QTL and association mapping for plant abiotic stress tolerance: trait characterization and introgression for crop improvement

Plant Abiotic Stress, Second Edition

Volumn , Issue , 2014, Pages 257-287

  Fleury, Delphine ^a   Langridge, Peter ^a  

^a Australian Centre for Plant Functional Genomics   (Australia)

Author keywords

Abiotic stress tolerance traits; Crop improvement; Environments; Plants; Quantitative trait loci (QTL); Trait characterization

Indexed keywords

EID: 84927063424     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118764374.ch10     Document Type: Chapter

References (137)

1. Abdi N, Darvishzadeh R, Jafari M, Pirzad A, Haddadi P. 2012. Genetic analysis and QTL mapping of agro-morphological traits in sunflower (Helianthus annuus L.) under two contrasting water treatment conditions. Plant Omics 5(2):149-158.
2. Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J. 2004. BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20(14):2324-2326.
3. Asfaw A, Blair MW, Struik PC. 2012. Multienvironment quantitative trait loci analysis for photosynthate acquisition, accumulation, and remobilization traits in common bean under drought stress. G3 (Bethesda) 2(5):579-595.
4. Beales J, Turner A, Griffiths S, Snape JW, Laurie DA. 2007. A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theor Appl Genet 115(5):721-733.
5. Bennett D, Izanloo A, Reynolds M, Kuchel H, Langridge P, Schnurbusch T. 2012a. Genetic dissection of grain yield and physical grain quality in bread wheat (Triticum aestivum L.) under water-limited environments. Theor Appl Genet 125(2):255-271.
6. Bennett D, Reynolds M, Mullan D, Izanloo A, Kuchel H, Langridge P, Schnurbusch T. 2012b. Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and high yield potential environments. Theor Appl Genet 125(7):1473-1485.
7. Berger B, Parent B, Tester M. 2010. High-throughput shoot imaging to study drought responses. J Exp Bot 61(13):3519-3528.
8. Blum A. 1988. Plant Breeding for Stress Environments. Boca Raton, FL: CRC Press.
9. Blum A. 2005. Drought resistance, water-use efficiency, and yield potential-are they compatible, dissonant, or mutually exclusive? Aust J Agric Res 56(11):1159-1168.
10. Bolaños J, Edmeades GO. 1996. The importance of the anthesis-silking interval in breeding for drought tolerance in tropical maize. Field Crops Res 48(1):65-80.
11. Bot AJ, Nachtergaele FO, Young A. 2000. Land resource potential and constraints at regional and country levels. World Soil Resour Rep FAO 90.
12. Caldwell KS, Russell J, Langridge P, Powell W. 2006. Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172(1):557-567.
13. Chen A, Gusta LV, Brule-Babel A, Leach R, Baumann U, Fincher GB, Collins NC. 2009. Varietal and chromosome 2H locus-specific frost tolerance in reproductive tissues of barley (Hordeum vulgare L.) detected using a frost simulation chamber. Theor Appl Genet 119(4):685-694.
14. Chen J, Chang SX, Anyia AO. 2012. Quantitative trait loci for water-use efficiency in barley (Hordeum vulgare L.) measured by carbon isotope discrimination under rain-fed conditions on the Canadian prairies. Theor Appl Genet 125(1):71-90.
15. Chenu K, Chapman SC, Tardieu F, McLean G, Welcker C, Hammer GL. 2009. Simulating the yield impacts of organ-level quantitative trait loci associated with drought response in maize: a "gene-to-phenotype" modeling approach. Genetics 183(4):1507-1523.
16. Chin JH, Gamuyao R, Dalid C, Bustamam M, Prasetiyono J, Moeljopawiro S, Wissuwa M, Heuer S 2011. Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application. Plant Physiol 156(3):1202-1216.
17. Chin JH, Lu X, Haefele SM, Gamuyao R, Ismail A, Wissuwa M, Heuer S. 2010. Development and application of gene-based markers for the major rice QTL Phosphorus uptake 1. Theor Appl Genet 120(6):1073-1086.
18. Chu Y, Su X, Huang Q, Zhang X. 2009. Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms. Genetica 137(2):141-150.
19. Collins NC, Tardieu F, Tuberosa R. 2008. Quantitative trait loci and crop performance under abiotic stress: where do we stand? Plant Physiol 147(2):469-486.
