Mining Elite Alleles For Grain Plumpness In Rice (Oryza Sativa L.)via Association Mapping

Rice(Oryza sativa L.)is a staple food that feeds more than 50%of world’s population.However,with the decreasing of arable land,the current yield of rice is not enough to meet the demands of the rapidly increasing population.The field application showed that the yield of hybrid rice was increased by 15%-20%compared with conventional rice.Therefore,the development of hybrid rice is necessary for the increase of world food.However,poor grain filling is still one of limited factors to reach yield potential of hybrid rice.Poor grain filling will seriously affect grain plumpness and the final yield of rice.Thus,the improvement of grain plumpness is very important for increasing the yield of rice.In this study,177 rice varieties were collected.The 177 varieties were planted in 2013 and 2014 at three locations,i.e.,Jiangpu Experimental Farm(118.62 ° E,32.07 ° N),Nanjing Agricultural University,Jiangsu,Yuanyang Farm(113.96 °E,35.05 °N)and Xinyang Farm(114.12 °E,32.10 °N),Henan Academy of Agricultural Sciences,Henan,China.Grain plumpness of 177 varieties was investigated after harvest.261 SSR markers were used to analyze genetic diversity,population structure and level of linkage disequilibrium.The genome-wide association analysis(GWAS)was conducted between grain plumpness and SSR markers in the general linear model(GLM)procedure in the TASSEL software to mine elite alleles.The main results obtained are as follows.1.Higher phenotypic variations for grain plumpness existed into the population composed of 177 rice varieties.The coefficient of variation ranged from 3.35%(2014 Nanjing)to 4.22%(2013 Xinyang).The broad-sense heritability for the grain plumpness was above 90%in each environment,ranging from 95.22%(2013 Nanjing)to 98.61%(2014 Yuanyang).2.Abundant genetic diversity existed into the population studied.261 SSR markers were used to analyze the genetic diversity of 177 varieties:1948 alleles were detected in the population,the average number of alleles per SSR locus was 7.46,the average gene diversity was 0.6734 and the average PIC value was 0.6395.3.Seven subgroups were detected in the population studied,and significant LD was found in the seven subgroups.Population structure was analyzed by two different analysis methods,i.e.,STRUCTURE analysis and PowerMarker cluster analysis based on Nei1s genetic distance.The results found that the population was divided into seven subgroups,viz.from SG1 to SG7.The varieties in SG3 and SG4 were mainly from Vietnam and the varieties of the rest subgroups were from China.The analysis of the levels of LD found that LD decay distances from SG1 to SG7 were 42.52 cM,38.37 cM,29.96 cM,27.39 cM,33.56 cM,44.70 cM and 50.40 cM respectively.The result showed that there were significant LD in the seven subgroups and that LD decay velocity varied among the seven subgroups.SG4 had fastest decay velocity,whereas SG7 had lowest decay velocity.4.Thirty-one trait-SSR marker loci associated with grain plumpness significantly(P<0.01)were detected,i.e.,RM8095,RM5,RM14,RM5340,RM300,RM573,RM450,RM263,RM5480,RM148,RM7563,RM153,RM159,RM3193,RM8109,RM510,RM2530,RM505,RM3589,RM506,RM1235,RM6863,RM544,RM331,RM8206,RM201,RM5629,RM590,RM511,RM1246 and RM5479.These marker loci were located on chromosomes 1,2,3,4,5,6,7,8,9,10 and 12.Of these marker loci,RM14,RM450,RM5480,RM1235,RM6863 and RM331 were detected only in three environments simultaneously,RM2530 was detected only in six environments simultaneously and the rest markers were detected only in two environments simultaneously.Compared with previous studies,we found that 19 marker loci were novel detected in this study.5.Based on marker loci detected,73 elite alleles and the varieties carried these alleles were mined for grain plumpness improvement.For example,RM5340-205bp,RM573-240bp,RM5-120bp,RM159-245bp,RM159-270bp and RM263-185bp,and the varieties carried them were ’Yuedao 22’,’Ligengqing’,’Huangsanshi’,’Qiaobinghuang’,’Yueda0 19’ and ’Yujing 6’ respectively.6.On the basis of elite alleles mined,7 parental combinations for grain plumpness improvement were predicted,i.e.,Yuedao 5 × Yuedao 19,Maozitou × Yuedao 19,Chiguhong × Yuedao 5,Chiguhong × Maozitou,Ligengqing × Yuedao 5,Qiutiandaxiedao× Chiguhong,Ligengqing × Qiutiandaxiedao.