Genome-Wide-Association Analysis And Excavation Of Allelic Variation Of Pre-Harvest Sprouting Resistance Genes In Wheat

As one of the most important staple crops,wheat provides approximately one fifth calorie and protein for 35%population in the world.The wheat prone to sprout before harvest,when grown/stored under a hot-and-humid condition,with its grain yield and quality seriously affected.To identify pre-harvest sprouting resistance genes in wheat and excavate germplasms with new allelic variation in these genes,we performed the genome-wide-association analysis in a winter wheat population and conducted the cloning of several reported pre-harvest sprouting resistance genes.For the first aspect,a GWAS panel comprising of 383 winter wheat accessions grown in 2016-2017 and 2017-2018 at Zhaoxian were conducted to the evaluation of the pre-harvest sprouting resistance,with seed germination tests and sprouting test using whole spikes.The phenotype data and the genotype data determined by Wheat660K SNP arrays were performed to the association calculation with Tassel V5.2 using MLM.The GWAS identified 17 stable significant associated loci(SAL),and a distinct SAL was identified between the seed-germination-rate and spike-germination-rate.Among which,the SAL on chromosome 3AL,3BL and 3DL explained the most phenotypic variation and showed a strong correlation with spike-germination-rate,and they were overlapped with the TaMYB10 which controlling the color of the seed coat in wheat.Hence,the H-value that indicates the grain color was measured and performed to the GWAS,and this providing SAL co-localized with that of spike-germination-rate and overlapped with TaMYB10,suggesting spike-germination-rate was significantly affected by the color of the seed coat.Secondly,ten major pre-harvest sprouting resistance genes in wheat,rice,maize and Arabidopsis were cloned and sequenced using SMRT~?PacBio RS II sequencing platform in 288 winter wheat accessions to excavate allelic variation of these genes.The 1-bp deletion in the promoter region of TaMYB10-A resulted in a 0.24 reduction in spike-germination-rate,whileitwaswithoutsignificanteffectonthe seed-germination-rate.For the GA20ox-B,a G>A SNP in the first exon could causes the hydrophobic alanine replaced by a hydrophilic threonine 12-aa away from the C-terminal of iron/ascorbate dioxygenase domain,which was expected to bring in changes in the secondary structure and affect the enzymatic activity of GA20ox.