Genome-wide RAD-Seq analysis revealed subpopulation structures of the pecan (Carya illinoinensis) germplasm collection and their relationship to geographical distribution patterns
Pecan (Carya illinoinensis) is a large and deciduous tree that is native to North America and grown in diverse environments throughout the world. Due to the importance of pecan as a nut tree, many genetic resources have been preserved and investigated. The genetic diversity of pecan, however, has never been evaluated based on genome-wide marker polymorphisms. In this study, we performed restriction site associated DNA sequencing (RAD-Seq) of ca. 860 Carya primarily pecan accessions to analyze genetic structure existing among the accessions, and found a significant relationship between population structure and geographic origin. After filtering out low-quality SNPs based on various criteria (e.g., minor allele frequency, average read depth, missing genotype rate), we obtained more than 7500 reliable SNPs across the accessions. In population structure analysis using ADMIXTURE, accessions were divided into 10 subpopulations. Accessions belonging to the same subpopulation tended to originate from the same geographic region. The results suggest a strong relationship between geographical distribution and genome-wide SNPs.
Ishimori, M., Takanashi, H., Fukami, K., Cervantes, K., Nagano, A.J., Kajiya-Kanegae, H., Grauke, L.J., Tsutsumi, N., Randall, J. and Iwata, H. (2021). Genome-wide RAD-Seq analysis revealed subpopulation structures of the pecan (Carya illinoinensis) germplasm collection and their relationship to geographical distribution patterns. Acta Hortic. 1318, 177-184
pecan, genome-wide SNP markers, population structure, genetic background, principal component analysis