20. Comadran J, Thomas WTB, van Eeuwijk FA, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, Romagosa I, Hackett CA, Russell JR. 2009. Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet 119(1):175-187.
21. 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(2):824-834.
22. Cooper M, van Eeuwijk FA, Hammer GL, Podlich DW, Messina C. 2009. Modeling QTL for complex traits: detection and context for plant breeding. Curr Opin Plant Biol 12(2):231-240.
23. del Pozo A, Castillo D, Inostroza L, Matus I, Mendez AM, Morcuende R. 2012. Physiological and yield responses of recombinant chromosome substitution lines of barley to terminal drought in a Mediterraneantype environment. Ann Appl Biol 160(2):157-167.
24. Ding X, Li X, Xiong L. 2011. Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice. Theor Appl Genet 123(5):815-826.
25. Dixit S, Swamy BP, Vikram P, Ahmed HU, Sta Cruz MT, Amante M, Atri D, Leung H, Kumar A. 2012. Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities. Theor Appl Genet 125(1):155-169.
26. Duvick DN. 2001. Biotechnology in the 1930s: the development of hybrid maize. Nat Rev Genet 2(1):69-74.
27. Edwards J. 2011. A genetic analysis of drought related traits in hexaploid wheat. PhD thesis, University of Adelaide, Australia.
28. Ellis H, Spielmeyer W, Gale R, Rebetzke J, Richards A. 2002. "Perfect" markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat. Theor Appl Genet 105(6-7):1038-1042.
29. Foley JA, Defries R, Asner GP, Barford C, Bonan G, Carpenter SR, Chapin FS, Coe MT, Daily GC, Gibbs HK, Helkowski JH, Holloway T, Howard EA, Kucharik CJ, Monfreda C, Patz JA, Prentice IC, Ramankutty N, Snyder PK. 2005. Global consequences of land use. Science 309(5734):570-574.
30. Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M. 2008. Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice. Proc Natl Acad Sci USA 105(34):12623-12628.
31. Fukao T, Xu K, Ronald PC, Bailey-Serres J. 2006. A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18(8):2021-2034.
32. Gasperini D, Greenland A, Hedden P, Dreos R, Harwood W, Griffiths S. 2012. Genetic and physiological analysis of Rht8 in bread wheat: an alternative source of semi-dwarfism with a reduced sensitivity to brassinosteroids. J Exp Bot doi: 10.1093/jxb/ERS138.
33. Genc Y, McDonald GK, Tester M. 2007. Reassessment of tissue Na(+) concentration as a criterion for salinity tolerance in bread wheat. Plant Cell Environ 30(11):1486-1498.
34. Genc Y, Oldach K, Verbyla AP, Lott G, Hassan M, Tester M, Wallwork H, McDonald GK. 2010. Sodium exclusion QTL associated with improved seedling growth in bread wheat under salinity stress. Theor Appl Genet 121(5):877-894.
35. Genc Y, Verbyla A, Torun A, Cakmak I, Willsmore K, Wallwork H, McDonald G. 2009. Quantitative trait loci analysis of zinc efficiency and grain zinc concentration in wheat using whole genome average interval mapping. Plant Soil 314(1-2):49-66.
36. Gilad Y, Rifkin SA, Pritchard JK. 2008. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 24(8):408-415.
37. Gonzalez-Martinez SC, Ersoz E, Brown GR, Wheeler NC, Neale DB. 2006. DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L. Genetics 172(3):1915-1926.
38. Gonzalez-Martinez SC, Huber D, Ersoz E, Davis J, Neale DB. 2008. Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredita 101:19-26.
39. Graham R, Ascher J, Ellis P, Shepherd K. 1987. Transfer to wheat of the copper efficiency factor carried on rye chromosome arm 5RL. Plant Soil 99:107-114.
40. Gupta P, Langridge P, Mir R. 2010. Marker-assisted wheat breeding: present status and future possibilities. Mol Breed doi: 10.1007/s11032-009-9359-7.
41. Hao Z, Li X, Xie C, Weng J, Li M, Zhang D, Liang X, Liu L, Liu S, Zhang S. 2011. Identification of functional genetic variations underlying drought tolerance in maize using SNP markers. J Integr Plant Biol 53(8):641-652.
42. Haseneyer G, Stracke S, Piepho HP, Sauer S, Geiger HH, Graner A. 2010. DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits. BMC Plant Biol 10(5).
43. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li J, Han B. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42(11):961-967.
44. International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763-768.
45. Jefferies S. 2000. Marker assisted backcrossing for gene introgression in barley (Hordeum vulgare L.). PhD thesis, University of Adelaide, Australia.
46. Jefferies SP, Pallotta MA, Paull JG, Karakousis A, Kretschmer JM, Manning S, Islam A, Langridge P, Chalmers KJ. 2000. Mapping and validation of chromosome regions conferring boron toxicity tolerance in wheat (Triticum aestivum). Theor Appl Genet 101(5-6):767-777.
47. Jiang Z, Han Y, Teng W, Li Y, Zhao X, Zhang Z, Man W, Li W. 2012. Impact of epistasis and QTL × environmental interaction on the mass filling rate during seed development of soybean. Genet Res (Camb) 94(2):63-71.
48. Kazmi RH, Khan N, Willems LA, Vanh AW, Ligterink W, Hilhorst HW. 2012. Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium. Plant Cell Environ 35(5):929-951.
49. Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R. 2009. A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5(7):e1000551.
50. Kuchel H, Williams K, Langridge P, Eagles HA, Jefferies SP. 2007. Genetic dissection of grain yield in bread wheat. II. QTL-by-environment interaction. Theor Appl Genet 115(7):1015-1027.
51. Kumar S, Sehgal SK, Kumar U, Prasad PVV, Joshi AK, Gill BS. 2012. Genomic characterization of drought tolerance-related traits in spring wheat. Euphytica 186(1):265-276.
52. Laird NM, Lange C. 2006. Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet 7(5):385-394.
53. Lewis S, Faricelli ME, Appendino ML, Valarik M, Dubcovsky J. 2008. The chromosome region including the earliness per se locus Eps-Am1 affects the duration of early developmental phases and spikelet number in diploid wheat. J Exp Bot 59(13):3595-3607.
54. Li HB, Vaillancourt R, Mendham N, Zhou MX. 2008. Comparative mapping of quantitative trait loci associated with waterlogging tolerance in barley (Hordeum vulgare L.). BMC Genomics 9.
55. Lonergan PF, Pallotta MA, Lorimer M, Paull JG, Barker SJ, Graham RD. 2009. Multiple genetic loci for zinc uptake and distribution in barley (Hordeum vulgare). New Phytol 184(1):168-179.
56. Lu Y, Xu J, Yuan Z, Hao Z, Xie C, Li X, Shah T, Lan H, Zhang S, Rong T, Xu Y. 2012. Comparative LD mapping using single SNPs and haplotypes identifies QTL for plant height and biomass as secondary traits of drought tolerance in maize. Mol Breed 30(1):407-418.
57. Lu Y, Zhang S, Shah T, Xie C, Hao Z, Li X, Farkhari M, Ribaut JM, Cao M, Rong T, Xu Y. 2010. Joint linkagelinkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize. Proc Natl Acad Sci USA 107(45):19585-19590.
58. Lynch M, Walsh B. 1998. Genetics and Analysis of Quantitative Traits. Sunderland, MA: Sinauer Associates.
59. Ma HX, Bai GH, Carver BF, Zhou LL. 2005. Molecular mapping of a quantitative trait locus for aluminum tolerance in wheat cultivar Atlas 66. Theor Appl Genet 112(1):51-57.
60. Ma J, Li HB, Zhang CY, Yang XM, Liu YX, Yan GJ, Liu CJ. 2010. Identification and validation of a major QTL conferring crown rot resistance in hexaploid wheat. Theor Appl Genet 120(6):1119-1128.
61. Maccaferri M, Sanguineti MC, Corneti S, Ortega JL, Salem MB, Bort J, DeAmbrogio E, del Moral LF, Demontis A, El-Ahmed A, Maalouf F, Machlab H, Martos V, Moragues M, Motawaj J, Nachit M, Nserallah N, Ouabbou H, Royo C, Slama A, Tuberosa R. 2008. Quantitative trait loci for grain yield and adaptation of durum wheat (Triticum durum Desf.) across a wide range of water availability. Genetics 178(1):489-511.
62. Maccaferri M, Sanguineti MC, Demontis A, El-Ahmed A, Garcia del Moral L, Maalouf F, Nachit M, Nserallah N, Ouabbou H, Rhouma S, Royo C, Villegas D, Tuberosa R. 2011. Association mapping in durum wheat grown across a broad range of water regimes. J Exp Bot 62(2):409-438.
