L, Yu S, Tong C, Zhao Y, Liu Y, Song C, Zhang Y, Zhang X, Wang Y, Hua W, Li D, Li D, Li F, Yu J, Xu C, Han X, Huang S, Tai S, Wang J, Xu X, Li Y, Liu S, Varshney RK, Wang J, Zhang X (2014) Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol 15:R39
Waterhouse PM, Graham MW, Wang MB (1998) Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl Acad Sci U S A 95:13959–13964
Watkinson JI, Hendricks L, Sioson AA, Heath LS, Bohnert HJ, Grene R (2008) Tuber development phenotypes in adapted and acclimated, drought-stressed Solanum tuberosum ssp. andigena have distinct expression profiles of genes associated with carbon metabolism. Plant Physiol Biochem 46:34–45
Watson JD, Crick FHC (1953) Molecular structure of nucleic acids. Nature 171:737–738
Watson JM, Fusaro AF, Wang M, Waterhouse PM (2005) RNA silencing platforms in plants. FEBS Lett 579:5982–5987
Wei LQ, Yan LF, Wang T (2011) Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol 12(6):R53
Weigel D, Ahn JH, Blazquez MA, Borevitz J, Christensen SK, Fankhauser C, Ferrandiz C, Kardailsky I, Malancharuvil EJ, Neff MM, Nguyen JT, Sato S, Wang Z, Xia Y, Dixon RA, Harrison MJ, Lamb CJ, Yanofsky MK, Chory J (2000) Activation tagging in Arabidopsis. Plant Physiol 122:1003–1013
Weil CF (2009) TILLING in grass species. Plant Physiol 149:158–164
Wesley SV, Helliwell CA, Smith NA, Wang MB, Rouse DT, Liu Q, Gooding PS, Singh SP, Abbott D, Stoutjesdijk PA (2001) Constructs for efficient, effective and high throughput gene silencing in plants. Plant J 27:581–590
Winfield MO, Wilkinson PA, Allen AM, Barker GL, Coghill JA, Burridge A, Hall A, Brenchley RC, D’Amore R, Hall N, Bevan MW, Richmond T, Gerhardt DJ, Jeddeloh JA, Edwards KJ (2012) Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotechnol J 10:733–742
Winkler HL (1920) Verbreitung und Ursache der Parthenogenesis im Pflanzen-and Tierreiche. Verlag Fischer, Jena
Wisman E, Hartmann U, Sagasser M, Baumann E, Palme K, Hahlbrock K, Saedler H, Weisshaar B (1998) Knockout mutants from an En-1 mutagenized Arabidopsis thaliana population generate phenylpropanoid biosynthesis phenotypes. Proc Natl Acad Sci U S A 95:12432–12437
Wu C, Li X, Yuan W, Chen G, Kilian A, Li J, Xu C, Li X, Zhou DX, Wang S, Zhang Q (2003) Developments of enhancer trap lines for functional analysis of the rice genome. Plant J 5:418–427
Wu JL, Wu C, Lei C, Baraoidan M, Bordeos A, Madamba MR, Ramos PM, Mauleon R, Portugal A, Ulat VJ, Bruskiewich R, Wang G, Leach J, Khush G, Leung H (2005) Chemical- and Irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol Biol 59:85–97
Wu N, Matand K, Wu H, Li B, Li Y, Zhang X, He Z, Qian J, Liu X, Conley S, Bailey M, Acquaah G (2013) De novo next-generation sequencing, assembling and annotation of Arachis hypogaea L. Spanish botanical type whole plant transcriptome. Theor Appl Genet 126:1145–1149
Xiang CC, Chen Y (2000) cDNA microarray technology and its applications. Biotechnol Adv 18:35–46
Xiao J, Jin X, Jia X, Wang H, Cao A, Zhao W, Pei H, Xue Z, He L, Chen Q, Wang X (2013) Transcriptome-based discovery of pathways and genes related to resistance against Fusarium head blight in wheat landrace Wangshuibai. BMC Genomics 14:197
Xie Z et al (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2:E104
Xin Z, Wang ML, Barkley NA, Burow G, Franks C, Pederson G, Burke J (2008) Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population. BMC Plant Biol 8:103
Xin M, Wang X, Peng H, Yao Y, Xie C, Han Y, Ni Z, Sun Q (2012) Transcriptome comparison of susceptible and resistant wheat in response to powdery mildew infection. Genomics Proteomics Bioinformatics 10:94–106
Xiong AS, Yao QH, Peng RH, Li X, Han PL, Fan HQ (2004) Different effects on ACC oxidase gene silencing triggered by RNA interference in transgenic tomato. Plant Cell Rep 23:639–646
Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407
Xu JJ, Zhao QA, Du P, Xu CW, Wang BH, Feng Q, Liu QQ, Tang SZ, Gu MH, Han B, Liang GH (2010) Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genomics 11:656
Xu P, Wu X, Luo J, Wang B, Liu Y, Ehlers JD, Wang S, Lu Z, Li G (2011a) Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding. BMC Genomics 12:467
Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, Li Y, Yu C, Kristiansen K, Zhang X, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W (2011b) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30:105–111
Yamagishi N, Yoshikawa N (2009) Virus-induced gene silencing in soybean seeds and the emergence stage of soybean plants with Apple latent spherical virus vectors. Plant Mol Biol 71:15–24
Yamaguchi T, Nakayama K, Hayashi T, Yazaki J, Kishimoto N, Kikuchi S, Koike S (2004) cDNA microarray analysis of rice anther genes under chilling stress at the microsporogenesis stage revealed two genes with DNA transposon Castaway in the 5′-flanking region. Biosci Biotechnol Biochem 68:1315–1323
Yamamoto M, Shitsukawa N, Yamada M, Kato K, Takumi S, Kawaura K, Ogihara Y, Murai K (2013) Identification of a novel homolog for a calmodulin-binding protein that is upregulated in alloplasmic wheat showing pistillody. Planta 237:1001–1013
Yamatani H, Sato Y, Masuda Y, Kato Y, Morita R, Fukunaga K, Nagamura Y, Nishimura M, Sakamoto W, Tanaka A, Kusaba M (2013) NYC4, the rice ortholog of Arabidopsis THF1, is involved in the degradation of chlorophyll – protein complexes during leaf senescence. Plant J. doi:10.1111/tpj.12154
Yamazaki M, Tsugawa H, Miyao A, Yano M, Wu J, Yamamoto S, Matsumoto T, Sasaki T, Hirochika H (2001) The rice retrotransposon Tos17 prefers low-copy-number sequences as integration targets. Mol Genet Genomics 265:336–344
Yang Y, Wu Y, Pirrello J, Regad F, Bouzayen M, Deng W, Li Z (2010) Silencing Sl-EBF1 and Sl-EBF2 expression causes constitutive ethylene response phenotype, accelerated plant senescence, and fruit ripening in tomato. J Exp Bot 61:697–708
Yang H, Tao Y, Zheng Z, Li C, Sweetingham MW, Howieson JG (2012a) Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics 13:318
Yang T, Bao SY, Ford R, Jia TJ, Guan JP, He YH, Sun XL, Jiang JY, Hao JJ, Zhang XY, Zong XX (2012b) High-throughput novel microsatellite marker of faba bean via next generation sequencing. BMC Genomics 13:602
Yokosho K, Yamaji N, Ueno D, Mitani N, Ma JF (2009) OsFRDL1 is a citrate transporter required for efficient translocation of iron in rice. Plant Physiol 149:297–305
You FM, Huo N, Deal KR, Gu YQ, Luo MC, McGuire PE, Dvorak J, Anderson OD (2011) Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics 12:59
Young ND, Debelle F, Oldroyd GE, Geurts R et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520–524
Yu LX, Setter TL (2003) Comparative transcriptional profiling of placenta and endosperm in developing maize kernels in response to water deficit. Plant Physiol 131:568–582
Yu J, Pressoir G, Briggs WH, Vroh BI, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB et al (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208
Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551
Yu H, Xie W, Wang J, Xing Y, Xu C, Li X, Xiao J, Zhang Q (2011a) Gains in QTL detection using an ultra-high density SNP map based on population sequencing relate to traditional RFLP/SSR markers. PLoS One 6:e17595
Yu LX, Lorenz A, Rutkoski J, Singh RP, Bhavani S, Huerta-Espino J, Sorrells ME (2011b) Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor Appl Genet 123:1257–1268
Yu X, Bai G, Liu S, Luo N, Wang Y, Richmond DS, Pijut PM, Jackson SA, Yu J, Jiang Y (2013) Association of candidate genes with drought tolerance traits in diverse perennial ryegrass accessions. J Exp Bot 64:1537–1551
