Genome-Wide Association Analysis Of Flour Color Related Traits In Common Wheat

Wheat is an important food crop that is not only because its high nutritional value,but also conferred by various products,such as noodles,steamed buns,bread,dumplings,biscuits,processed from wheat flour.The color of wheat flour and its products is a vital index to evaluate its processing quality.In this study,the wheat660 K SNP chip was used for genotyping the association analysis population consisted with 207 wheat germplasms.The association population was planted under multi locations for measuring five wheat flour colour related traits: flour whiteness,grain yellow content,flour brightness,flour redness and flour yellowness.The genetic loci and key genes controlling wheat flour color were elucidated.The main results are as follows:1.The heritability of wheat flour color parameters(including flour whiteness,flour brightness,redness and yellowness)and wheat grain yellow pigment content were all >0.91,and the phenotypes were normally distributed which indicated all the five traits controlled by multiple genes.A total of 76 Peak SNPs were identified for flour colour parameters by genome-wide association analysis(GWAS),and they distributed on 19 chromosomes except 3A and 6B.The SNPs accounted for 7.9%-16.5% of the phenotypic variation,among which 29 polymorphic SNPs controlled more than 2 flour color related traits.2.Ten of the Peak SNPs were converted to Kompetitive Allele-Specific PCR(KASP)markers.Furthermore,three of the Peak SNPs located on chromosome 1BS,4BL and 7AL,respectively,were revealed influencing the flour colour related traits by additive effect.In addition,AX-111746023,a KASP marker developed from the Peak SNP located on the short arm of chromosome 1B,can be used for identification of1B/1R translocation lines.3.Candidate genes TaPsyA1 and TaPsyB1 were found near the multi effect SNP AX-108932464 and AX-94460336 on chromosomes 7AL and 7BL,respectively,and they were annotated the function of Phytoene synthase.SSR polymorphisms with TC repeat units were found in the promoter region of Psy A1-a,the TaPsyA1 functional allele,in the association analysis population.There were 7 variants detected in this SSR region in the association population.The germplasms with the allele of longer SSR(21 or more repeat units)was classified into Type 1,and shorter SSR(less than21 repeat units)was grouped into Type 2.The flour color indexes in Type 1germplasms were significantly better than those in Type 2,while the expression level of TaPsyA1 was significantly lower than that in Type 2.The polymorphism in the candidate gene TaPsyB1 which located in chromosome7 BL was also caused by a SSR with GA as the repeat unit at the promoter region.TaPsyB1 revealed 7 different variants in the association population.The germplasms with the shorter SSR allele(with the amplified fragment length of 371 bp)was classified as Type 1,and the germplasms contained the longer allele(with the amplified fragment length longer than 371 bp)was grouped as Type 2.The flour color indexes of Type 1 was significantly better than Type 2,and the expression level of TaPsyB1 in Type 1 germplasms was significantly lower than that in Type 2.Therefore,the length of SSR sequences in both of the Psy A1-a promoter region and TaPsyB1 promoter region can regulate gene expression,thus affect the color of wheat flour products.4.The third candidate gene,Ta GELP-B1,was found near the Peak SNP AX-111746023 on chromosome 1BS.The gene was annotated the function of GDSL esterase/lipase.Two polymorphisms were detected in the Ta GELP-B1 promoter region in non-1B/1R translocation lines of associated populations: 55 bp insertion/deletion,and a 22 bp insertion/deletion.According to the polymorphisms,the germplasms in the association population were divided into three genotypes.The FPKM and Luc/Ren value of GELP-B1 a allele were significantly lower than those of GELP-B1 b and GELP-B1 c.Correspondingly,the yellow pigment content of GELP-B1 a was significantly higher than that of GELP-B1 b.Therefore,the polymorphism of Ta GELP-B1 promoter region affects gene expression,and it is speculated that it reduces the content of yellow pigment in wheat grains.