Favorable Alleles Mining For Gelatinization Temperature,Gel Consistency And Amylose Content Of Milled Rice By Association Mapping

During the last 20 years,the success of hybrid rice in China was a significant step to improve rice grain yield,the yield of hybrid rice was 15-20 percent higher than that of high-yielding conventional varieties.The annual planting acreage for hybrid Indica rice in China accounted for approximately 80%of the total Indica rice area,while hybrid japonica rice only accounted for approximately 5%of the total japonica rice area.One of the main reasons for the slow development of hybrid japonica rice is that the grain eating and cooking qualities(ECQs)are not as good as conventional japonica rice.With the development of advanced sciences and technologies,improving the gelatinization temperature(GT),gel consistency(GC)and amylose content(AC)for parental grain eating and cooking qualities(ECQs)are key factors for enhancing average grain ECQs for hybrid japonica rice.In this study,a genome-wide association mapping for ECQs was performed on a selected sample of 462 rice accessions from 7 ecological regions in 5 environments using 262 simple sequence repeat markers,the Mixed Linear Model(MLM)in TASSEL software was used to analyze the association between marker and phenotypic variation.The main results are as follows:1.In the population constituted of 462 rice accessions,phenotypic variation of GT,GC and AC traits was large,the corresponding coefficient of variation was 41.24%,51.96%and 32.85%,respectively.The heritability in broad sense of each trait was 95%,94%and 98%,respectively and it was basically stable over the five environments.2.The genetic diversity of the 462 accessions was measured using 262 SSR markers,the analysis resulted in a total of 2462 alleles being detected.Furthermore,there were 379 unique alleles(allele frequencies<0.5%),848 rare alleles(0.5%?allele frequencies<5%),1231 polymorphic alleles(5%?allele frequencies?95%)and 4 fixed alleles(allele frequencies?95%)of the 2462 alleles,its corresponding proportions were 15.39%,34.44%,50.00%and 0.16%,respectively.Numbers of alleles per locus ranged from 2(at locus RM206 on chromosome11)to 25(RM7545 on chromosome10)with an average of 9.40 alleles per locus.The genetic diversity averaged 0.4685 ranging from 0.0068(RM7403 on chromosome3)to 0.7569(RM128 on chromosomel).The average PIC value was 0.4208,ranging from 0.0067(RM7403 on chromosome3)to 0.7444(RM128 on chromosome1).3.STRUCTURE analysis with 262 SSR markers combined with the Neighbor-Joining cluster method and Principal component analysis(PCA)for each subpopulation showed that the 462 accessions could be divided into five subpopulations,viz.from subpopulation 1 to subpopulation 5.The number of accessions contained from subpopulation 1 to subpopulation 5 were 97,115,105,97,96 and 48,respectively.There was a certain degree of Linkage Disequilibrium(LD)between SSR marker loci of either intra-chromosome or inter-chromosome within each subpopulations.The D' mean values of the standard disequilibrium coefficient from subpopulation 1 to subpopulation 5 were 0.692,0.673,0.786,0.751 and 0.787,respectively.The minimum distance of delay(D'<0.5)from subpopulation 1 to subpopulation 5 were 41.8 cM,79.3 cM,83.3 cM,76.4 cM and 63.4 cM,respectively.4.We totally identified 35 QTLs for rice ECQs(FDR<0.05),some of these loci were overlapping with starch synthesis-related genes.8 QTLs that were associated with the GT located on chromosomes 2,3,5,7,9,10 and 11 with a corresponding PVE rang of 2.56%to 10.12%,of which RM232-chr3,RM135-chr3 and RM3600-chr9 were novel detected in this study;9 QTLs were associated with the GC trait in five environments,and distributed on seven chromosomes 3,4,6,7,8,11 and 12 with a corresponding PVE rang of 1.84%to 10.54%,of which RM232-chr3,RM6712-chr3,RM348-chr4,RM234-chr7,RM6327-chrll and RM309-chr12 were novel detected;18 QTLs were associated with AC and distributed on chromosomes 2,3,4,5,6,7,8,10,11 and 12 with a corresponding PVE rang of 1.95%to 12.87%,of which RM6712-chr3,RM122-chr5,RM159-chr5,RM3754-chr8,RM258-chr10 and RM6327-chrl1 were novel detected.5.The QTLs detected associated with the rice ECQs over the five environments had 87 favorable alleles,20 favorable alleles had phenotypic effect of decreasing the GT,of which the allele RM3600-90bp showed the largest positive phenotypic effect value(1.49 grade)of reducing the GT,and with the typical carrier accession being 'Longdun105'.24 favorable alleles had phenotypic effect of increasing the GC,of which the allele RM6327-175bp showed the largest positive phenotypic effect value(21.94mm)of increasing the GC,and with the typical carrier accession being 'Hongnong5'.43 favorable alleles had phenotypic effect of increasing the AC,of which the allele RM6327-175bp showed the largest positive phenotypic effect value(-2.42%)of reducing the AC,and with the typical carrier accession being‘Baimangnuo'.6.Fifteen excellent parental combinations by pyramiding favorable alleles into one single plant for improving GT,GC and AC traits.Taking the GT trait as an example,'Zhongjing212'crossed with 'Longdun105',all of the favorable alleles could be combined into a single plant,and the ASS of this variety could be theoretically increased by 4.2 grade.For GC trait,'Hongnong5' crossed with 'Xudao4',the GC of this variety could be theoretically increased by 148.4mm.For AC trait,'Hongnong5' crossed with 'Buxuenuo',the AC of this variety could be theoretically reduced by 37.3%.