Genome-wide association mapping for yellow rust resistance in a population of 454 whole-genome sequenced diverse wheat genotypes

Yellow rust infections were evaluated in seven different field experiments based on natural or artificial inoculations and using a 1-to-9 scoring scale [1: complete absence of symptoms, 9: severe infection]. Best linear unbiased estimators (BLUEs) across experiments were used as phenotypes for genome-wide association studies (GWAS). GWAS was conducted for 454 whole-genome sequenced (WGS) wheat genotypes considering a kinship matrix computed from genotyping-by-sequencing (GBS) markers. SNP-based GWAS was conducted using WGS variants mapped to Chinese Spring (RefSeq v1.0) while k-mer-based GWAS was performed using the presence/absence of 31-bp-long sequence motifs. For further details on input files and R codes, please read the “README.txt” files.

本研究基于自然或人工接种，在七个不同田间试验中评估了黄锈病的感染情况，采用1至9分的评分标准[1：症状完全缺失，9：严重感染]。利用实验间的最佳线性无偏估计量（BLUEs）作为全基因组关联研究（GWAS）的表型。针对454个全基因组测序（WGS）的 wheat 基因型，通过从基因分型测序（GBS）标记计算出的亲缘矩阵进行了GWAS。基于SNP的GWAS采用映射到中国春（RefSeq v1.0）的WGS变异体进行，而基于k-mer的GWAS则通过31碱基长度的序列模式的存在/缺失进行。有关输入文件和R代码的更详细信息，请参阅“README.txt”文件。