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Towards Enriching Genomic Resources in Legumes

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Legumes in the Omic Era

Abstract

Food legumes, mainly comprising dry beans, dry peas, soybean, chickpea, pigeonpea, groundnut, greengram, blackgram, cowpea, lentil and lathyrus, have considerable area under cultivation globally and these are important constituents of cereal-based vegetarian diets. Keeping in view their tremendous importance for diversification and intensification of contemporary agriculture, systematic efforts towards their genetic improvement have been undertaken with classical breeding tools, lately complemented by the use of genomic tools. These genomic tools provide comprehensive information on genes involved in biochemical pathways leading upto nutritional compounds and can be used to understand the genetics of traits of interest and consequently, helping in marker assisted breeding. During the last two decades powerful genetic and genomic tools such as establishment of genetic and physical maps, expressed sequence tags, bioinformatic tools, genome-wide sequence data, genomic and metabolomic platforms, etc. have been developed for many legume species. These efforts have led to development of large scale molecular markers, identification of various marker trait associations, construction of genetic and linkage maps, expressed sequence tags database, partial or whole genome sequences, physical and molecular maps, DNA chips and bacterial artificial chromosome (BAC) libraries. After the genome sequencing of three model species, Medicago, Lotus and Glycine, draft genome sequences have recently been made available in agronomically important food legumes, pigeonpea and chickpea while similar efforts are underway in groundnut and greengram. The new generation sequencing (NGS) and genotyping platforms such as 454/FLX sequencing and Illumina GoldenGate/Solexa have revolutionized plant genomic research as these generate millions of ESTs per run. With the increased amount of genomic resources, there are now tremendous opportunities to integrate these with the genetic resources for their widespread use in routine legume improvement programmes by integrating them with conventional breeding tools. As a result, the genomics assisted breeding (GAB) can now be successfully used in legume improvement and development of improved genotypes having improved agronomic and quality traits and resistance to biotic and abiotic stresses. This chapter discusses the developments made in development of legume genomics and their role in overall improvement of food legumes.

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References

  • Allen RS, Millgate AM, Chitty JA, Thistleton J, Miller JAC, Fist AJ, Gerlach WL, Larkin PJ (2004) RNAi-mediated replacement of morphine with the non-narcotic alkaloid reticuline in opium poppy. Nat Biotechnol 22:1559–1566

    PubMed  CAS  Google Scholar 

  • Alzate-Marin AL, Menarim H, Arruda MCC, Chagas JM, Barros EG, Moreira MA (1999) Backcross assisted by RAPD markers for introgression of Co-4 and Co-6 anthracnose resistant genes in common bean cultivars. Ann Rep Bean Improv Coop 42:15–16

    Google Scholar 

  • Arelli PR, Young LD (2009) Jtn-5109 soybean germplasm resistant to nematode population infecting cv. Hartwig. Agronomy Society of America, The Abstracts 268–18: 133 (http://a-c-s.confex.com/crops/2009am/webprogram/Paper51979.html)

  • Arelli PR, Young LD, Mengistu A (2006) Registration of high yielding and multiple disease resistant soybean germplasm Jtn-5503. Crop Sci 46:2723–2724

    Google Scholar 

  • Arelli PR, Pantalone VR, Allen FL, Mengistu A (2007) Registration of soybean germplasm Jtn-5303. J Plant Reg 1:69–70

    Google Scholar 

  • Ashraf N, Ghai D, Barman P, Basu S, Gangisetty N, Mandal R, Chakraborty N, Datta A, Chakraborty S (2009) Comparative Analysis of genotype dependent expressed sequenced tag and stress responsive transcriptome of chick pea will illustrate predicted and unpredicted genes and novel regulators of plant immunity. BMC Genomics 10:415

    PubMed  Google Scholar 

  • Aziz N, Paiva NL, May GD, Dixon RA (2005) Transcriptome analysis of alfalfa glandular trichomes. Planta 221:28–38

    PubMed  CAS  Google Scholar 

  • Baier MC, Barsch A, Kuster H, Hohnjec N (2007) Antisense repression of the Medicago truncatula nodule-enhanced sucrose synthase leads to a handicapped nitrogen fixation mirrored by specific alterations in the symbiotic transcriptome and metabolome. Plant Physiol 145:1600–1618

    PubMed  CAS  Google Scholar 

  • 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 1:28–35

    PubMed  Google Scholar 

  • Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, Kakar K, Wandrey M, Verdier J, Zuber H, Ott T, Sandra M, Andreas N, Tancred F, Georg W, Ji H, Xinbin D, Patrick ZX, Yuhong T, Michael KU (2008) A gene expression atlas of the model legume Medicago truncatula. Plant J 55:504–513