Yuan X, Zhang S, Liu S, Yu M, Su H, Shu H, Li X (2013) Global analysis of ankyrin repeat domain C3HC4-Type RING finger gene family in plants. PLoS One 8:e58003
Zamore PD, Tuschl T, Sharp PA, Bartel DP (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101:25–33
Zha W, Peng X, Chen R, Du B, Zhu L, He G (2011) Knockdown of midgut genes by dsRNA-transgenic plant-mediated RNA interference in the hemipteran insect Nilaparvata lugens. PLoS One 6(5):e20504
Zhang L, Zhou W, Velculescu VE, Kern SE, Hruban RH, Hamilton SR, Vogelstein B, Kinzler KW (1997) Gene expression profiles in normal and cancer cells. Science 276:1268–1272
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189–1201
Zhang L, Lavery L, Gill U, Gill K, Steffenson B, Yan G, Chen X, Kleinhofs A (2009) A cation/proton-exchanging protein is a candidate for the barley NecS1 gene controlling necrosis and enhanced defense response to stem rust. Theor Appl Genet 118:385–397
Zhang C, Grosic S, Whitham SA, Hill JH (2012a) The requirement of multiple defense genes in soybean Rsv1-mediated extreme resistance to soybean mosaic virus. Mol Plant Microbe Interact 25:1307–1313
Zhang J, Liang S, Duan J, Wang J, Chen S, Cheng Z, Zhang Q, Liang X, Li Y (2012b) De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.). BMC Genomics 13:90
Zhang Z, Liu X, Wang X, Zhou M, Zhou X, Ye X, Wei X (2012c) An R2R3 MYB transcription factor in wheat, TaPIMP1, mediates host resistance to Bipolaris sorokiniana and drought stresses through regulation of defense- and stress-related genes. New Phytol 196:1155–1170
Zhao MM, An RD, Zhao J, Huang GH, He ZH, Chen JY (2006) Transiently expressed short hairpin RNA targeting 126 kDa protein of tobacco mosaic virus interferes with virus infection. Acta Biochim Biophys Sin 38:22–28
Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P et al (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:e4
Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, Wang XJ (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 10:3
Zhou H, Steffenson BJ (2013) Association mapping of septoria speckled leaf blotch resistance in US barley breeding germplasm. Phytopathology 103:600–609
Zhou ML, Zhang Q, Zhou M, Qi LP, Yang XB, Zhang KX, Pang JF, Zhu XM, Shao JR, Tang YX, Wu YM (2012) Aldehyde dehydrogenase protein superfamily in maize. Funct Integr Genomics 12:683–691
Zhou ZS, Yang SN, Li H, Zhu CC, Liu ZP, Yang ZM (2013a) Molecular dissection of mercury-responsive transcriptome and sense/antisense genes in Medicago truncatula. J Hazard Mater 252–253C:123–131
Zhou Q, Yu Q, Wang Z, Pan Y, Lv W, Zhu L, Chen R, He G (2013b) Knockdown of GDCH gene reveals reactive oxygen species-induced leaf senescence in rice. Plant Cell Environ 36:1476–1489
Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20
Zhu Y, Cao Z, Xu F, Huang Y, Chen M, Guo W, Zhou W, Zhu J, Meng J, Zou J, Jiang L (2012) Analysis of gene expression profiles of two near-isogenic lines differing at a QTL region affecting oil content at high temperatures during seed maturation in oilseed rape (Brassica napus L.). Theor Appl Genet 124:515–531
Zuo R, Hu R, Chai G, Xu M, Qi G, Kong Y, Zhou G (2012) Genome-wide identification, classification, and expression analysis of CDPK and its closely related gene families in poplar (Populus trichocarpa). Mol Biol Rep 40:2645–2662
Zou Z, Ishida M, Li F, Kakizaki T, Suzuki S, Kitashiba H, Nishio T (2013) QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L. PLoS One 8:e53541
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Jha, U.C., Bhat, J.S., Patil, B.S., Hossain, F., Barh, D. (2015). Functional Genomics: Applications in Plant Science. In: Barh, D., Khan, M., Davies, E. (eds) PlantOmics: The Omics of Plant Science. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2172-2_4
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