Acu?a T L B, Lafitte H R, Wade L J. 2008. Genotype ? environment interactions for grain yield of upland rice backcross lines in diverse hydrological environments. Field Crops Res, 108(2): 117–125.
Ashikari M, Sakakibara H, Lin S Y, Yamamoto T, Takashi T, Nishimura A, Angeles E R, Qian Q, Kitano H, Matsuoka M. 2005. Cytokinin oxidase regulates rice grain production. Science, 309: 741–745.
Bai X F, Luo L J, Yan W H, Kovi M R, Zhan W, Xing Y Z. 2010. Genetic dissection of rice grain shape using a recombinant inbred line population derived from two contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7. BMC Genet, 11: 16.
Breseghello F, Sorrells M E. 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics, 172(2): 1165–1177.
Brown M E, Funk C C. 2008. Food security under climate change. Science, 319: 580–581.
Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol Ecol, 14(8): 2611–2620.
Fan C C, Xing Y Z, Mao H L, Lu T T, Han B, Xu C G, Li X H, Zhang Q F. 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(6): 1164–1171.
Gowda V R P, Henry A, Vadez V, Shashidhar H E, Serraj R. 2012. Water uptake dynamics under progressive drought stress in diverse accessions of the OryzaSNP panel of rice (Oryza sativa). Funct Plant Biol, 39(5): 402–411.
Gravois K A, McNew R W. 1993. Genetic relationships among and selection for rice yield and yield components. Crop Sci, 33: 249–252.
Henry A, Gowda V R P, Torres R O, McNally K L, Serraj R. 2011. Variation in root system architecture and drought response in rice (Oryza sativa): Phenotyping of the OryzaSNP panel in rainfed lowland fields. Field Crops Res, 120(2): 205–214.
Heuberger A L, Lewis M R, Chen M H, Brick M A, Leach J E, Ryan E P. 2010. Metabolomic and functional genomic analyses reveal varietal differences in bioactive compounds of cooked rice. PLoS One, 5(9): e12915.
Hu Z J, He H H, Zhang S Y, Sun F, Xin X Y, Wang W X, Qian X, Yang J S, Luo X J. 2012. A kelch motif-containing serine/threonine protein phosphatase determines the large grain QTL trait in rice. J Integr Plant Biol, 54(12): 979–990.
Huang X H, Wei X H, Sang T, Zhao Q, Feng Q, Zhao Y, Li C Y, Zhu C R, Lu T T, Zhang Z W, Li M, Fan D L, Guo Y L, Wang A H, Wang L, Deng L W, Li W J, Lu Y Q, Weng Q J, Liu K Y, Huang T, Zhou T Y, Jing Y F, Li W, Lin Z, Buckler E S, Qian Q, Zhang Q F, Li J Y, Han B. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet, 42: 961–967.
Huang X Z, Qian Q, Liu Z B, Sun H Y, He S Y, Luo D, Xia G M, Chu C C, Li J Y, Fu X D. 2009. Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet, 41(4): 494–497.
Jahn C E, Mckay J K, Mauleon R, Stephens J, McNally K L, Bush D R, Leung H, Leach J E. 2011. Genetic variation in biomass traits among 20 diverse rice varieties. Plant Physiol, 155(1): 157–168.
Jiang S H, Zhou H, Lin D Z, Dong Y J, Ye S H, Zhang X M. 2013. Identification and gene mapping of a thermo-sensitive leaf-color mutant at seedling stage in rice. Chin J Rice Sci, 27(4): 359–364. (in Chinese with English abstract)
Jiao Y Q, Wang Y H, Xue D W, Wang J, Yan M X, Liu G F, Dong G J, Zeng D L, Lu Z F, Zhu X D, Qian Q, Li J Y. 2010. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet, 42: 541–544.
Khush G S. 2001. Challenges for meeting the global food and nutrient needs in the new millennium. Proc Nutr Soc, 60: 15–26.
Kondo M, Pablico P P, Aragones D V, Agbisit R, Abe J, Morita S, Courtois B. 2003. Genotypic and environmental variations in root morphology in rice genotypes under upland field conditions. Plant Soil, 255(1): 189–200.
Li J M, Xiao J H, Grandillo S, Jiang L Y, Wan Y Z, Deng Q Y, Yuan L P, McCouch S R. 2004. QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian (O. sativa L.) and African (O. glaberrima S.) rice. Genome, 47(4): 697–704.
Li X B, Yan W G, Agrama H, Jia L M, Shen X H, Jackson A, Moldenhauer K, Yeater K, McClung A, Wu D X. 2011. Mapping QTLs for improving grain yield using the USDA rice mini-core collection. Planta, 234(2): 347–361.
Lipka A E, Tian F, Wang Q S, Peiffer J, Li M, Bradbury P J, Gore M A, Buckler E S, Zhang Z W. 2012. GAPIT: Genome association and prediction integrated tool. Bioinformatics, 28(18): 2397–2399.
Lu C F, Shen L S, Tan Z, Xu Y B, He P, Chen Y, Zhu L H. 1996. Comparative mapping of QTLs for agronomic traits of rice across environments using a doubled haploid population. Theor Appl Genet, 93: 1211–1217.