    PubMed  CAS  Google Scholar 

  • Benlloch R, D’Erfurth I, Ferrandiz C, Cosson V, Beltran JP, Canas LA, Kondorosi A, Madueno F, Ratet P (2006) Isolation of mtpim proves Tnt1 a useful reverse genetics tool in Medicago truncatula and uncovers new aspects of AP1 functions in legumes. Plant Physiol 142:972–983

    PubMed  CAS  Google Scholar 

  • Bennett MD, Leitch IJ (2012) Plant DNA C-values database. Available at: http://www.kew.org/cvalues/. Accessed 2 Apr 2013

  • Bernardo R, Charcosset A (2006) Usefulness of gene information in marker-assisted recurrent selection: a simulation appraisal. Crop Sci 46:614–621

    Google Scholar 

  • Blair MW, Pedraza F, Buendia HF, Gatian-Soils E, Beebe SE, Gepts P, Tohme J (2003) Development of a genome-wide anchors microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107:1362–1374

    PubMed  CAS  Google Scholar 

  • Bohra A, Dubey A, Saxena RK, Penmetsa RV, Poornima KN, Kumar N (2011) Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.). BMC Plant Biol 11:56

    PubMed  CAS  Google Scholar 

  • Bohra A, Saxena RK, Gnanesh BN, Saxena K, Byregowda M, Rathore A, Kavi Kishor PB, Cook DR, Varshney RK (2012) An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations. Theor Appl Genet 125:1325–1338. http://link.springer.com/journal/122

    Google Scholar 

  • Briñez B, Blair MW, Kilian A, Carbonell SAM, Chiorato AF, Rubiano LB (2011) A whole genome DArT assay to assess germplasm collection diversity in common beans. Mol Breed. doi:10.1007/s11032-011-9609-3

    Google Scholar 

  • Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH (2005) Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC Plant Biol 5:16–29

    PubMed  Google Scholar 

  • Buitink J, Leger JJ, Guisle I, Vu BL, Wuilleme S, Lamirault G, Le Bars A, Le Meur N, Becker A, Kuster H, Leprince O (2006) Transcriptome profiling uncovers metabolic and regulatory processes occurring during the transition from desiccation-sensitive to desiccation-tolerant stages in Medicago truncatula seeds. Plant J 47:735–750

    PubMed  CAS  Google Scholar 

  • Chaky JM, Specht JE, Cregan PB (2003) Advanced backcross QTL analysis in a mating between Glycine max and Glycine soja. Plant Anim Genome Abstr 545

    Google Scholar 

  • Chamarthi SK, Kumar A, Vuong TD, Blair MW, Gaur PM, Nguyen HT (2011) Trait mapping and molecular breeding. In: Pratap A, Kumar J (eds) Biology and breeding of food legumes. CABI, Oxfordshire, UK, pp 297–313

    Google Scholar 

  • Chandran D, Sharopova N, Ivashuta S, Gantt JS, Vandenbosch KA, Samac DA (2008) Transcriptome profiling identified novel genes associated with aluminum toxicity, resistance and tolerance in Medicago truncatula. Planta 228:151–166

    PubMed  CAS  Google Scholar 

  • Choudhary S, Gaur R, Gupta S, Bhatia S (2012) EST derived genetic molecular marker: development and utilization for generating an advanced transcript map of chick pea. Theor Appl Genet 124:1449–1462

    PubMed  CAS  Google Scholar 

  • Chu Y, Wu CL, Holbrook CC, Tillman BL, Person G, Ozias-Akins P (2011) Marker-assisted selection to pyramid nematode resistance and the high oleic trait in peanut. Plant Genome 4:110–117

    CAS  Google Scholar 

  • Concibido VC, Vallee BL, Mclaird P, Pineda N, Meyer J, Hummel L, Yang J, Wu K, Delannay X (2003) Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars. Theor Appl Genet 106:575–582

    PubMed  CAS  Google Scholar 

  • Concibido VC, Diers BW, Arelli PR (2004) A decade of QTL mapping for cyst nematode resistance in soybean. Crop Sci 44:1121–1131

    CAS  Google Scholar 

  • Constantin GD, Krath BN, MacFarlane SA, Nicolaisen M, Johansen IE, Lund OS (2004) Virus-induced gene silencing as a tool for functional genomics in a legume species. Plant J 40:622–631

    PubMed  CAS  Google Scholar 

  • Coram TE, Pang ECK (2005a) Isolation and analysis of candidate Ascochyta blight defence genes in chickpea. Part I. Generation and analysis of an expressed sequence tag (EST) library. Physiol Mol Plant Pathol 66:192–200

    CAS  Google Scholar 

  • Coram TE, Pang ECK (2005b) Isolation and analysis of candidate Ascochyta blight defence genes in chickpea. Part II. Microarray expression analysis of putative defence-related ESTs. Physiol Mol Plant Pathol 66:201–210

