Genome-wide Association Study Of Seed Reserve Utilization Efficiency During Seed Germination With SSR Markers In Rice(Oryza Sativa.l.)

Rice(Oryza sativa L.)is the main food crop for about 3.5 billion populations in the world.To adapt to the development of domestic economy,the transfer of rural surplus labor force,the decrease of fresh water and the crop cultivation practices,mechanization,and patterned,direct-seeded rice is an inevitable trend which has a wide application prospect.An essential condition of direct-seeded rice is possessing seedling vigor.SRUE(seed reserve utilization efficiency)is an important indicator of energy metabolism,a yardstick of efficient conversion of storage in the process of seed germination,and an evaluation criterion of seed vigor.Therefore,the improvement of SRUE has an important significance for seed germination,seedling growth,direct-seeded rice and increase rice yield.In order to discover elite alleles for enhancing rice seed vigor,five hundred and seventy rice varieties were genotyped with 262 simple sequence repeat(SSR)markers.We surveyed the SRUE trait of 570 varieties during germination(dark culture 10days)from 2013 to 2014 and detected the trait-marker associations.We determine elite alleles using GWAS(genome-wide association study)and identified the carrier varieties carrying these elite alleles and predicted the excellent parental combinations for improving SRUE.The main results are summarized as follows:1.There were significant differences for seed reserve utilization efficiency in the population consisted of 570 rice varieties.The mean was 0.5682mg/mg,SD was 0.0423,ranged from 0.430 1mg/mg(Yuedao 62)to 0.7266mg/mg(Zidao).There were 282 varieties larger than the mean,and the top 10 SRUE varieties were Zidao,Songjing 12,Mudanjiang 27,Diediezhong,Sujing 353,Puxidadaotou,Beidao 3 hao,24248,Shengtangqing and Yaxuenuo,respectively.2.3110 alleles were detected in 262 pairs of SSR markers in the population studied.There were 3 SSR markers(RM280,RM437 and RM216)amplified had 4 alleles were found detected among 570 varieties.SSR marker RM7445 had 26 alleles detected,with an average of 11.87 alleles per marker locus.The average gene diversity of population was 0.7453,ranged from 0.1308 to 0.9421.An average of PIC was 0.7192,ranged from 0.1275 to 0.9391.3.In natural population,13 marker-SRUE associations were detected(p<0.01).13 loci distributed on chromosome 1,2,4,5,6,7,8,11,and they were RM8095_Chrl(S),RM5356_Chr2(S),RM573_Chr2(L),RM518_Chr4(S),RM159_Chr5(S),RM437_Chr5(S),RM7309_Chr6(L),RM5753_Chr6(L),RM162_Chr6(L),RM2530_Chr7(L),RM6863_Chr8(S),RM72_Chr8(S)and RM287_Chrll(L)respectively.The explanation SRUE variation of a single site was different ranged from 2.77%-10.94%.4.36 positive elite alleles were identified and there were 3,3,2,3,4,1,3,4,2,4、2,2 and 3 elite alleles on the locus of RM8095,RM5356,R M573,RM518,RM159,RM437,RM7309,RM5753,RM162,RM2530,RM6863,RM72 and RM287 respectively.The mean range for the positive allele increasing SRUE phenotypic effect value was 0.0008mg/mg(RM2530-160bp)-0.0229mg/mg(RM159-245bp).There were 396 rice varieties,accounted for 77.3%,carrying the positive elite allele RM437-275bp in nature population.There were 16 varieties,accounted for 3.13%,carrying the rare allele RM437-270bp.5.There were 13 carrier varieties of Zidao,Songjing 12,Mudanjiang 27,Diediezhong,Sujing 353,Puxidadaotou,Shengtangqing,Yaxuenuo,Bodao,Yingtoudao,Yuedao 69,Longjing 25 and Zhongshuyangzhongdao.Among then,the effect values of Yaxuenuo,Zidao,Mudanjiang and Bodao were all more than 0.015mg/mg.6.The best 10 excellent parental combinations were predicted.They were YaxuenuoxBodao,Zidao×Jiangfeng 4 hao,Bodao×Yuedao 69,Bodao×Jiangfeng 4 hao,Bodao×Longjing 25,Bodao×Sihao4230,ShengtangqingxBodao,Bodao×Zhongshuyangzhongdao,Sujing 353×Longjing 25 and Sujing 353×Zhongshuyangzhongdao.