Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Swamy, BP Mallikarjuna ^a   Vikram, Prashant ^a   Dixit, Shalabh ^a   Ahmed, HU ^a   Kumar, Arvind ^a  

^a INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BARLEY; CEREAL; DROUGHT; GENE CLUSTER; GENE MAPPING; GENETIC ANALYSIS; GENETIC SELECTION; GRAIN YIELD; GRASS; MAIZE; MARKER GENE; MORPHOLOGICAL TRAIT; PLANT CHROMOSOME; PLANT LEAF; PLANT ROOT; QUANTITATIVE TRAIT LOCUS; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; WHEAT; AGRICULTURE; CHROMOSOME MAP; CONSENSUS; GENETIC MARKER; GENETICS; GENOMICS; GROWTH, DEVELOPMENT AND AGING; META ANALYSIS; METHODOLOGY; PLANT GENE; POACEAE; REPRODUCIBILITY;

HORDEUM; POACEAE; TRITICUM AESTIVUM; ZEA MAYS;

AGRICULTURE; CEREALS; CHROMOSOME MAPPING; CONSENSUS; DROUGHTS; GENES, PLANT; GENETIC MARKERS; GENOMICS; POACEAE; QUANTITATIVE TRAIT LOCI; REPRODUCIBILITY OF RESULTS;

EID: 80051579192     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-319     Document Type: Article

References (42)