    CAS  Google Scholar 

  • Córdoba JM, Chavarro C, Schlueter JA, Jackson SA, Blair MW (2010) Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers. BMC Genomics 11:436

    PubMed  Google Scholar 

  • Cortés AJ, Chavarro MC, Blair MW (2011) SNP marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 123:827–845

    PubMed  Google Scholar 

  • Coyne CJ, McClendon MT, Walling JG, Timmerman-Vaughan GM, Murray S, Meksem K, Lightfoot DA, Shultz JL, Keller KE, Martin RR, Inglis DA, Rajesh PN, McPhee KE, Weeden NF, Grusak MA, Li CM, Storlie EW (2007) Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes. Genome 50:871–875

    PubMed  CAS  Google Scholar 

  • Cregan PB, Mudge J, Fickus EW, Danesh D, Denny R, Young ND (1996) Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor Appl Genet 99:811–818

    Google Scholar 

  • Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG et al (1999) An integrated genetic linkage map of the soybean genome. Crop Sci 39:1464–1490

    CAS  Google Scholar 

  • D’Erfurth I, Cosson V, Eschstruth A, Lucas H, Kondorosi A, Ratet P (2003) Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula. Plant J 34:95–106

    PubMed  Google Scholar 

  • Dubey A, Farmer A, Schlueter J, Cannon SB, Abernathy B, Tuteja R (2011) Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.). DNA Res 18:153–164

    PubMed  CAS  Google Scholar 

  • Dutta S, Kumawat G, Singh BP, Gupta DK, Singh S, Dogra V (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea (Cajanus cajan (L.) Millspaugh). BMC Plant Biol 11:17

    PubMed  CAS  Google Scholar 

  • Eathington SR, Crosbie TM, Edwards MD, Reiter RS, Bull JK (2007) Molecular markers in a commercial breeding program. Crop Sci 47:S154–S163

    Google Scholar 

  • Ender M, Terpstra K, Kelly JD (2008) Marker-assisted selection for white mold resistance in common bean. Mol Breed 21:149–157

    CAS  Google Scholar 

  • Endre G, Kereszt A, Kevei Z, Mihacea S, Kalo P, Kiss GB (2002) A receptor kinase gene regulating symbiotic nodule development. Nature 417:962–966

    PubMed  CAS  Google Scholar 

  • Faleiro FG, Ragagnin VA, Carvalho GA, Paula TJ Jr, Moreira MA, Barros EG (2001) Development of common bean lines resistant to rust and anthracnose by molecular marker-assisted backcrossing. Annu Rep Bean Improvement Coop 44:1130–1133

    Google Scholar 

  • Firnhaber C, Puhler A, Kuster H (2005) EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods. Planta 222:269–283

    PubMed  CAS  Google Scholar 

  • Foncéka D, Hodo-Abalo T, Rivallan R, Faye I, Sall MN, Ndoye O (2009) Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid. BMC Plant Biol 9:103

    PubMed  Google Scholar 

  • Galeano CH, Fernandez AC, Franco-Herrera N, Cichy KA, McClean PE (2011) Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean. PLoS One 6(12):e28135. doi:10.1371/journal.pone.0028135

    PubMed  CAS  Google Scholar 

  • Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G (2011a) Gene discovery and tissue-specific transcriptome analysis in Chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol 156:1661–1678

    PubMed  CAS  Google Scholar 

  • Garg R, Patel RK, Tyagi AK, Jain M (2011b) De Novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18:53–63

    PubMed  CAS  Google Scholar 

  • Gaur R, Sethy NK, Choudhary S, Shokeen B, Gupta V, Bhatia S (2011) Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.). BMC Genomics 12:117

    PubMed  CAS  Google Scholar 

  • Gaur PM, Jukanti AK, Varshney RK (2012) Impact of genomic technologies on chickpea breeding strategies. Agronomy 2:199–221

    Google Scholar 

  • Gepts P, Beavis WD, Brummer CE, Shoemaker RC, Stalker TH, Weeden NF, Young ND (2005) Legumes as a model plant family. Genomics for food and feed report of the cross-legume advances through genomics conference. Plant Physiol 137:1228–1235

    PubMed  CAS  Google Scholar 

  • Gepts P, Aragão F, de Barros E, Blair MW, Brondani R, Broughton W, Galasso I, Hernández G, Kami J, Lariguet P, McClean P, Melotto M, Miklas P, Pauls P, Pedrosa-Harand A, Porch T, Sánchez F, Sparvoli F, Yu K (2008) Genomics of Phaseolus beans, a major source of dietary protein and micronutrients in the tropics. In: Moore P, Ming R (eds) Genomics of tropical crop plants. Springer, New York, NY, pp 113–143

