Population structure analysis and genome-wide association study of a hexaploid oat landrace and cultivar collection

作者：Lei Wang, Jinqing Xu, Handong Wang, Tongrui Chen, En You, Haiyan Bian, Wenjie Chen, Bo Zhang, Yuhu Shen · 发表于：Frontiers in Plant Science · 年份：2023 · DOI：10.3389/fpls.2023.1131751 · 被引用次数：20 · 研究领域：Wheat and Barley Genetics and Pathology、Genetic Mapping and Diversity in Plants and Animals、Genetic diversity and population structure

Introduction Oat ( Avena sativa L.) is an important cereal crop grown worldwide for grain and forage, owing to its high adaptability to diverse environments. However, the genetic and genomics research of oat is lagging behind that of other staple cereal crops. Methods In this study, a collection of 288 oat lines originating worldwide was evaluated using 2,213 single nucleotide polymorphism (SNP) markers obtained from an oat iSelect 6K-beadchip array to study its genetic diversity, population structure, and linkage disequilibrium (LD) as well as the genotype–phenotype association for hullessness and lemma color. Results The average gene diversity and polymorphic information content (PIC) were 0.324 and 0.262, respectively. The first three principal components (PCs) accounted for 30.33% of the genetic variation, indicating that the population structure of this panel of oat lines was stronger than that reported in most previous studies. In addition, accessions could be classified into two subpopulations using a Bayesian clustering approach, and the clustering pattern of accessions was closely associated with their region of origin. Additionally, evaluation of LD decay using 2,143 mapped markers revealed that the intrachromosomal whole-genome LD decayed rapidly to a critical r 2 value of 0.156 for marker pairs separated by a genetic distance of 1.41 cM. Genome-wide association study (GWAS) detected six significant associations with the hullessness trait. Four of these six markers...