Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants

Journal of Biosciences

Volumn 38, Issue 5, 2013, Pages 971-987

  Kujur, Alice ^a   Saxena, Maneesha S ^a   Bajaj, Deepak ^a   Laxmi, ^a   Parida, Swarup K ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

Complex quantitative traits; genomics; molecular breeding; SNP; SSR

Indexed keywords

BIOTECHNOLOGY; CROP PLANT; GENOME; GENOMICS; GENOTYPE; MOLECULAR ANALYSIS; QUANTITATIVE ANALYSIS;

ABIOTIC STRESS; AGRONOMIC TRAIT; BIOTIC STRESS; BREEDING METHOD; CLIMATE CHANGE; CROP IMPROVEMENT; EPIGENETICS; GENETIC IMPROVEMENT; GENETIC RESOURCE; GENETIC SELECTION; GENOTYPE; HIGH THROUGHPUT SEQUENCING; MICROSATELLITE MARKER; NONHUMAN; PHENOTYPE; PLANT BREEDING; PLANT GENOME; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAIT LOCUS MAPPING; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTOMICS; VARIETAS;

ANIMALS; CHROMOSOME MAPPING; CLIMATE CHANGE; CROPS, AGRICULTURAL; DATABASES, GENETIC; DNA SHUFFLING; FOOD QUALITY; GENETIC MARKERS; GENOME, PLANT; GENOMICS; HUMANS; QUANTITATIVE TRAIT LOCI;

EID: 84891277402     PISSN: 02505991     EISSN: 09737138     Source Type: Journal    
DOI: 10.1007/s12038-013-9388-6     Document Type: Review

References (144)

1. Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, et al. 2012 Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol. 30 174-178
2. Akimoto K, Katakami H, Kim HJ, Ogawa E, Sano CM, Wada Y and Sano H 2007 Epigenetic inheritance in rice plants. Ann. Bot. 100 205-217
3. Anderson PK, Cunningham AA, Patel NG, Morales FJ, Epstein PR and Daszak P 2004 Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 19 535-544
4. Baroux C, Raissig MT and Grossniklaus U 2011 Epigenetic regulation and reprogramming during gamete formation in plants. Curr. Opin. Genet. Dev. 21 124-133
5. Basavaraj SH, Singh VK, Singh A, Singh A, Singh A, Yadav S, Ellur RK, Singh D, et al. 2010 Marker-assisted improvement of bacterial blight resistance in parental lines of Pusa RH10, a superfine grain aromatic rice hybrid. Mol. Breed. 2 293-305
6. Bernstein BE, Meissner A and Lander ES 2007 The mammalian epigenome. Cell 128 669-681
7. Boerjan W and Vuylsteke M 2009 Integrative genetical genomics in Arabidopsis. Nat. Genet. 41 144-145
8. Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, et al. 2012 Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491 705-710
9. Chakraborty S 2013 Migrate or evolve: options for plant pathogens under climate change. Glob. Chang. Biol. 19 1985-2000
10. Chia JM and Ware D 2011Sequencing for the cream of the crop. Nat Biotechnol. 29 138-139
11. Chinnusamy V and Zhu JK 2009 Epigenetic regulation of stress responses in plants. Curr. Opin. Plant Biol. 12 133-139
12. Choudhary S, Gaur R and Gupta S 2012 EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. Theor. Appl. Genet. 124 1449-1462
13. Choudhary S, Sethy NK, Shokeen B and Bhatia S 2009 Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor. Appl. Genet. 118 591-608
14. Clark R, Maccurdy R, Jung J, Shaff J, McCouch SR, Aneshansley D and Kochian L 2011 3-dimensional root phenotyping with a novel imaging and software platform. Plant Physiol. 156 455-465
15. Coakley SM, Scherm H and Chakraborty S 1999 Climate change and plant disease management. Annu. Rev. Phytopathol. 37 399-426
16. Cubas P, Vincent C and Coen E 1999 An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401 157-161
17. Du Z, Li H, Wei Q, Zhao X, Wang C, Zhu Q, Yi X, Xu W, et al. 2013 Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. Mol. Plant 6 1463-1472
18. Eckardt NA 2009 Deep sequencing maps the maize epigenomic landscape. Plant Cell 21 1024-1026
19. Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, et al. 2011 Heritable epigenetic variation among maize inbreds. PLoS Genet. 7 e1002372
20. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, et al. 2008 Genetics of gene expression and its effect on disease. Nature 452 423-428
21. Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV and McCouch SR 2011 Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet. 7 e1002221
22. Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X and Zhang Q 2006 GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 112 1164-1171
23. Fukai E, Stougaard J and Hayashi M 2013 Activation of an endogenous retrotransposon associated with epigenetic changes in Lotus japonicus: A tool for functional genomics in legumes. Plant Genome doi 10.3835/plantgenome2013.04. 0009
24. Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, et al. 2011b Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol. 156 1661-1678
25. Garg R, Patel RK, Tyagi AK and Jain M 2011a De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 18 53-63
26. Garrett KA, Dendy SP, Frank EE, Rouse MN and Travers SE 2006 Climate change effects on plant disease: genomes to ecosystems. Annu. Rev. Phytopathol. 44 489-509
27. Gaur PM, Jukanti AK and Varshney RK 2012a Impact of genomic technologies on chickpea breeding strategies. Agronomy 2 199-221
28. Gaur R, Azam S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, et al. 2012b High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res. 19 357-373
29. Gopalakrishnan S, Sharma RK, Rajkumar KA, Joseph M, Singh VP, Singh AK, Bhat KV, Singh NK, et al. 2008 Integrating marker-assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice. Plant Breed. 127 131-139
30. Gregory PJ, Johnson SN, Newton AC and Ingram JSI 2009 Integrating pests and pathogens into the climate change/food security debate. J. Exp. Bot. 60 2827-2838.
31. Gujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Bhanu Prakash A, Farmer A, Bhide M, et al. 2011 Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theor. Appl. Genet. 122 1577-1589
32. Harvell CD, Mitchell CE, Ward JR, Altizer S, Dobson AP, Ostfeld RS and Samuel MD 2002 Climate warming and disease risks for terrestrial and marine biota. Science 296 2158-2162
33. He G, Elling AA and Deng XW 2011 The epigenome and plant development. Annu. Rev. Plant Biol. 62 411-435
34. He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, et al. 2010 Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22 17-33
35. Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, Bhanuprakash A, et al. 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
36. Hiremath PJ, Kumar A, Penmetsa RV, Farmer A, Schlueter JA, Chamarthi SK, Whaley AM, Carrasquilla-Garcia N, et al. 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. 10 716-732
37. Huang BE, George AW, Forrest KL, Kilian A, Hayden MJ, Morell MK and Cavanagh CR 2012a A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol J. 10 826-839
38. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, et al. 2009 High-throughput genotyping by whole-genome resequencing. Genome Res. 19 1068-1076
39. Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, et al. 2012b A map of rice genome variation reveals the origin of cultivated rice. Nature 490 497-501
40. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, et al. 2010 Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 42 961-967
41. Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q, Li W, Guo Y, et al. 2012c Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet. 44 32-39
42. International Barley Genome Sequencing Consortium (IBGSC) 2012 A physical, genetic and functional sequence assembly of the barley genome. Nature 491 711-716
43. International Rice Genome Sequencing Project (IRGSP) 2005 The map-based sequence of the rice genome. Nature 436 793-800
44. Jain M 2012 Next-generation sequencing technologies for gene expression profiling in plants. Brief. Funct. Genomics 11 63-70
45. Jain M, Misra G, Patel RK, Priya P, Jhanwar S, Khan AW, Shah N, Singh VK, et al. 2013 A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J. 74 715-729
46. Jannink JL, Lorenz AJ and Iwata H 2010 Genomic selection in plant breeding: from theory to practice. Brief Funct. Genomics 9 166-177
47. Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK and Jain M 2012 Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol. J. 10 690-702
48. Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, et al. 2013 Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496 91-95
49. Joseph M, Gopala Krishnan S, Sharma RK, Singh VP, Singh AK, Singh NK and Mohapatra T 2004 Combining bacterial blight resistance and Basmati quality characteristics by phenotypic and molecular marker-assisted selection in rice. Mol. Breed. 13 377-387
50. Kapazoglou A, Engineer C, Drosou V, Kalloniati C, Tani E, Tsaballa A, Kouri ED, Ganopoulos I, et al. 2012 The study of two barley type I-like MADS-box genes as potential targets of epigenetic regulation during seed development. BMC Plant Biol. 12 166
51. Kashkush K, Feldman M, Levy AA 2003 Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet. 33 102-106
52. Kashkush K, Khasdan V 2007 Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 177 1975-1985
53. Kharabian-Masouleh A, Waters DLE, Reinke RF, Ward R and Henry RJ 2012 SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci. Rep. 2 557
54. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, et al. 2003 Rice Full-Length cDNA Consortium; Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301 376-379
55. Kim TY, Kim HU and Lee SY 2010 Data integration and analysis of biological networks. Curr. Opin Biotechnol. 21 78-84
56. Kohler C, Wolff P and Spillane C 2012 Epigenetic mechanisms underlying genomic imprinting in plants. Annu. Rev. Plant Biol. 63 18.1-18.22
57. Kota R, Varshney RK, Prasad M, Zhang H, Stein N and Graner A 2007 EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome. Funct. Integr. Genomics 8 223-233
58. Kujur A, Bajaj D, Saxena MS, Tripathi S, Upadhyaya HD, Gowda CL, Singh S, Jain M, et al. 2013 Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Res. 20 355-374
59. Langridge P and Fleury D 2011 Making the most of 'omics' for crop breeding. Trends Biotechnol. 29 33-40
60. Li H, Freeling M and Lisch D 2010 Epigenetic reprogramming during vegetative phase change in maize. Proc. Natl. Acad. Sci. USA 107 22184-22189
61. Li X, Wang X, He K, Ma Y, Su N, He H, Stolc V, Tongprasit W, et al. 2008 High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 20 259-276
62. Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, et al. 2011 Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet. 43 1266-1269
63. Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, et al. 2013 Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496 87-90
64. Lobell DB and Field CB 2007 Global scale climate-crop yield relationships and the impacts of recent warming. Environ. Res. Lett 2 004000 7 pp
65. Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, et al. 2010 Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res. 20 1238-1249
66. Manning K, Tör M, Poole M, Hong Y, Thompson AJ, King GJ, Giovannoni JJ and Seymour GB 2006 A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet. 38 948-952
67. Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X and Zhang Q 2010 Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc. Natl. Acad. Sci. USA 107 19579-19584
68. McCouch SR, Sweeney M, Li J, Jiang H, Thomson M, Septiningsih E, Edwards J, Moncada P, et al. 2007 Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica 154 317-339
69. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, et al. 2002 Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9 199-207
70. McNally KL, Bruskiewich R, Mackill D, Buell CR, Leach JE and Leung H 2006 Sequencing multiple and diverse rice varieties: connecting whole-genome variation with phenotypes. Plant Physiol. 141 26-31
71. McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, et al. 2009 Genome-wide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl. Acad. Sci. USA 106 12273-12278
72. Metzker ML 2010 Sequencing technologies-the next generation. Nat. Rev. Genet. 11 31-46
73. Meuwissen TH, Hayes BJ and Goddard ME 2001 Prediction of total genetic value using genome-wide dense marker maps. Genetics 157 1819-1829
74. Mir RR, Zaman-Allah M, Sreenivasulu N, Trethowan R and Varshney RK 2012 Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. Theor. Appl. Genet. 125 625-645