    Google Scholar 

  • Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185

    CAS  Google Scholar 

  • Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Sci 49:1–12

    CAS  Google Scholar 

  • Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R (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

    PubMed  CAS  Google Scholar 

  • Hiremath PJ, Kumar A, Penmetsa RV, Farmer A, Schlueter JA, Chamarthi SK (2012) Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol J. doi:10.1111/j.1467-7652.2012.00710.x

    PubMed  Google Scholar 

  • Hofer J, Turner L, Moreau C, Ambrose M, Isaac P, Butcher S, Weller J, Dupin A, Dalmais M, Le Signor C, BendahmaneA EN (2009) Tendril-less regulates tendril formation in pea leaves. Plant Cell 21:420–428

    PubMed  CAS  Google Scholar 

  • Horst I, Welham T, Kelly S, Kaneko T, Sato S, Tabata S, Parniske M, Wang TL (2007) TILLING mutants of Lotus japonicus reveal that nitrogen assimilation and fixation can occur in the absence of nodule-enhanced sucrose synthase. Plant Physiol 144:806–820

    PubMed  CAS  Google Scholar 

  • Hospital F (2005) Selection in backcross programmes. Phil Trans R Soc B 360:1503–1511

    PubMed  CAS  Google Scholar 

  • Hyten DL, Song O, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor Corrales M, Cregan PB (2010) High-throughput SNP discovery and assay development in common bean. BMC Genomics 11:475

    PubMed  Google Scholar 

  • Isemura T, Kaga A, Tabata S, Somta P, Srinives P et al (2012) Construction of a genetic linkage map and genetic analysis of domestication related traits in mungbean (Vigna radiata). PLoS One 7(8):e41304. doi:10.1371/journal.pone.0041304

    PubMed  CAS  Google Scholar 

  • Jackson SA, Rokhsar D, Stacey G, Shoemaker RC, Schmutz J, Grimwood J (2006) Toward a reference sequence of the soybean genome: a multiagency effort. Crop Sci 46:555–561

    Google Scholar 

  • Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genom Prot 9:166–177

    CAS  Google Scholar 

  • Jayashree B, Buhariwalla HK, Shinde S, Crouch JH (2005) A legume genomics resource: the chickpea root expressed sequence tag database. Electron J Biotechnol 8:128–133

    CAS  Google Scholar 

  • Jones KM, Sharopova N, Lohar DP, Zhang JQ, VandenBosch KA, Walker GC (2008) Differential response of the plant Medicago truncatula to its symbiont Sinorhizobium meliloti or an exopolysaccharide-deficient mutant. Proc Natl Acad Sci U S A 105:704–709

    PubMed  CAS  Google Scholar 

  • Kaczorowski KA, Kim KS, Diers BW, Hudson ME (2008) Microarray-based genetic mapping using soybean near-isogenic lines and generation of SNP markers in the Rag1 aphid-resistance interval. Plant Genome 1:89–98

    CAS  Google Scholar 

  • Kassa MT, Penmetsa RV, Carrasquilla-Garcia N, Sarma BK, Datta S, Upadhyaya HD (2012) Genetic patterns of domestication in pigeonpea (Cajanus cajan (L.) Millsp.) and wild Cajanus relatives. PLoS One 7:e39563

    PubMed  CAS  Google Scholar 

  • Kudapa H, Bharti AK, Cannon SB, Farmer AD, Mulaosmanovic B, Kramer R (2012) A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using Sanger and second-generation sequencing platforms. Mol Plant 1–9; doi:10.1093/mp/ssr111

  • Kuester H, Hohnjec N, Krajinski F, El Yahyaoui F, Manthey K, Gouzy J, Dondrup M, Meyer F, Kalinowski J, Brechenmacher L, van Tuinen D, Gianinazzi-Pearson V, Pühler A, Gamas P, Becker A (2004) Construction and validation of cDNA-based Mt6k-RIT macroarray and microarray to explore root endosymbioses in the model legume Medicago truncatula. J Biotechnol 108:95–113

    Google Scholar 

  • Kuhar K, Gupta VK, Kansal R, Gupta VK (2012) Isolation and in silico characterization of cDNA encoding cyclophilin from etiolated Vigna mungo seedlings. Braz J Plant Physiol 24:69–73

    CAS  Google Scholar 

  • Kumar J, Choudhary A, Solanki RK, Pratap A (2011) Towards marker-assisted selection in pulses—a review. Plant Breed 130:297–313

    CAS  Google Scholar 

  • Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, AntonescuV CA, Cheung F, Quackenbush J (2005) The TIGR gene indices: clustering and assembling EST and known genes and integration witheukaryotic genomes. Nucleic Acids Res 33:D71–D74

