Genome-wide Association Study Of Seed Dormancy And Fine Mapping Of Qsd3.1 In Rice

Seed dormancy is an important agronomic trait,which affects yield and quality of crops.At maturity stage,weak dormant seeds of rice varieties often appear a pre-harvest sprouting phenomenon under high temperature and humidity conditions,while,strong dormant seeds inhibit germination at sowing time.Either weak or strong dormant varieties are likely to affect plant growth and development,and to decrease the yield and quality of rice.Therefore,breeding of moderate seed-dormant varieties has a significance role in crop productivity.In the present study,we conducted genome-wide QTL analyses for seed dormancy and germination performance using the NIP/ZS97 chromosome segment substitution lines and a core collection of 252 rice varieties.We further validated and finely mapped a major QTL qsd3.1 that associated with seed dormancy and germination characteristics.The main results are as follows:1.Germination experiment of the freshly harvested seeds demonstrates that ZS97 has a weak or non-dormant seeds,while NIP is moderate dormant.The seed dormancy was broken after 43 ? oven treatment,however,the difference in germination rate between ZS97 and NIP still existed at 25? germination temperature condition.2.By using a ridge regression method to detect QTLs in 146 NIP/ZS97 CSSLs,we identified a total of 28 QTLs for seed dormancy distributes in 12 chromosomes.Of them,9 QTLs detected affecting all the six indexes(7dGR,3dGR,AUC,T50,U80-20,GI),4 QTLs including qsd3.2,qsd7.2,qsd7.4 and qsd10.4 are consitent with those reported or cloned previously.The remaining 24 QTLs such as some weak dormant QTLs(qsdl.1,qsd3.3,qsd5.1,qsd5.2,qsd5.3,qsd6.2,qsd8.1,qsd9.1,qsd10.1,qsd11.2)are newly detected in this inverstigation,which reflects precision and accuracy of the QTL detection using the CSSLs population.3.The principal component analysis divided the six indexes into two principal components,PC1 and PC2,which explained 51%and 41%phenotypic variances in CSSLs,respectively.7dGR and AUC can be classified as PC2,reflecting the final status of germination.The other four indexes classified as PC1,reflecting the germinate rate of seeds.4.Using a F2 population derived from a CSSL(NQ96)that contains a target substitution region on chromosome 3,qsd3.1 was confirmed as a major QTL for the 6 indexes.It located in the intervial of RM14238-MP030012 explaining 67.53%(7dGR),56.87%(3dGR),35.99%(AUC),24.64%(T50),36.08%(GI),68.30%(U80-20)of the phenotypic varation in the F2 population.We selected recombinant individuals in the target region from the F2 population and narrowed qsd3.1 down to an introgressed region between MP03009 and MP030012 with 92 kb in length.5.The germination test using the near isogenic lines indicated that the qsd3.1 is one of the moderate dormant QTLs.The dormancy of newly harvested seeds disappears after storaged 12 d at room temperature.The dehulled seed test using the near isogenic lines showed that the coat of seed may have a certain inhibitor suppress germination,while the permeability of seeds was no difference between the dormant and non-dormant near isogenic lines.Exogenous hormones treatment of the near isogenic lines showed that,GA and ethylene can break seed dormancy,and ABA affects the germination behavours.6.We detect a total of 62 QTLs using GWAS with the core collection of rice.Among them 12 common QTLs were identifited in CSSLs.These results provide a wealth of QTLs information for further improving resistance to pre-harvest sprouting in rice.