63. Magalhaes JV, Liu J, Guimaraes CT, Lana UG, Alves VM, Wang YH, Schaffert RE, Hoekenga OA, Pineros MA, Shaff JE, Klein PE, Carneiro NP, Coelho CM, Trick HN, Kochian LV. 2007. A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum. Nat Genet 39(9):1156-1161.
64. Marguerit E, Brendel O, Lebon E, Van Leeuwen C, Ollat N. 2012. Rootstock control of scion transpiration and its acclimation to water deficit are controlled by different genes. New Phytol 194(2):416-429.
65. Maron LG, Pineros MA, Guimaraes CT, Magalhaes JV, Pleiman JK, Mao C, Shaff J, Belicuas SN, Kochian LV. 2010. Two functionally distinct members of the MATE (multi-drug and toxic compound extrusion) family of transporters potentially underlie two major aluminum tolerance QTLs in maize. Plant J 61(5):728-740.
66. Mathews KL, Malosetti M, Chapman S, McIntyre L, Reynolds M, Shorter R, van Eeuwijk F. 2008. Multi-environment QTL mixed models for drought stress adaptation in wheat. Theor Appl Genet 117(7):1077-1091.
67. McIntyre CL, Mathews KL, Rattey A, Chapman SC, Drenth J, Ghaderi M, Reynolds M, Shorter R. 2009. Molecular detection of genomic regions associated with grain yield and yield-related components in an elite bread wheat cross evaluated under irrigated and rainfed conditions. Theor Appl Genet 120(3):527-541.
68. McWilliam J. 1989. The dimensions of drought. In: F Baker, ed., Drought Resistance in Cereals. Wallingford, UK: CAB International, 1-11.
69. Mengistu N, Baenziger PS, Eskridge KM, Dweikat I, Wegulo SN, Gill KS, Mujeeb-Kazi A. 2012. Validation of QTL for grain yield-related traits on wheat chromosome 3A using recombinant inbred chromosome lines. Crop Sci 52(4):1622-1632.
70. Merewitz EB, Belanger FC, Warnke SE, Huang B. 2012. Identification of quantitative trait loci linked to drought tolerance in a colonial × creeping bentgrass hybrid population. Crop Sci 52(4):1891-1901.
71. Miura K, Ashikari M, Matsuoka M. 2011. The role of QTLs in the breeding of high-yielding rice. Trends Plant Sci 16(6):319-326.
72. Mullan DJ, Mirzaghaderi G, Walker E, Colmer TD, Francki MG. 2009. Development of wheat-Lophopyrum elongatum recombinant lines for enhanced sodium "exclusion" during salinity stress. Theor Appl Genet 119(7):1313-1323.
73. Munns R, Tester M. 2008. Mechanisms of salinity tolerance. Annu Rev Plant Biol 59:651-681.
74. Navakode S, Weidner A, Varshney RK, Lohwasser U, Scholz U, Borner A. 2009. A QTL analysis of aluminium tolerance in barley, using gene-based markers. Cereal Res Commun 37(4):531-540.
75. Naz AA, Ehl A, Pillen K, Leon J. 2012. Validation for root-related quantitative trait locus effects of wild origin in the cultivated background of barley (Hordeum vulgare L.). Plant Breed 131(3):392-398.
76. Nezhad KZ, Weber WE, Roeder MS, Sharma S, Lohwasser U, Meyer RC, Saal B, Boerner A. 2012. QTL analysis for thousand-grain weight under terminal drought stress in bread wheat (Triticum aestivum L.). Euphytica 186(1):127-138.
77. Nikolic A, Ignjatovic-Micic D, Dodig D, Andelkovic V, Lazic-Jancic V. 2012. Identification of QTLs for yield and drought-related traits in maize: assessment of their causal relationships. Biotechnol Biotechnol Equip 26(3):2952-2960.
78. Paliwal R, Roder MS, Kumar U, Srivastava JP, Joshi AK. 2012. QTL mapping of terminal heat tolerance in hexaploid wheat (T. aestivum L.). Theor Appl Genet 125(3):561-575.
79. Pallotta M, Graham R, Langridge P, Sparrow D, Barker S. 2000. RFLP mapping of manganese efficiency in barley. Theor Appl Genet 101:1100-1108.