    PubMed  CAS  Google Scholar 

  • Lewers K, Heinz R, Beard H, Marek L, Matthews B (2002) A physical map of a gene- dense region in soybean linkage group A2 near the black seed coat and Rhg4 loci. Theor Appl Genet 104:254–260

    PubMed  CAS  Google Scholar 

  • Li X, Han Y, Teng W, Zhang S, Yu K, Poysa V, Anderson T, Ding J, Li W (2010) Pyramided QTL underlying tolerance to phytophthora root rot in mega-environments from soybean cultivars Conrad and Hefeng 25. Theor Appl Genet. doi:10.1007/S00122-010-1337-2

    Google Scholar 

  • Liu N, Shan Y, Wang FP, Xu G, Peng KM, Li XH, Zhang Q (2001) Identification of an 85-kb DNA fragment containing pms 1, a locus for photoperiod-sensitive genic male-sterility in rice. Mol Genet Genomics 266:271–275

    PubMed  CAS  Google Scholar 

  • Liu J, Blaylock LA, Endre G, Cho J, Town CD, VandenBosch KA, Harrison MJ (2003) Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of an arbuscular mycorrhizal symbiosis. Plant Cell 15:2106–2123

    PubMed  CAS  Google Scholar 

  • Lohar DP, Sharopova N, Endre G, Penuela S, Samac D, Town C, Silverstein KAT, VandenBosch KA (2006) Transcript analysis of early nodulation events in Medicago truncatula. Plant Physiol 140:221–234

    PubMed  CAS  Google Scholar 

  • Lucas MR, Diop N, Wanamaker S, Ehlers JD, Roberts PA, Close TJ (2011) Cowpea–soybean synteny clarified throughan improved genetic map. Plant Genome 4:218–225

    CAS  Google Scholar 

  • Mallikarjuna N, Senapathy S, Jadhav DR, Saxena KB, Sharma HC, Upadhyaya HD (2011) Progress in the utilization of Cajanus platycarpus in pigeonpea improvement. Plant Breed 130:507–514

    CAS  Google Scholar 

  • Mantri NL, Ford R, Coram TE, Pang ECK (2007) Transcriptional profiling of chickpea genes differentially regulated in response to high-salinity, cold and drought. BMC Genomics 8:303–316

    PubMed  Google Scholar 

  • Mantri NL, Coram TE, Ford R, Pang ECK (2010) Evidence of unique and shared responses to major biotic and abiotic stresses in chickpea. Environ Exp Bot 69:286–292

    Google Scholar 

  • Mayor PJ, Bernardo R (2009) Genomewide selection and marker-assisted recurrent selection in doubled haploid versus F2 populations. Crop Sci 49:1719–1725

    Google Scholar 

  • Meyers BC, Galbraith DW, Nelson T, Agrawal V (2004) Methods for transcriptional profiling in plants: be fruitful and replicate. Plant Physiol 135:637–652

    PubMed  CAS  Google Scholar 

  • Miklas PN (2002) Marker assisted selection for disease resistance in common beans. Ann Rep Bean Improv Coop 45:1–3

    Google Scholar 

  • Miklas PN, Kelly JD, Singh S (2003) Registration of anthracnose resistant pinto bean germplasm line USPT-ANT-1. Crop Sci 43:1889–1890

    Google Scholar 

  • 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 9:553–580

    PubMed  Google Scholar 

  • Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA, Close TJ (2009) A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proc Natl Acad Sci 106:18159–18164

    PubMed  CAS  Google Scholar 

  • Mustafa BM, Coram TE, Pang ECK, Taylor PWJ, Ford R (2009) A cDNA microarray approach to decipher Ascochyta blight resistance in lentil. Austr Plant Pathol 38:617–631

    CAS  Google Scholar 

  • Mutlu N, Urrea CA, Miklas PN, Steadman JR, Pastor Corrales MA, Lindgren DT, Reiser J, Vidaver AK, Coyne DP (2008) Registration of common bacterial blight, rust and bean common mosaic resistant great northern bean germplasm line Abc-weighing. J Plant Reg 2:120–124

    Google Scholar 

  • Narasimhamoorthy B, Bouton JH, Olsen KM, Sledge MK (2007) Quantitative trait loci and candidate gene mapping of aluminum tolerance in diploid alfalfa. Theor Appl Genet 114:901–913

    PubMed  CAS  Google Scholar 

  • Navarro FM, Sass ME, Nienhuis J (2009) Marker-facilitated selection for a major QTL associated with root rot resistance in snap bean (Phaseolus Vulgaris L.). Crop Sci 49:850–856

    CAS  Google Scholar 

  • Nayak SN, Zhu H, Varghese N, Datta S, Choi HK, Horres R (2010) Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theor Appl Genet 120:1415–1441

