Reconciliation Of Wheat 90K And 660K SNP Assay And Their Utilization In Yield- And Dough Rheological-Related Traits

Bread wheat is the staple food of 35-40% people in the world,and can be made into kinds of food as its sepecail gluten character.It is also the international trade and aid food.With the gradually decrease of cultivated area and rapidly increase of population,high stable yield and quality wheat are always the key target of wheat breeding.This study updated the physical positions of widely used wheat 90 K and 660 K SNP assay,and applied them into the association and linkage anslysis of yield-and dough rheological-related traits,the results are as follows:1.The flanking sequences of wheat 90 K and 660 K SNP assay were aligned to the Aikang58 reference genome.The BLAST results can be classified into the following 5 types.Type_I,unique best hits were identified on the same chromosomes as the original arrays.Type_II,unique best hits were identified,but their chromosomes were not same as the original,and we updated both their physical positions and chromosomes.Type_III,more than one best hit was identified in the same chromosomes as the original arrays.Type_IV,more than one best hit was identified,but these hits were not located on the same chromosomes as the original arrays.Type_V,no hits were identified.In the 660 K SNP array,565583(92.28%),10993(1.79%),10358(1.69%),1040(0.17%),and24934(4.07%)SNP were classified into Type_I,Type_II,Type_III,Type_IV,and Type_V,respectively.The percentages of Type_I SNP on most chromosomes exceeded 90%,especially chromosomes 1A,2A,3B,4B,and 4D(the percentages exceeded 95%).In the 90 K SNP array,67656(83.09%),6070(7.45%),1973(2.42%),900(1.11%)and 4824(5.92%)were classified as Type_I,Type_II,Type_III,Type_IV and Type_V SNP,respectively.The percentages of Type_I SNP on most chromosomes exceeded 80%,especially chromosomes 1A,1D,2A,2B,2D,3D,4B,4D,and 5A(percentages exceeded 85%).The dominant percentage of Type_I markers indicated the reliability of BLAST results.The results of 90 K SNP array aligned to the Chinese Spring reference genome V1.0 indicated that 77126(86.77%)markers showed the unique physical positions.Physical positions comparison of 90 K SNP assay in the Aikang58 and Chinese Spring reference genome V1.0 indicated that the tendency of physical positions in the two genomes was consistent,big difference was only found at the start and end of each chromosome.2.Genome-wide association studies were conductd for 13 yield-related traits in 163 bread wheat cultivars characterized by Wheat 90 K SNP genotyping assay in Yellow and Huai Valley ofChina.Phenotyping were investigated in 14 environments at three locations over three years.Totally 1,769 significant loci were identified and explained,on average,~20% of the phenotypic variation.SNP on chromosomes 6AS,6AL,6BS,5BL,and 7AS were significantly linked to thousand kernel weight(TKW),and consistently identified in 12 and 13 of the 14 environments.Kernel length-related SNP were mainly identified on chromosomes 7BS,6AS,5AL,and 5BL.Plant height-related SNP on chromosomes 4DS,6DL,2DS and 1BL were respectively identified in more than 11 environments,with averaged PVE of ~55%.Four SNPs were confirmed to be important genetic loci in two RIL populations.Based on repetivity and PVE,a total of 41 SNP loci possibly played the key role in modulating yield-related traits of the cultivars surveyed.Distribution of superior alleles at the 41 SNP loci indicated that superior alleles were getting popular with time and modern cultivars had integrated many superior alleles,especially for peduncle length-and plant height-related superior alleles.However,there were still 19 SNP loci showing less than percentages of 50% in modern cultivars,suggesting they should be paid more attention to improve yield-related traits of cultivars in the Yellow and Huai wheat region.This study could provide useful information for dissection of yield-related traits and valuable genetic loci for marker-assisted selection in Chinese wheat breeding program.3.Genome-wide association studies of 9 dough rheological properties of Chinese bread wheat were conducted in two association panels.The association population I containing 435 introgression lines,and characterized by the Wheat 660 K SNP assay;the association population II containing 163 cultivars,and characterized by the Wheat 90 K SNP assay.Phenotyping were investigated by Mixolab.The GWAS totally indicated 26 significant intervals composed of 1032 SNPs associated with 9 quality traits in multiple environments over 4 years.Before being updated,the significant interval for stability time on 1D was 407875297-416222857 bp based on the 660 K SNP array and1011346-2290849 bp based on the 90 K SNP array in two populations,and their distance was ≈ 405 Mb.After being updated,their positions were 410958209-419370971 bp and410958467-436196126 bp,respectively,with an 8.4-Mb region overlapped.Linkage analysis indicated that the QST.henau-1D.2 for stability time was detected within the overlapped interval and could narrow to 1.64 Mb.Haplotype analysis indicated that this interval increased stability time by an average of 3.1 min.Collinearity analysis identified 9 annotated genes in this interval.This study revealed important genetic loci affecting wheat-processing quality.