80. 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.
81. Passioura J. 2007. The drought environment: physical, biological and agricultural perspectives. J Exp Bot 58(2):113-117.
82. Peleg Z, Fahima T, Krugman T, Abbo S, Yakir D, Korol AB, Saranga Y. 2009. Genomic dissection of drought resistance in durum wheat × wild emmer wheat recombinant inbreed line population. Plant Cell Environ 32(7):758-779.
83. Pinto RS, Reynolds MP, Mathews KL, McIntyre CL, Olivares-Villegas JJ, Chapman SC. 2010. Heat and drought adaptive QTL in a wheat population designed to minimize confounding agronomic effects. Theor Appl Genet 121(6):1001-1021.
84. Rafalski JA. 2010. Association genetics in crop improvement. Curr Opin Plant Biol 13(2):174-180.
85. 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(11):957-966.
86. Raman H, Zhang K, Cakir M, Appels R, Garvin DF, Maron LG, Kochian LV, Moroni JS, Raman R, Imtiaz M, Drake-Brockman F, Waters I, Martin P, Sasaki T, Yamamoto Y, Matsumoto H, Hebb DM, Delhaize E, Ryan PR. 2005. Molecular characterization and mapping of ALMT1, the aluminium-tolerance gene of bread wheat (Triticum aestivum L.). Genome 48(5):781-791.
87. Rebetzke G, Appels R, Morrison A, Richards R, McDonald G, Ellis M, Spielmeyer W, Nonnett D. 2001. Quantitative trait loci on chromosome 4B for coleoptile length and early vigour in wheat (Triticum aestivum L.). Aust J Agric Res 52:1221-1234.
88. Rebetzke GJ, Condon AG, Farquhar GD, Appels R, Richards RA. 2008a. Quantitative trait loci for carbon isotope discrimination are repeatable across environments and wheat mapping populations. Theor Appl Genet 118(1):123-137.
89. Rebetzke GJ, van Herwaarden A, Jenkins C, Weiss M, Lewis D, Ruuska S, Tabe L, Fettell N, Richards R. 2008b. Quantitative trait loci for water-soluble carbohydrates and associations with agronomic traits in wheat. Aust J Agric Res 59:891-905.
90. Ren Y, He X, Liu D, Li J, Zhao X, Li B, Tong Y, Zhang A, Li Z. 2012. Major quantitative trait loci for seminal root morphology of wheat seedlings. Mol Breed 30(1):139-148.
91. Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX. 2005. A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37(10): 1141-1146.
92. Reymond M, Muller B, Leonardi A, Charcosset A, Tardieu F. 2003. Combining quantitative trait loci analysis and an ecophysiological model to analyze the genetic variability of the responses of maize leaf growth to temperature and water deficit. Plant Physiol 131(2):664-675.
93. Reymond M, Muller B, Tardieu F. 2004. Dealing with the genotype × environment interaction via a modeling approach: a comparison of QTLs of maize leaf length or width with QTLs of model parameters. J Exp Bot 55(407):2461-2472.
94. Reynolds M, Manes Y, Izanloo A, Langridge P. 2009. Phenotyping approaches for physiological breeding and gene discovery in wheat. Ann Appl Biol 155(3):309-320.
95. Rizhsky L, Liang HJ, Shuman J, Shulaev V, Davletova S, Mittler R. 2004. When defense pathways collide: the response of Arabidopsis to a combination of drought and heat stress. Plant Physiol 134(4): 1683-1696.
96. Sabadin PK, Malosetti M, Boer MP, Tardin FD, Santos FG, Guimaraes CT, Gomide RL, Andrade CLT, Albuquerque PEP, Caniato FF, Mollinari M, Margarido GRA, Oliveira BF, Schaffert RE, Garcia AAF, van Eeuwijk FA, Magalhaes JV. 2012. Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences. Theor Appl Genet 124(8):1389-1402.
97. Salekdeh GH, Reynolds M, Bennett J, Boyer J. 2009. Conceptual framework for drought phenotyping during molecular breeding. Trends Plant Sci 14(9):488-496.
98. Sasaki T, Yamamoto Y, Ezaki B, Katsuhara M, Ahn SJ, Ryan PR, Delhaize E, Matsumoto H. 2004. A wheat gene encoding an aluminum-activated malate transporter. Plant J 37(5):645-653.