    PubMed  CAS  Google Scholar 

  • Nunberg A, Bedell JA, Budiman MA, Citek RW, Clifton SW, Fulton L, Pape D, Cai Z, Joshi T, Nguyen H, Xu D, Stacey G (2006) Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats. Funct Plant Biol 33:765–773

    Google Scholar 

  • Nunes AC, Vianna GR, Cuneo F, Amaya-Farfan J, deCap deville G, Rech EL, Aragao FJ (2006) RNAi-mediated silencing of the myo-inositol-1-phosphate synthase gene (GmMIPS1) in transgenic soybean inhibited seed development and reduced phytate content. Planta 224:125–132

    PubMed  CAS  Google Scholar 

  • O’Rourke IJA, Charlson DV, Gonzalez DO, Vodkin LO, Graham MA, Cianzio SR, Grusak MA, Shoemaker RC (2007) Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines. BMC Genomics 8:476–488

    PubMed  Google Scholar 

  • Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN et al (2012) Advances in Arachis genomics for peanut improvement. Biotechnol Adv 30:639–651

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Perry J, Brachmann A, Welham T, Binder A, Charpentier M, Groth M, Haage K, Markmann K, Wang TL, Parniske M (2009) TILLING in Lotus japonicas identified large allelic series for symbiosis genesand revealed a bias in functionally defective ethyl methane sulfonate alleles toward glycine replacements. Plant Physiol 151:1281–1291

    PubMed  CAS  Google Scholar 

  • Polegri L, Negri V (2010) Molecular markers for promoting agro-biodiversity conservation: a case study from Italy. How cowpea landraces were saved from extinction. Genet Res Crop Evol 57:867–880

    CAS  Google Scholar 

  • Pratap A, Gupta SK, Kumar J, Solanki RK (2012) Soybean. In: Gupta SK (ed) Technological innovations in major world oil crops, Vol I. Breeding. Springer Science + Business Media, New York, NY, pp 293–321

    Google Scholar 

  • Rajesh PN, Coyne C, Meksem K, DerSharma K, Gupta V, Muehlbauer FJ (2004) Construction of a HindIII bacterial artificial chromosome library and its use in identification of clones associated with disease resistance in chickpea. Theor Appl Genet 108:663–669

    PubMed  CAS  Google Scholar 

  • Raju NL, Gnanesh BN, Pazhamala L, Jayashree B, Pande S, Hiremath PJ, Byregowda M et al (2010) The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.). BMC Plant Biol 10:45

    PubMed  Google Scholar 

  • Reddy MS, Dinkins RD, Collins GB (2003) Gene silencing in transgenic soybean plants transformed via particle bombardment. Plant Cell Rep 21:676–683

    PubMed  CAS  Google Scholar 

  • Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K, Fujishiro T, Katoh M, Kohara M, Kishida Y, Minami C, Nakayama S, Nakazaki N, Shimizu Y, Shinpo S, Takahashi C, Wada T, Yamada M, Ohmido N, Hayashi M, Fukui K, Baba T, Nakamichi T, Mori H, Tabata S (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15:227–239

    PubMed  CAS  Google Scholar 

  • Saxena KB, Nadarajan N (2010) Prospects of pigeonpea hybrids in Indian agriculture. Electron J Plant Breed 1:1107–1117

    Google Scholar 

  • Schlueter JA, Goicoechea JL, Collura K, Gill N, Lin JY, Yu Y, Kudrna D, Zuccolo A, Vallejos CE, Muñoz-Torres M, Blair MW, Tohme J, Tomkins J, McClean P, Wing RA, Jackson SA (2008) BAC-end sequence analysis and a draft physical map of the common bean (Phaseolus vulgaris L.) genome. Trop Plant Biol 1:40–48

    CAS  Google Scholar 

  • Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183

    PubMed  CAS  Google Scholar 

  • Shi A, Chen P, Li D, Zheng C, Zhang B, Hou A (2009) Pyramiding multiple genes for resistance to soybean mosaic virus in soybean using molecular markers. Mol Breed 23:113–124

    CAS  Google Scholar 

  • Shoemaker RC, Schlueter JA, Cregan P, Vodkin L (2003) The status of soybean genomics and its role in the development of soybean biotechnologies. Agric Bio Forum 6:4–7

    Google Scholar 

  • Simpson CE, Krapovickas A, Valls JFM (2001) History of Arachis including evidence of A. hypogaea L. progenitors. Peanut Sci 28:78–79

    Google Scholar 

  • Singh NK, Gupta DK, Jayaswal PK, Mahato AK, Dutta S (2012) The first draft of the pigeon pea genome sequence. J Plant Biochem Biotechnol. doi:10.1007/s13562-011-0088-8

    Google Scholar 

  • Smith J (2010) USDA, ARS, National Genetic Resources Program. Germplasm Resources Information Network – (GRIN) [Online Database]. National Germplasm Resources Laboratory, Beltsville, MD. http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl. Accessed 17 May 2013

