Abstract
In the past decade, innovations in high-throughput sequencing (next-generation sequencing) technologies have accelerated whole-genome sequencing of various non-model crop species. Taking advantage of huge polymorphic sequence data provided by the results of whole-genome sequencing, we can easily develop novel molecular markers. It may boost the use of forward genetics approach to isolating the corresponding genes for QTLs in non-model crops. Furthermore, this forward genetics approach is a steady and robust method but it is still difficult to increase its throughput. The sequenced genes have been annotated on the basis of sequence similarity; however, the functions of most genes (and the resulting phenotypes) are still obscure. Although we can easily obtain multiple crop genomic sequences from public databases, it is necessary to increase the throughput of functional genomics. Reverse genetics, which uses mutants or transgenic lines for the genes of interest, is an attractive approach to determine gene function. Mutant-based reverse genetics has several advantages over transgene-based reverse genetics: (a) its higher throughput, (b) the absence of restrictions for growing non-transgenic mutants in the field and (c) the possibility to use the mutants directly for traditional cross-breeding programs as valuable genetic resources of non-model crops. This chapter describes recent advances in functional genomics research on non-model crops, with a focus on mutant-based reverse genetics approaches.
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References
AGI Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
Alonso JM, Stepanova AN, Leisse TJ et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653–657
Anai T (2012) Potential of a mutant-based reverse genetic approach for functional genomics and molecular breeding in soybean. Breed Sci 61:462–467
Argout X, Salse J, Aury JM et al (2011) The genome of Theobroma cacao. Nat Genet 43:101–108
Ashikari M, Sakakibara H, Lin S et al (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745
Bolger ME, Weisshaar B, Scholz U et al (2014) Plant genome sequencing – applications for crop improvement. Curr Opin Biotechnol 26:31–37
Bolon Y-T, Haun WJ, Xu WW et al (2011) Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiol 156:240–253
Botticella E, Sestili F, Hernandez-Lopez A et al (2010) High resolution melting analysis for the detection of EMS induced mutations in wheat SbeIIa genes. BMC Plant Biol 11:156
Boualem A, Fleurier S, Troadec C et al (2014) Development of a Cucumis sativus TILLinG platform for forward and reverse genetics. PLoS One 9:e97963
Chantreau M, Grec S, Gutierrez L et al (2013) PT-Flax (phenotyping and TILLinG of flax): development of a flax (Linum usitatissimum L.) mutant population and TILLinG platform for forward and reverse genetics. BMC Plant Biol 13:159
Colbert T, Till BJ, Tompa R et al (2001) High-throughput screening for induced point mutations. Plant Physiol 126:480–484
Cong L, Ran FA, Cox D et al (2013) Multiplex genome engineering using CRISPR/cas systems. Science 339:819–823
Cooper JL, Till BJ, Laport RG et al (2008) TILLING to detect induced mutations in soybean. BMC Plant Biol 8:9
D’Hont A, Denoeud F, Aury JM et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488:213–217
Garcia-Mas J, Benjak A, Sanseverino W et al (2012) The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A 109:11872–11877
Gengyo-Ando K, Mitani S (2000) Characterization of mutations induced by ethyl methanesulfonate, UV, and trimethylpsoralen in the nematode Caenorhabditis elegans. Biochem Biophys Res Comm 269:64–69
Goff SA, Ricke D, Lan TH, Presting G et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100
Greene EA, Codomo CA, Taylor NE et al (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics 164:731–740
Guo S, Zhang J, Sun H et al (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45:51–58
Hoshino T, Takagi Y, Anai T (2010) Novel GmFAD2-1b mutant alleles created by reverse genetics induce marked elevation of oleic acid content in soybean seed in combination with GmFAD2-1a mutant alleles. Breed Sci 60:419–425
Huang S, Li R, Zhang Z et al (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275–1281
IBGS Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716
Ichikawa T, Nakazawa M, Kawashima M et al (2006) The FOX hunting system: an alternative gain-of-function gene hunting technique. Plant J 48:974–985
International Peach Genome Initiative (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494
Jaillon O, Aury JM, Noel B et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467
Jung K-H, An G, Ronald PC (2008) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat Rev Genet 9:91–101
Kazama Y, Hirano T, Saito H, Liu Y et al (2011) Characterization of highly efficient heavy-ion mutagenesis in Arabidopsis thaliana. BMC Plant Biol 11:161
Knoll JE, Ramos ML, Zeng Y et al (2011) TILLING for allergen reduction and improvement of quality traits in peanut (Arachis hypogaea L.). BMC Plant Biol 11:81
Krishnan A, Guiderdoni E, An G et al (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol 149:165–170
Kumar APK, Boualem A, Bhattacharya A et al (2013) SMART – Sunflower mutant population and reverse genetic tool for crop improvement. BMC Plant Biol 13:38
Li X, Song Y, Century K et al (2001) A fast neutron deletion mutagenesis-based reverse genetics system for plants. Plant J 27:235–242
Li T, Liu B, Spalding MH et al (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30:390–392
Lloyd A, Plaisier CL, Carroll D, Drews GN (2005) Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proc Natl Acad Sci U S A 102:2232–2237
Maluszynski M, Ahloowalia BS, Sigurbjörnsson B (1995) Application of in vivo and in vitro mutation techniques for crop improvement. Euphytica 85:303–315
Mayer KFX, Martis M, Hedley PE et al (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249–1263
McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeted screening for induced mutations. Nat Biotechnol 18:455–457
Ming R, Hou S, Feng Y, Yu Q (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–996
Minoia S, Petrozza A, D’Onofrio O et al (2010) A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Res Notes 3:69
Miyao A, Tanaka K, Murata K et al (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15:1771–1780
Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556
Potato Genome Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195
Powell ALT, Nguyen CV, Hill T et al (2012) Uniform ripening encodes a golden 2-like transcription factor regulating tomato fruit chloroplast development. Science 336:1711–1715
Riedelsheimer C, Czedik-Eysenberg A, Grieder C et al (2012) Genomic and metabolic prediction of complex heterotic traits in hybrid maize. Nat Genet 44:217–220
Rigola D, van Oeveren J, Janssen A et al (2009) High-throughput detection of induced mutations and natural variation using KeyPointâ„¢ technology. PLoS One 4:e4761
Sato Y, Shirasawa K, Takashashi Y et al. (2006) Mutant selection from progeny of gamma-ray-irradiated rice by DNA heteroduplex cleavage using Brassica petiole extract. Breed Sci 56:179–183.