99. Sayed MA, Schumann H, Pillen K, Naz AA, Leon J. 2012. AB-QTL analysis reveals new alleles associated to proline accumulation and leaf wilting under drought stress conditions in barley (Hordeum vulgare L.). BMC Genet 13(1):61.
100. Schranz ME, Song BH, Windsor AJ, Mitchell-Olds T. 2007. Comparative genomics in the Brassicaceae: a family-wide perspective. Curr Opin Plant Biol 10:168-175.
101. Sehgal D, Rajaram V, Armstead IP, Vadez V, Yadav YP, Hash CT, Yadav RS. 2012. Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci. BMC Plant Biol 12:9.
102. Seo M, Aoki H, Koiwai H, Kamiya Y, Nambara E, Koshiba T. 2004. Comparative studies on the Arabidopsis aldehyde oxidase (AAO) gene family revealed a major role of AAO3 in ABA biosynthesis in seeds. Plant Cell Physiol 45(11):1694-1703.
103. Setter TL, Yan J, Warburton M, Ribaut JM, Xu Y, Sawkins M, Buckler ES, Zhang Z, Gore MA. 2011. Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought. J Exp Bot 62(2):701-716.
104. Shavrukov Y, Langridge P, Tester M, Nevo E. 2010. Wide genetic diversity of salinity tolerance, sodium exclusion and growth in wild emmer wheat, Triticum dicoccoides. Breed Sci 60:426-435.
105. Shinozaki K, Yamaguchi-Shinozaki K. 2007. Gene networks involved in drought stress response and tolerance. J Exp Bot 58(2):221-227.
106. Smita S, Lenka SK, Katiyar A, Jaiswal P, Preece J, Bansal KC. 2011. QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice. Database (Oxford) 2011:bar037.
107. Sourdille P, Snape JW, Cadalen T, Charmet G, Nakata N, Bernard S, Bernard M. 2000. Detection of QTLs for heading time and photoperiod response in wheat using a doubled-haploid population. Genome 43(3):487-494.
108. Spielmeyer W, Hyles J, Joaquim P, Azanza F, Bonnett D, Ellis ME, Moore C, Richards RA. 2007. A QTL on chromosome 6A in bread wheat (Triticum aestivum) is associated with longer coleoptiles, greater seedling vigour and final plant height. Theor Appl Genet 115(1):59-66.
109. Su J, Zheng Q, Li H, Li B, Jing R, Tong Y, Li Z. 2009. Detection of QTLs for phosphorus use efficiency in relation to agronomic performance of wheat grown under phosphorus sufficient and limited conditions. Plant Sci 176(6):824-836.
110. Sutton T, Baumann U, Hayes J, Collins N, Shi B, Schnurbusch T, Hay A, Mayo G, Pallotta M, Tester M, Langridge P. 2007. Boron-toxicity tolerance in barley arising from efflux transporter amplification. Science 318(5855):1446-1449.
111. Swamy BP, Vikram P, Dixit S, Ahmed HU, Kumar A. 2011. Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. BMC Genomics 12:319.
112. Tardieu F. 2003. Virtual plants: modelling as a tool for the genomics of tolerance to water deficit. Trends Plant Sci 8(1):9-14.
113. Teulat B, Merah O, Sirault X, Borries C, Waugh R, This D. 2002. QTLs for grain carbon isotope discrimination in field-grown barley. Theor Appl Genet 106(1):118-126.
114. Teulat B, Zoumarou-Wallis N, Rotter B, Ben Salem M, Bahri H, This D. 2003. QTL for relative water content in field-grown barley and their stability across Mediterranean environments. Theor Appl Genet 108(1):181-188.
115. Toktay H, McIntyre CL, Nicol JM, Ozkan H, Elekcioglu HI. 2006. Identification of common root-lesion nematode (Pratylenchus thornei Sher et Allen) loci in bread wheat. Genome 49(10):1319-1323.
116. Turner NC. 1979. Drought resistance and adaptation to water deficits in crop plants. In: H Mussell, C Staples, eds., Stress Physiology in Crop Plants. New York: Wiley, 343-372.