  • Solanki RK, Singh S, Kumar J (2010) Molecular marker-assisted testing of hybridity of F1 plants in lentil. J Food Leg 23:21–24

    Google Scholar 

  • Stavely JR (2000) Pyramiding rust and viral resistance genes using traditional and marker techniques in common bean. Ann Rep Bean Improv Coop 43:1–3

    Google Scholar 

  • Stracke S, Kistner C, Yoshida S, Mulder L, Sato S, Kaneko T, Tabata S, Sandal N, Stougaard J, Szczyglowski K, Parniske M (2002) A plant receptor-like kinase required for both bacterial and fungal symbiosis. Nature 417:959–962

    PubMed  CAS  Google Scholar 

  • Subramanian S, Graham MY, Yu O, Graham TL (2005) RNA interference of soybean isoflavone synthase genes leads to silencing in tissues distal to the transformation site and to enhanced susceptibility to Phytophthora sojae. Plant Physiol 137:1345–1353

    PubMed  CAS  Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

    PubMed  CAS  Google Scholar 

  • Tao Q, Chang YL, Wang J, Chen H, Islam-Faridi MN, Scheuring C, Wang B, Stelly DM, Zhang HB (2001) Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 158:1711–1724

    PubMed  CAS  Google Scholar 

  • Taunk J, Yadav NR, Yadav RC, Kumar R (2012) Genetic diversity among green gram (Vigna radiata L. Wilczek) genotypes varying in micronutrient content using RAPD. Ind J Bitechnol 11:48–53

    CAS  Google Scholar 

  • Thudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Penmetsa RV (2011) Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PLoS One 6:e27275

    PubMed  CAS  Google Scholar 

  • Timko MP, Rushton PJ, Laudeman TW, Bokowiec MT, Chipumuro E, Cheung F, Town CD, Chen X (2008) Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics 9:103

    PubMed  Google Scholar 

  • Triques K, Sturbois B, Gallais S, Dalmais M, Chauvin S, Clepet C, Aubourg S, Rameau C, Caboche M, Bendahmane A (2007) Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea. Plant J 51:1116–1125

    PubMed  CAS  Google Scholar 

  • Van de Wouw M, Van Hinten T, Kik C, Van Treuren R, Visser B (2010) Genetic diversity trends in twentieth century crop cultivars: a meta analysis. Theor Appl Genet 120:1241–1252

    Google Scholar 

  • Vance CP, Graham PH, Allan DL (2000) Biological nitrogen fixation phosphorus: a critical future need. In: Pedrosa FO, Hungria M, Yates MG, Newton WE (eds) Nitrogen fixation: from molecules to crop productivity. Kluwer, Dordrecht, pp 506–514

    Google Scholar 

  • Vanden Bosch K, Stacey G (2003) Summaries of legume genomics projects from around the globe. Community resources for crops and models. Plant Physiol 131:840–865

    Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55

    PubMed  CAS  Google Scholar 

  • Varshney RK, Bertioli DJ, Moretzsohn MC, Vadez V, Krishnamurthy L, Aruna R, Nigam SN, Moss BJ, Seetha K, Ravi K, He G, Knapp SJ, Hoisington DA (2009a) The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theor Appl Genet 118:729–739

    PubMed  CAS  Google Scholar 

  • Varshney RK, Close TJ, Singh NK, Hoisington DA, Cook DR (2009b) Orphan legume crops enter the genomics era! Curr Opin Plant Biol 12:1–9

    Google Scholar 

  • Varshney RK, Thudi M, May GD, Jakson SA (2010) Legume genomics and breeding. Plant Breed Rev 33:257–304

    Google Scholar 

  • Varshney RK, Kudapa H, Roorkiwal M, Thudi M, Pandey MK, Saxena RK et al (2012) Advances in genomics research and molecular breeding applications in SAT legume crops by using next generation sequencing and high-throughput genotyping technologies. J Biosci 37:811–820

    PubMed  CAS  Google Scholar 

  • 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, Lu MC, Thudi M, Gowda CLL, 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 S, Wang J, Cook DR (2013a) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol. doi:10.1038/nbt.2491

    PubMed  Google Scholar 

  • Varshney RK, Mohan SM, Gaur PM, Gangarao NVPR, Pandey MK, Bohra A, Sawargaonkar SL, Gorantla A, Kimurto PK, Janila P, Saxena KB, Fikre A, Sharma M, Rathore A, Pratap A, Tripathi S, Datta S, Chaturvedi SK, Mallikarjuna N, Anuradha G, Babbar A, Choudhary AK, Mhase MB, Bharadwaj Ch, Mannur DM, Harer PN, Guo B, Liang X, Nadarajan N, Gowda CLL (2013b) Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv (http://dx.doi.org/10.1016/j.biotechadv.2013.01.001)