1. Lanceras CJ, Pantuwan G, Jongdee B, Toojinda T. Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiology 2004, 135:384-399. 10.1104/pp.103.035527, 429392, 15122029.
2. Venuprasad R, Dalid CO, Del Valle M, Zhao D, Espiritu M, Sta Cruz MT, Amante M, Kumar A, Atlin GN. Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis. Theoretical and Applied Genetics 2009, 120:177-190. 10.1007/s00122-009-1168-1, 19841886.
3. Wassmann R, Jagadish SVK, Sumfleth K, Pathak H, Howell G, Ismail A, Serraj R, Redoña E, Singh RK, Heuer S. Regional vulnerability of climate change impacts on Asian rice production and scope for adaptation. Advances in Agronomy 2009, 102:91-133.
4. Bates BC, Kundzewicz ZW, Wu S, Palutikof JP. Climate change and water. In technical paper of the Intergovernmental Panel on Climate Change 2008, 210. IPCC Secretariat, Geneva., http://www.ipcc.ch/
5. Bernier J, Kumar A, Ramaiah V, Spaner D, Atlin GN. A large-effect QTL for grain yield under reproductive-stage drought stress in upland Rice. Crop Science 2007, 47:507-518.
6. Podlich DW, Winkler CR, Cooper M. Mapping as you go: an effective approach for marker-assisted selection of complex traits. Crop Science 2004, 44:1560-1571.
7. Collins NC, Tardieu F, Tuberosa R. Quantitative trait loci and crop performance under abiotic stress: Where do we stand?. Plant Physiology 2008, 147:469-486. 10.1104/pp.108.118117, 2409033, 18524878.
8. Swamy BPM, Sarla N. Yield enhancing QTLs from wild species. Biotechnology Advances 2008, 26:106-111. 10.1016/j.biotechadv.2007.09.005, 17949936.
9. Khowaja FS, Norton GJ, Courtois B, Price AH. Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis. BMC Genomics 2009, 10:276. 10.1186/1471-2164-10-276, 2708188, 19545420.
10. Courtois B, Ahmadi N, Khowaja F, Price A, Rami JF, Frouin J, Hamelin C, Ruiz M. Rice root genetic architecture: meta-analysis from a QTL database improves resolution to a few candidate genes. Rice 2009, 2:115-128.
11. Goffinet B, Gerber S. Quantitative trait loci: a meta-analysis. Genetics 2000, 155:463-473. 1461053, 10790417.
12. Ballini E, Morel JB, Droc G, Price AH, Courtois B, Nottehem JL, Tharreau DA. Genome wide meta analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Molecular and Microbe Interaction 2008, 21:859-868.
13. Rong J, Feltus FA, Waghmare VN, Pierce GJ, Chee PW, Draye X, Saranga Y, Wright RJ, Wilkins TA, May OL, Smith CW, Gannaway JR, Wendel JF, Paterson AH. Meta-analysis of polyploid cotton QTL shows unequal contributions of sub genomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 2007, 176:2577-2588. 10.1534/genetics.107.074518, 1950656, 17565937.
14. Guo B, Sleper DA, Lu P, Shannon JG, Nguyen HT, Arelli PR. QTLs associated with resistance to soybean cyst nematode in soybean meta-analysis of QTL locations. Crop Science 2006, 46:202-208.
15. Loffler M, Schon CC, Miedaner T. Revealing the genetic architecture of FHB resistance in hexaploid wheat (Triticum aestivum L.) by QTL meta-analysis. Molecular Breeding 2009, 23:473-488.
16. Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murigneux A, Charcosset A. Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with rice genome. Genetics 2004, 168:2169-2185. 10.1534/genetics.104.032375, 1448716, 15611184.
17. Hao Z, Li X, Liu X, Xie C, Li M, Zhang D, Zhang S. Meta-analysis of constitutive and adaptive QTL for drought tolerance in maize. Euphytica 2010, 174:165-177.
18. Lanaud C, Fouet O, Clement D, Boccara M, Risterucci AM, Maharaj SS, Legavre T, Argout X. A meta-QTL analysis of disease resistance traits of Theobroma cacao L. Molecular Breeding 2009, 24:361-374.
19. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch SR. Computational and experimental analysis of microsatellite in rice (Oryza sativa L.): frequency, length variation, transposon associations and genetic marker potential. Genome Research 2001, 1:1441-1452.
20. Darvasi A, Soller M. A simple method to calculate resolving power and confidence interval of QTL map location. Behavioural Genetics 1997, 27:125-132.
21. Hirotugu A. A new look at the statistical model identification. IEEE Transactions on Automatic Control 1974, 19:716-723.
22. Beena. Studies on physio-morphological traits and genetic markers associated with drought response in rice (O. sativa). 2005, Tamil Nadu Agricultural University, Coimbatore, India, PhD thesis..
23. Prashant V. Development and morpho-molecular analysis of Swarna (Oryza sativa L.) introgression lines for drought tolerance. 2010, Veer Bahadur Singh Purvanchal University, Jaunpur, Uttar Pradesh, India.
24. Price AH. Believe it or not, QTLs are accurate. Trends in Plant Science 2006, 11:213-216. 10.1016/j.tplants.2006.03.006, 16617032.
25. Ashikari M, Matsuoka M. Identification, isolation and pyramiding of quantitative trait loci for rice breeding. Trends in Plant Science 2006, 11:344-350. 10.1016/j.tplants.2006.05.008, 16769240.
26. Ashikari M, Sakakibara H, Lin S, Ymamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M. Cytokinin oxidase regulates rice grain production. Science 2005, 309:741-745. 10.1126/science.1113373, 15976269.
27. Sakamoto T, Morinaka Y, Ohnishi T, Sunohara H, Fujioka S, Tanaka MU, Mizutani M, Sakata K, Takatsuto S, Yoshida S, Tanaka H, Kitano H, Matsuoka M. Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice. Nature Biotechnology 2005, 24:105-109.
28. Bentolila S, Alfonso AA, Hanson MR. A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proceedings of the National Academy of Sciences, USA 2002, 99:10887-10892.
29. Daniel A, Cushing E, Nancy R, Daniel R, Daniel M. Arabidopsis emb175 and other ppr knockout mutants reveal essential roles for pentatricopeptide repeat (PPR) proteins in plant embryogenesis. Planta 2005, 221:424-436. 10.1007/s00425-004-1452-x, 15647901.
30. Mukhopadhyay A, Vij S, Tyagi AK. Overexpression of a zinc-finger protein gene from rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco. Proceedings of the National Academy of Sciences, USA 2004, 101:6309-6314.
31. Wang L, Xu Y, Zhang C, Ma Q, Joo SH, Kim SK, Xu Z, Chong K. OsLIC, a novel CCCH-type zinc finger protein with transcription activation, mediates rice architecture via brassinosteroids signaling. PLOS One 2008, 3:e3521. 10.1371/journal.pone.0003521, 2567845, 18953406.
32. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP. F-box proteins in rice: genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiology 2007, 143:1467-1483. 10.1104/pp.106.091900, 1851844, 17293439.
33. Xiang Y, Tang N, Du H, Ye H, Xiong L. Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiology 2008, 48:1938-1952.
34. Jeong JS, Kim YS, Baek KH, Jung H, Ha SH, Choi YD, Kim M, Reuzeau C, Kim JK. Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiology 2010, 153:185-197. 10.1104/pp.110.154773, 2862432, 20335401.
35. Masle J, Gilmore SR, Farquhar GD. The ERECTA gene regulates plant transpiration efficiency in Arabidopsis. Nature 2005, 436:866-870. 10.1038/nature03835, 16007076.
36. Ito Y, Katsura K, Maruyama K, Taji T, Kobayashi M, Seki M, Shinozaki K, Shinozaki KY. Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant and Cell Physiology 2006, 47:141-153.
37. Chandra Babu R, Nguyen BD, Chamarerk V, Shanmugasundaram P, Chezhian P, Jeyaprakash P, Ganesh SK, Palchamy A, Sadasivam S, Sarkarung S, Wade LJ, Nguyen HT. Genetic analysis of drought resistance in rice by molecular markers: association between secondary traits and field performance. Crop Science 2003, 43:1457-1469.
38. Yue B, Xiong L, Xue W, Xing Y, Luo L, Xu C. Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil. Theoretical and Applied Genetics 2005, 111:1127-1136. 10.1007/s00122-005-0040-1, 16075205.
39. Zou GH, Mei HW, Liu HY, Liu GL, Hu SP, Yu XQ, Li MS, Wu JH, Luo LJ. Grain yield responses to moisture regimes in a rice population: association among traits and genetic markers. Theoretical and Applied Genetics 2005, 112:106-113. 10.1007/s00122-005-0111-3, 16231161.
40. Yue B, Xue W, Xiong L, Yu X, Luo L, Cui K, Jin D, Xing Y, Zhang Q. Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance. Genetics 2006, 172:1213-1228. 1456219, 16272419.
41. Gomez MS, Satheesh Kumar S, Jeyaprakash P, Suresh R, Biji KR, Boopathi NM, Price AH, Chandra Babu R. Mapping QTLs linked to physio-morphological and plant production traits under drought stress in rice (Oryza sativa L.) in the target environment. American Journal of Biochemistry and Biotechnology 2006, 2:161-169.
42. Kumar R, Venuprasad R, Atlin GN. Genetic analysis of rainfed lowland rice drought tolerance under naturally-occurring stress in eastern India: heritability and QTL effects. Field Crops Research 2007, 103:42-52.