QTL Analysis And Favorable Alleles Mining For Seed Reserve Utilization Efficiency In Oryza Sativa Using Natural And Segregation Populations

Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice that saves water and reduces labor requirement.Improving SRUE is a key factor to facilitate the application of this technology and improve the production.However,the QTLs controlling this trait are poorly investigated.In this study,we determine favorable alleles using GWAS(genome-wide association study)and identified the carrier accessions carrying these favorable alleles and predicted the excellent parental combinations for improving SRUE.Furthermore,QTL underlying SRUE were detected,verified and mined in JL-CSSL population which was constructed by 9522(as the recurrent parent)and Ludao(as the donor parent)by applying molecular marker-assisted selection method and successive backcross.The main results are summarized as follows.1.There were significant differences for seed reserve utilization efficiency in the population consisted of 542 rice accessions.The average of SRUE over 542 accessions was 0.52mg.mg-1 ranging from 0.22 mg.mg-1(Hongnong5)to 0.93 mg.mg-1(Yue40),with coefficient of variation 22.66%.31.55%of total accessions had SRUE value of 0.55mg.mg1 and 30.44%of total accessions had SRUE value of 0.65mg.mg-1.2879 alleles were detected in 542 rice accessions.The average number of alleles per SSR locus was 10.82.The variation ranges were from 2(RM437 on chromosome5,RM7163 on chromosome11)to 38(RM3428 on chromosome 11).The average genetic diversity of all SSR loci was 0.74 and the variation range was 0.08(RM7163 on chromosomell)-0.9506(RM3428 on chromosomell).The average PIC value was 0.71,ranging from 0.08(RM7163 on chromosome11)to 0.9484(RM3428 on chromosome11)2.Total 13 SSR marker loci associated with SRUE were detected by GLM,and two loci were also detected by MLM analyses,with PVE>5%.The 13 SSR markers associated with SRUE(P<0.01)were located on all chromosomes except chromosome 11,with PVE ranging from 5.05%(RM5158 on chromosome 5)to 12%(RM297 on chromosome 1).The two loci(RM7309 on chromosome 6 and RM434 on chromosome 9)revealed by both models were detected in both years.Twenty-three favorable alleles were identified with phenotypic effect values ranging from 0.10 mg.mg-1(RM7309-135bp on chromosome 9)to 0.45 mg.mg-1(RM297-180bp on chromosome 1).RM297-180bp showed the largest phenotypic effect value(0.44 mg.mg-1 in 2016 and 0.45 mg.mg-1 in 2017)with 6.72%of the accessions carrying this allele and the typical carrier accession was Manyedao,followed by RM297-175bp(0.43 mg.mg-1 in 2016 and 0.44 mg.mg-1 in 2017).The 5 typical carriers were Daniaodao,Manyedao,SuWujing,Yue 40 and Baimangnuo possessing the favorable alleles.Among them,the effect values of Daniaodao and Manyedao were all more than 0.3 mg.mg-1.Nine novel SSR marker loci associated with SRUE were identified comparing with previous studies.The best 5 excellent parental combinations were predicted.They were Yue40 × Manyedao,Yue40 × Daniaodao,Manyedao × Suwujing,Suwujing ×Baimangnuo and Daniaodao × Suwujing.Those top optimal parental combinations for pyramiding more favorable alleles for SRUE could be used for breeding rice accessions suitable for wet direct seeding in the future.3.A total of 5 QTL,which controls the SRUE and its component traits,were detected by RSTEP-LRT method in the JL-CSSL population.They were distributed on chromosome 6 and 9.One QTL was detected in seed dry weight trait(DW),on chromosome 9 with negative effect value on DW and the favorable alleles was from Ludao decreasing the dry weight phenotypic effect by 16.41mg(RM6971-200bp).One QTL was detected in seedling dry weight trait(SDW)on chromosome 6,and the favorable alleles was from Ludao,increasing the seedling dry weight phenotypic effect by 1.62mg(RM162-220bp).Two QTL were detected in remaining seed dry weight(RSDW),on chromosome 6,one with negative effect value on RSDW decreasing the phenotypic effect by 0.32mg(RM345180bp from the donor parent)and another with positive effect on RSDW increasing the phenotypic effect by 1.93mg(RM162-250bp from the recurrent parent).One QTL was detected in Seed reserve utilization efficiency trait(SRUE),on chromosome 6,and the favorable allele was from Ludao,increasing SRUE phenotypic effect by 0.08 mg.mg-1(RM162-220bp).One marker was linked with pleiotropic QTLs;RM162 located on chromosome 6 was linked to SDW,RSDW and SRUE.4.This study showed significant differences in SRUE in JLCSSL population,one QTL coming from the donor parent(Ludao)was detected for SRUE located on chromosomes 6(RM162-220;PVE 16.12%)has led to increase SRUE and the material numbers carrying this QTL were CSSL40 and CSSL41.Present results suggest that the Ludao genome has a potential to improve SRUE and can be used to breed for this important trait and the newly developed CSSL population will provide a foundation for rice accession improvement and proved to be a useful tool for both gene identification and mapbased cloning.5.In both association mapping and linkage mapping markers on chromosome 6 were detected to be related to SRUE.In the natural population,RM7309 on the long arm of chromosome 6(2629723 8-26297595bp)was confirmed to be related to SRUE using GLM and MLM models.The mean value for RM7309-135bp increasing SRUE phenotypic effect was 0.10mg.mg-1.As for the,CSSL population,RM162 on the long arm of chromosome6(24035491-24035615 bp)was identified by RSTEP-LRT method of linkage mapping and the elite allele RM162-220bp coming from the donor parent Ludao had increased SRUE by 0.08mg.mg-1.