Ma L Y, Yang C D, Zeng D L, Cai J, Li X M, Ji Z J, Xia Y W, Qian Q, Bao J S. 2009. Mapping QTLs for heading synchrony in a doubled haploid population of rice (Oryza sativa L.) in two environments. J Genet Genom, 36(5): 297–304.
Malosetti M, van der Linden C G, Vosman B, van Eeuwijk F A. 2007. A mixed-model approach to association mapping using pedigree information with an illustration of resistance to phytophthora infestans in potato. Genetics, 175(2): 879–889.
Manneh B, Stam P, Struik P C, Bruce-Oliver S, van Eeuwijk F A. 2007. QTL-based analysis of genotype-by-environment interaction for grain yield of rice in stress and non-stress environments. Euphytica, 156(1): 213–226.
Mei H W, Li Z K, Shu Q Y, Guo L B, Wang Y P, Yu X Q, Ying C S, Luo L J. 2005. Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations. Theor Appl Genet, 110(4): 649–659.
McNally K L, Childs K L, Bohnert R, Davidson R M, Zhao K Y, Ulat V J, Zeller G, Clark R M, Hoen D R, Bureau T E, Stokowski R, Ballinger D G, Frazer K A, Cox D R, Padhukasahasram B, Bustamante C D, Weigel D, Mackill D J, Bruskiewich R M, R?tsch G, Buell C R, Leung H, Leach J E. 2009. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci USA, 106: 12273–12278.
Miura K, Ikeda M, Matsubara A, Song X J, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M. 2010. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet, 42: 545–549.
Nordborg M, Tavaré S. 2002. Linkage disequilibrium: What history has to tell us. Trends Genet, 18(2): 83–90.
Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155(2): 945–959.
Risch N, Merikangas K. 1996. The future of genetic studies of complex human diseases. Science, 273: 1516–1517.
Samonte S O P B, Wilson L T, McClung A M. 1998. Path analyses of yield and yield-related traits of fifteen diverse rice genotypes. Crop Sci, 38(5): 1130–1136.
Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M. 2008. Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet, 40: 1023–1028.
Shrestha R, Al-Shugeairy Z, Al-Ogaidi F, Munasinghe M, Radermacher M, Vandenhirtz J, Price A H. 2014. Comparing simple root phenotyping methods on a core set of rice genotypes. Plant Biol, 16(3): 632–642.
Song X J, Huang W, Shi M, Zhu M Z, Lin H X. 2007. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet, 39: 623–630.
Takeda S, Matsuoka M. 2008. Genetic approaches to crop improvement: Responding to environmental and population changes. Nat Rev Genet, 9: 444–457.
Tan Y F, Xing Y X, Li J X, Yu S B, Xu C G, Zhang Q F. 2000. Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. Theor Appl Genet, 101: 823–829.
Tian Z X, Qian Q, Liu Q Q, Yan M X, Liu X F, Yan C J, Liu G F, Gao Z Y, Tang S Z, Zeng D L, Wang Y H, Yu J M, Gu M H, Li J Y. 2009. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA, 106: 21760–21765.
Wang M L, Zhu C S, Barkley N A, Chen Z B, Erpelding J E, Murray S C, Tuinstra M R, Tesso T, Pederson G A, Yu J M. 2009. Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection. Theor Appl Genet, 120: 13–23.
Wang S K, Wu K, Yuan Q B, Liu X Y, Liu Z B, Lin X Y, Zeng R Z, Zhu H T, Dong G J, Qian Q, Zhang Q F, Fu X D. 2012. Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet, 44: 950–954.
Weng J F, Gu S H, Wan X Y, Gao H, Guo T, Su N, Lei C L, Zhang X, Cheng Z J, Guo X P, Wang J L, Jiang L, Zhai H Q, Wan J M. 2008. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res, 18: 1199–1209.
Yu J M, Buckler E S. 2006. Genetic association mapping and genome organization of maize. Curr Opin Biotechnol, 17(2): 155–160.
Yu J M, Pressoir G, Briggs W H, Brigges W H, Vroh Bi I, Yamasaki M, Doebley J F, McMullen M D, Gaut B S, Nielsen D M, Holland J B, Kresovich S, Buckler E S. 2005. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet, 38: 203–208.
Zhang X J, Wang J F, Huang J, Lan H X, Wang C L, Yin C F, Wu Y Y, Tang H J, Qian Q, Li J Y, Zhang H S. 2012. Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proc Natl Acad Sci USA, 109(52): 21534–21539.
Zhao K Y, Tung C W, Eizenga G C, Wright M H, Ali M L, Price A H, Norton G J, Islam M R, Reynolds A, Mezey J, Mcclung A M, Bustamante C D, McCouch S R. 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun, 2: 467–477.
Zhuang J Y, Fan Y Y, Wu J L, Xia Y W, Zheng K L. 2001. Comparison of the detection of QTL for yield traits in different generations of a rice cross using two mapping approaches. Acta Genet Sin, 28(5): 458–464. (in Chinese with English abstract)