    Google Scholar 

  • Verdier J, Kakar K, Gallardo K, Le Signor C, Aubert G, Schlereth A, Town CD, Udvardi MK, Thompson RD (2008) Gene expression profiling of Medicago truncatula transcription factors identifies putative regulators of grain legume seed filling. Plant Mol Biol 67:567–580

    PubMed  CAS  Google Scholar 

  • Vodkin LO, Khanna A, Shealy R, Clough SJ, Gonzalez DO, Philip R, Zabala G, Thibaud-Nissen F, Sidarous M, Stromvik MV, Shoop E, Schmidt C, Retzel E, Erpelding J, Shoemaker RC, Rodriguez-Huete AM, Polacco JC, Coryell V, Keim P, Gong G, Liu L, Pardinas J, Schweitzer P (2004) Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC Genomics 5:73–90

    PubMed  Google Scholar 

  • Warrington CV, Zhu S, Parrot WA, All JN, Boerma HR (2008) Seed yield of near isogenic soybean lines introgressed with quantitative trait loci conditioning resistance to corn earworm (Lepidopter: Noctuidae) and soybean looper (Lepidoptera: Noctuidae) from PI 229358. J Econ Entomol 101:1471–1477

    PubMed  CAS  Google Scholar 

  • Wu C, Sun S, Nimmakayala P, Santos FA, MeksemK SR, Ding K, Lightfoot DA, Zhang HB (2004) A Bac- and Bibac-based physical map of the soybean genome. Genome Res 14:319–326

    PubMed  CAS  Google Scholar 

  • Xu M, Song J, Cheng Z, Jiang J, Korban SS (2001) A bacterial artificial chromosome (BAC) library of Malus floribunda 821 and contig construction for positional cloning of the apple scab resistance gene Vf. Genome 44:1104–1113

    PubMed  CAS  Google Scholar 

  • Yahyaoui FE, Kuster H, Amor BB, Hohnjec N, Puhler A, Becker A, Gouzy J, Vernie T, Gough C, Niebel A, Godiard L, Gamas P (2004) Expression profiling in Medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbioticprogram. Plant Physiol 136:3159–3176

    PubMed  Google Scholar 

  • Yang SY, Saxena RK, Kulwal PA, Ash GJ, Dubey A, Harper DI (2011) The first genetic map of pigeonpea based on diversity arrays technology (DArT) markers. J Genet 90:103–109

    PubMed  Google Scholar 

  • Young ND, Udvardi M (2009) Translating Medicago truncatula genomics to crop legumes. Curr Opin Plant Biol 12:193–201

    PubMed  CAS  Google Scholar 

  • Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S (2005) Sequencing the gene spaces of Medicago truncatula and Lotus japonicus. Plant Physiol 137:1174–1181

    PubMed  CAS  Google Scholar 

  • Yu K (2012) Bacterial artificial chromosome libraries of pulse crops: Characteristics and applications. J Biomedicine Biotechnol. Article ID 493186 doi:10.1155/2012/493186

  • Zhang X, Scheuring CF, Zhang M, Dong JJ, Zhang Y, HuangJJ LMK, Abbo S, Sherman A, Shtienberg D, Chen W, Muehlbauer F, Zhang HB (2010) A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L. BMC Genomics 11:501

    PubMed  Google Scholar 

  • Zong X, Redden R, Liu Q, Wang S, Guan J, Liu J, Xu Y, Liu X, Gu J, Yan L, Ades P, Ford R (2009) Analysis of a diverse global Pisum sp. collection and comparison to a Chinese local P. sativum collection with microsatellite markers. Theor Appl Genet 118:193–204

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Crop Improvement Division, Indian Institute of Pulses Research, G.T. Road, Kanpur, Uttar Pradesh, 208024, India

    Aditya Pratap Ph.D., Rakhi Tomar M.Sc., Jitendra Kumar Ph.D., Nupur Malviya Ph.D. & Tuba K. Anjum M.Sc.

  2. Krishi Vigyan Kendra, Ramakrishna Mission Ashram, Ranchi, Jharkhand, India

    Neha Rajan M.Sc.

  3. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India

    Pooja Bhatnagar Mathur Ph.D.

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  1. Aditya Pratap Ph.D.
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  4. Jitendra Kumar Ph.D.
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Correspondence to Aditya Pratap Ph.D. .

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  1. Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

    Sanjeev Gupta

  2. Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

    Nagasamy Nadarajan

  3. Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA

    Debjyoti Sen Gupta

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Pratap, A. et al. (2014). Towards Enriching Genomic Resources in Legumes. In: Gupta, S., Nadarajan, N., Gupta, D. (eds) Legumes in the Omic Era. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8370-0_11

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