75. Mirouze M and Paszkowski J 2011 Epigenetic contribution to stress adaptation in plants. Curr. Opin. Plant Biol. 14 267-274
76. Mittler R 2006 Abiotic stress, the field environment and stress combination. Trends Plant Sci. 11 15-19
77. Miura K, Ashikari M and Matsuoka M 2011 The role of QTLs in the breeding of high-yielding rice. Trends Plant Sci. 16 319-326
78. Mukhopadhyay P, Singla-Pareek SL, Reddy MK and Sopory SK 2013 Stress-mediated alterations in chromatin architecture correlate with down-regulation of a gene encoding 60S rpL32 in rice. Plant Cell Physiol. 54 528-540
79. Nayak SN, Zhu H, Varghese N, Datta S, Choi HK, Horres R, Jüngling R, Singh J, et al. 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
80. Negrão S, Almadanim MC, Pires IS, Abreu IA, Maroco J, Courtois B, Gregorio GB, McNally KL, et al. 2013 New allelic variants found in key rice salt-tolerance genes: an association study. Plant Biotechnol. J. 11 87-100
81. Oliver SN, Finnegan EJ, Dennis ES, Peacock WJ and Trevaskis B 2009 Vernalization-induced flowering in cereals is associated with changes in histone methylation at the VERNALIZATION1 gene. Proc. Natl. Acad. Sci. USA 106 8386-8391
82. Pachauri RK and Reisinger A 2007 Intergovernmental Panel on Climate Change (IPCC); in Climate change synthesis report (eds) IPCC, Geneva
83. Parida SK, Dalal V, Singh NK and Mohapatra T 2009b Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups. BMC Genomics 10 140
84. Parida SK, Kalia SK, Kaul S, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, et al. 2009a Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor. Appl. Genet. 118 327-338
85. Parida SK, Mukerji M, Singh AK, Singh NK and Mohapatra T 2012 SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure. BMC Genomics 13 426
86. Parida SK, Rajkumar KA, Dalal V, Singh NK and Mohapatra T 2006 Unigene derived microsatellite markers for the cereal genomes. Theor. Appl. Genet. 112 808-817
87. Parida SK, Yadava DK and Mohapatra T 2010 Microsatellites in Brassica unigenes: Relative abundance, marker design and use in comparative physical mapping and genome analysis. Genome 53 55-67
88. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, et al. 2009 The Sorghum bicolor genome and the diversification of grasses Nature 457 551-556
89. Pautasso M, Döring TF, Garbelotto M, Pellis L and Jeger MJ 2012 Impacts of climate change on plant diseases opinions and trends. Eur. J. Plant Pathol. 133 295-313
90. Pfender WF and Vollmer SS 1999 Freezing temperature effect on survival of Puccinia graminis subsp. Graminicola in Festuca arundinacea and Lolium perenne. Plant Disease 83 1058-1062
91. Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA and Boyce-Jacino M 1999 Mining SNPs from EST databases. Genome Res. 9 167-174
92. Potato Genome Sequencing Consortium (PGSC) 2011 Genome sequence and analysis of the tuber crop potato. Nature 475 189-195
93. Raghavan C, Naredo MEB, Wang HH, Atienza G, Liu B, Qiu FL, McNally KL and Leung H 2007 Rapid method for detecting SNPs on agarose gels and its application in candidate gene mapping. Mol Breed. 19 87-101
94. Redden R 2013 New approaches for crop genetic adaptation to the abiotic stresses predicted with climate change. Agronomy 3 419-432
95. Reynolds MP and Ortiz R 2010 Adapting crops to climate change: a summary; in Climate change and crop production (eds) MP Reynolds (CAB international) 1-8 pp
96. Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL and Zilberman D 2013 Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proc. Natl. Acad. Sci. USA 110 7934-7939
97. Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, et al. 2013 Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res. 23 1663-1674
98. Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, et al. 2013 Patterns of population epigenomic diversity. Nature 495 193-198
99. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, et al. 2010 Genome sequence of the palaeopolyploid soybean. Nature 463 178-183
100. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, et al. 2009 The B73 maize genome: complexity, diversity, and dynamics. Science 326 1112-1115
101. Septiningsih EM, Pamplona AM, Sanchez DL, Neeraja CN, Vergara GV, Heuer S, Ismail AM and Mackill DJ 2009 Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond. Ann. Bot. 103 151-160
102. Sethy NK, Shokeen B, Edwards KJ and Bhatia S 2006 Development of microsatellite markers and analysis of intra-specific genetic variability in chickpea (Cicer arietinum L.). Theor. Appl. Genet. 112 1416-1428
103. Shitsukawa N, Tahira C, Kassai K, Hirabayashi C, Shimizu T, Takumi S, Mochida K, Kawaura K, et al. 2007 Genetic and epigenetic alteration among three homoeologous genes of a class E MADS box gene in hexaploid wheat. Plant Cell 19 1723-1737
104. Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D and Meyers BC 2009 Short-read sequencing technologies for transcriptional analyses. Annu. Rev. Plant Biol. 60 305-333
105. Singh AK, Gopalakrishnan S, Singh VP, Prabhu KV, Mohapatra T, Singh NK, SharmaTR, Nagarajan M, et al. 2011 Marker assisted selection: a paradigm shift in Basmati breeding. Indian J. Genet. 71 120-128
106. Sundaram RM, Vishnupriya MR, Biradar SK, Laha GS, Reddy GA, Shoba Rani N, Sarma NP and Sonti RV 2008 Marker assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite indica rice variety. Euphytica 160 411-422
107. Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD and McCouch SR 2007 Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet. 3 e133
108. Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, et al. 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
109. Tan L, Zhang P, Liu F, Wang G, Ye S, Zhu Z, Fu Y, Cai H, et al. 2008 Quantitative trait loci underlying domestication-and yield-related traits in an Oryza sativa x Oryza rufipogon advanced backcross population. Genome 51 692-704
110. Tardieu F and Tuberosa R 2010 Dissection and modelling of abiotic stress tolerance in plants. Curr. Opin. Plant Biol. 13 206-212
111. Terpstra IR, Snoek LB, Keurentjes JJ, Peeters AJ and van den Ackerveken G 2010 Regulatory network identification by genetical genomics: signaling downstream of the Arabidopsis receptor-like kinase ERECTA. Plant Physiol. 154 1067-1078
112. The Brassica rapa Genome Sequencing Project Consortium (BGSPC) 2011 The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43 1035-1039
113. Tian F, Li DJ, Fu Q, Zhu ZF, Fu YC, Wang XK and Sun CQ 2006 Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor. Appl. Genet. 112 570-580
114. Till BJ, Cooper J, Tai TH, Colowit P, Greene EA, Henikoff S and Comai L 2007 Mutant resources in rice discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol. 7 19
115. Tomato Genome Consortium (TGC) 2012 The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485 635-641
116. Upadhyaya HD and Ortiz R 2001 A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor. Appl. Genet. 102 1292-1298
117. Upadhyaya HD, Bramel PJ and Singh S 2001 Development of a chickpea core subset using geographic distribution and quantitative traits. Crop Sci. 41 206-210
118. Upadhyaya HD, Ortiz R, Bramel PJ and Singh S 2002 Phenotypic diversity for morphological and agronomic characteristics in chickpea core collection. Euphytica 123 333-342
119. Vahdati K and Leslie C 2013 Abiotic stress-plant responses and applications in agriculture (eds) InTech doi 10.5772/45842
120. Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MT, Azam S, et al. 2012 Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30 83-89
121. Varshney RK, Close TJ, Singh NK, Hoisington DA and Cook DR 2009a Orphan legume crops enter the genomics era. Curr. Opin. Plant Biol. 12 202-210
122. Varshney RK, Graner A and Sorrells ME 2005 Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23 48-55
123. Varshney RK, Hiremath PJ, Lekha PT, Kashiwagi J, Jayasree B, Deokar AA, Vadez V, Xiao Y, et al. 2009b A comprehensive resource of drought-and salinity-responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L). BMC Genomics 10 523
124. Varshney RK, Nayak SN, May GD and Jackson SA 2009c Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol. 27 522-530
125. Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, et al. 2013 Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 31 240-246
126. Wang C, Chen S and Yu S 2011 Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice. Theor. Appl. Genet. 122 905-913
127. Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, Zhang L, He W, et al. 2008 Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet. 40 1370-1374
128. Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, et al. 2009 Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21 1053-1069
129. Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh CT, Xu W, Schnable PS, Vaughn MW, et al. 2011 Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell 23 4221-4233
130. Waugh MM, Kim DH, Ferrin DM and Stanghellini ME 2003 Reproductive potential of Monosporascus cannonballus. Plant Disease 87 45-50
131. Wu JL, Wu C, Lei C, Baraoidan M, Bordeos A, Madamba MR, Ramos-Pamplona M, Mauleon R, et al. 2005 Chemical and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol. Biol. 59 85-97
132. Xie W, Feng Q, Yu H, Huang X, Zhao Q, Xing Y, Yu S, Han B, et al. 2010 Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc. Natl. Acad. Sci. USA 107 10578-10583
133. Xu Y, Lu Y, Xie C, Gao S, Wan J and Prasanna B 2012 Whole-genome strategies for marker-assisted plant breeding. Mol. Breed. 29 833-854
134. Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, et al. 2011 The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480 520-524
135. Yu H, Xie W, Wang J, Xing Y, Xu C, Li X, Xiao J and Zhang Q 2011 Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS One 6 e17595
136. Zavala JA, Casteel CL, Delucia EH and Berenbaum MR 2008 Anthropogenic increase in carbon dioxide compromises plant defense against invasive insects. Proc. Natl. Acad. Sci. USA 105 5129-5133
137. Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD and Zilberman D 2010 Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl. Acad. Sci. USA 107 18729-18734
138. Zhang H, Zhang D, Wang M, Sun J, Qi Y, Li J, Wei X, Han L, et al. 2011a A core collection and mini core collection of Oryza sativa L. in China. Theor. Appl. Genet. 122 49-61
139. Zhang M, Zhao H, Xie S, Chen J, Xu Y, Wang K, Zhao H, Guan H, et al. 2011b Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm. Proc. Natl. Acad. Sci. USA 108 20042-20047
140. Zhang X 2008 The epigenetic landscape of plants. Science 320 489-492
141. Zhang Z, Deng Y, Tan J, Hu S, Yu J and Xue Q 2007 A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Res. 14 37-45
142. Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, et al. 2011 Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2 467
143. Zhong S, Fei Z, Chen YR, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, et al. 2013 Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat. Biotechnol. 31 154
144. Zhu JK 2008 Epigenome sequencing comes of age. Cell 133 395-397