Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection

Abstract

Background Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources of variation and to leverage the power of genome-wide association studies (GWAS) to discover markers associated with traits of interest. We report an analysis of linkage disequilibrium (LD), population structure, and genetic diversity, and examine the ability of GWA to infer marker-trait associations in the U.S. peanut mini core collection genotyped with a 58 K SNP array. Results LD persists over long distances in the collection, decaying to r 2 = half decay distance at 3.78 Mb. Structure within the collection is best explained when separated into four or five groups (K = 4 and K = 5). At K = 4 and 5, accessions loosely clustered according to market type and subspecies, though with numerous exceptions. Out of 107 accessions, 43 clustered in correspondence to the main market type subgroup whereas 34 did not. The remaining 30 accessions had either missing taxonomic classification or were classified as mixed. Phylogenetic network analysis also clustered accessions into approximately five groups based on their genotypes, with loose correspondence to subspecies and market type. Genome wide association analysis was performed on these lines for 12 seed composition and quality traits. Significant marker associations were identified for arachidic and behenic fatty acid compositions, which despite having low bioavailability in peanut, have been reported to raise cholesterol levels in humans. Other traits such as blanchability showed consistent associations in multiple tests, with plausible candidate genes. Conclusions Based on GWA, population structure as well as additional simulation results, we find that the primary limitations of this collection for GWAS are a small collection size, significant remaining structure/genetic similarity and long LD blocks that limit the resolution of association mapping. These results can be used to improve GWAS in peanut in future studies – for example, by increasing the size and reducing structure in the collections used for GWAS. Electronic supplementary material The online version of this article (10.1186/s12864-019-5824-9) contains supplementary material, which is available to authorized users.

Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA

“…SNP distribution across the genome assessed by analyzing filtered SNP density shows the typical pattern of distinctly reduced recombination in pericentromeric regions and increased varying recombination rates in euchromatic regions for all chromosomes. Larger regions with no SNP coverage are usually found in large pericentromeric regions, where repetitive DNA makes it difficult to distinguish unique flanking regions around SNPs 26,27 . A similar distribution has been observed in Sorghum 28 , wild tomatoes 29 , and Prunus 30 .…”

GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data

“…For common bean, diversity data is available for two diverse collections of Phaseolus vulgaris : the Mesoamerican Diversity Panel (MDP) and the Andean Diversity Panel (ADP) [ 25 ]. The peanut data set contains the U.S. Peanut Mini Core Collection genotyped using the 58 K Affymetrix SNP array, Axiom Arachis [ 26 ].…”

Genotypic characterization of the U.S. peanut core collection

“…Of the 253 accessions, 35 were selected based on information from GRIN-Global (https://www.grin-global.org) and previous knowledge of heterogeneity (Otyama et al 2019).…”