Satoh H, Matsusaka H, Kumamaru T (2010) Use of N-methyl-N-nitrosourea treatment of fertilized egg cells for saturation mutagenesis of rice. Breed Sci 60:475–485
Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183
Schnable PS, Ware D, Fulton RS et al (2009) The b73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115
Schwab R, Ossowski S, Riester M et al (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18:1121–1133
Sessions A, Burke E, Presting G et al (2002) A high-throughput Arabidopsis reverse genetics system. Plant Cell 14:2985–2994
Shaked H, Melamed-Bessudo C, Levy AA (2005) High-frequency gene targeting in Arabidopsis plants expressing the yeast RAD54 gene. Proc Natl Acad Sci U S A 102:2232–2237
Shulaev V, Sargent DJ, Crowhurst RN et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109–116
Slade AJ, Fuerstenberg SI, Loeffler D et al (2005) A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 23:75–81
Stephenson P, Baker D, Girin T et al (2010) A rich TILLING resource for studying gene function in Brassica rapa. BMC Plant Biol 10:62
Suzuki T, Eiguchi M, Kumamaru T, Satoh H (2008) MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Mol Genet Genomics 279:213–223
Talamè V, Bovina R, Sanguineti MC et al (2008) TILLMore, a resource for the discovery of chemically induced mutants in barley. Plant Biotechnol J 6:477–485
Till BJ, Reynolds SH, Weil C et al (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:12
Till BJ, Cooper J, Tai TH, Colowit P (2007) Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol 7:19
Tissier AF, Marillonnet S, Klimyuk V et al (1999) Multiple independent defective suppressor-mutator transposon insertions in Arabidopsis: a tool for functional genomics. Plant Cell 11:1841–1852
Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641
Tuskan GA, Difazio S, Jansson S et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604
Uauy C, Paraiso F, Colasuonno P et al (2009) A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat. BMC Plant Biol 9:115
Varshney RK, Song C, Saxena RK et al (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246
Varshney RK, Terauchi R, McCouch SR (2014) Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol 12:e1001883
Velasco R, Zharkikh A, Troggio M et al (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One 2:e1326
Velasco R, Zharkikh A, Affourtit J et al (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833–839
Wang N, Wang Y, Tian F et al (2008) Functional genomics resource for Brassica napus: development of an EMS mutagenized population and discovery of FAE1 point mutations by TILLING. New Phytol 180:751–765
Wang X, Wang H, Wang J et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039
Watanabe S, Hideshima R, Xia Z et al (2009) Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics 182:1251–1262
Watanabe S, Xia Z, Hideshima R et al (2011) A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics 188:395–407
Waterhouse PM, Helliwell CA (2003) Exploring plant genomes by RNA-induced gene silencing. Nat Rev Genet 4:29–38
Wu J-L, Wu C, Lei C et al (2005) Chemical- and irradiation-induced mutants of Indica rice IR64 for forward and reverse genetics. Plant Mol Biol 59:85–97
Xia Z, Watanabe S, Yamada T et al (2012) Positional cloning and characterization reveal the molecular basis for soybean maturity locus e1 that regulates photoperiodic flowering. Proc Natl Acad Sci U S A 109:E2155–E2164
Xin Z, Wang ML, Barkley NA et al (2008) Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population. BMC Plant Biol 8:103
Xu Q, Chen LL, Ruan X et al (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45:59–66
Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92
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Anai, T. (2015). Mutant-Based Reverse Genetics for Functional Genomics of Non-model Crops. In: Al-Khayri, J., Jain, S., Johnson, D. (eds) Advances in Plant Breeding Strategies: Breeding, Biotechnology and Molecular Tools. Springer, Cham. https://doi.org/10.1007/978-3-319-22521-0_16
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DOI: https://doi.org/10.1007/978-3-319-22521-0_16
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