117. Uwimana B, Smulders MJ, Hooftman DA, Hartman Y, van Tienderen PH, Jansen J, McHale LK, Michelmore RW, van de Wiel CC, Visser RG. 2012. Hybridization between crops and wild relatives: the contribution of cultivated lettuce to the vigour of crop-wild hybrids under drought, salinity and nutrient deficiency conditions. Theor Appl Genet 125(6):1097-1111.
118. Vadez V, Krishnamurthy L, Thudi M, Anuradha C, Colmer TD, Turner NC, Siddique KHM, Gaur PM, Varshney RK. 2012. Assessment of ICCV 2 × JG 62 chickpea progenies shows sensitivity of reproduction to salt stress and reveals QTL for seed yield and yield components. Mol Breed 30(1):9-21.
119. Vagujfalvi A, Galiba G, Cattivelli L, Dubcovsky J. 2003. The cold-regulated transcriptional activator Cbf3 is linked to the frost-tolerance locus Fr-A2 on wheat chromosome 5A. Mol Gent Genomics 269(1):60-67.
120. Van Eeuwijk FA, Bink MC, Chenu K, Chapman SC. 2010. Detection and use of QTL for complex traits in multiple environments. Curr Opin Plant Biol 13(2):193-205.
121. Vikram P, Swamy BP, Dixit S, Ahmed HU, Teresa Sta Cruz M, Singh AK, Kumar A. 2011. qDTY(1).(1), a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genet 12:89.
122. Von Korff M, Grando S, Del Greco A, This D, Baum M, Ceccarelli S. 2008. Quantitative trait loci associated with adaptation to Mediterranean dryland conditions in barley. Theor Appl Genet 117(5):653-669.
123. Von Korff M, Wang H, Leon J, Pillen K. 2006. AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. spontaneum). Theor Appl Genet 112(7):1221-1231.
124. Wang A, Li Y, Zhang C. 2012a. QTL mapping for stay-green in maize (Zea mays). Can J Plant Sci 92(2):249-256.
125. Wang M, Jiang N, Jia T, Leach L, Cockram J, Comadran J, Shaw P, Waugh R, Luo Z. 2012b. Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor Appl Genet 124(2):233-246.
126. Wilhelm EP, Turner AS, Laurie DA. 2009. Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat (Triticum durum Desf.). Theor Appl Genet 118(2):285-294.
127. Williams KJ, Willsmore KL, Olson S, Matic M, Kuchel H. 2006. Mapping of a novel QTL for resistance to cereal cyst nematode in wheat. Theor Appl Genet 112(8):1480-1486.
128. Wu X, Chang X, Jing R. 2012. Genetic insight into yield-associated traits of wheat grown in multiple rain-fed environments. PLoS One 7(2):e31249.
129. Wu X, Wang Z, Chang X, Jing R. 2010. Genetic dissection of the developmental behaviours of plant height in wheat under diverse water regimes. J Exp Bot 61(11):2923-2937.
130. Yang DL, Jing RL, Chang XP, Li W. 2007. Identification of quantitative trait loci and environmental interactions for accumulation and remobilization of water-soluble carbohydrates in wheat (Triticum aestivum L.) stems. Genetics 176(1):571-584.
131. Yasui H, Yamagata Y, Yoshimura A. 2010. Development of chromosome segment substitution lines derived from indica rice donor cultivars DV85 and ARC10313 in the genetic background of japonica cultivar Taichung 65. Breed Sci 60(5):620-628.
132. Young ND, Udvardi M. 2009. Translating Medicago truncatula genomics to crop legumes. Curr Opin Plant Biol 12:193-201.
133. Yu J, Buckler ES. 2006. Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17(2):155-160.
134. Yu J, Holland JB, McMullen MD, Buckler ES. 2008. Genetic design and statistical power of nested association mapping in maize. Genetics 178(1):539-551.
135. Yuan L, Tang J, Wang X, Li C. 2012. QTL analysis of shading sensitive related traits in maize under two shading treatments. PLoS One 7(6):e38696.
136. Zhang XK, Xiao YG, Zhang Y, Xia XC, Dubcovsky J, He ZH. 2008. Allelic variation at the vernalization genes Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3 in Chinese wheat cultivars and their association with growth habit. Crop Sci 48(2):458-470.
137. Zwart R, Thompson J, Milgate A, Bansal U, Williamson P, Raman H, Bariana H. 2010. QTL mapping of multiple foliar disease and root-lesion nematode resistances in wheat. Mol Breed 26(1):107-124.