Genome-Wide Association Study of Major Agronomic Traits Related to Domestication in Peanut

Abstract

Peanut (Arachis hypogaea) consists of two subspecies, hypogaea and fastigiata, and has been cultivated worldwide for hundreds of years. Here, 158 peanut accessions were selected to dissect the molecular footprint of agronomic traits related to domestication using specific-locus amplified fragment sequencing (SLAF-seq method). Then, a total of 17,338 high-quality single nucleotide polymorphisms (SNPs) in the whole peanut genome were revealed. Eleven agronomic traits in 158 peanut accessions were subsequently analyzed using genome-wide association studies (GWAS). Candidate genes responsible for corresponding traits were then analyzed in genomic regions surrounding the peak SNPs, and 1,429 genes were found within 200 kb windows centerd on GWAS-identified peak SNPs related to domestication. Highly differentiated genomic regions were observed between hypogaea and fastigiata accessions using F_ST values and sequence diversity (π) ratios. Among the 1,429 genes, 662 were located on chromosome A3, suggesting the presence of major selective sweeps caused by artificial selection during long domestication. These findings provide a promising insight into the complicated genetic architecture of domestication-related traits in peanut, and reveal whole-genome SNP markers of beneficial candidate genes for marker-assisted selection (MAS) in future breeding programs.

Keywords: domestication; genome-wide association studies; peanut; selective sweeps; single-nucleotide polymorphisms (SNPs).

Figure 1

Phenotypic variation of eight traits among 158 peanut accessions.

Figure 2

Principal component analysis (PCA), phylogenetic tree construction and population structure analysis of the 158 peanut accessions. (A) Scatter plots of the first two principal components. The horizontal and vertical coordinates represent PC1 (with variance explain 8.16%) and PC2 (with variance explain 5.23%). Each dot represents an accession. (B) Phylogenetic tree constructed with 17,338 high quality SNPs. (C) Population structure dividing the accessions into two groups (ΔK value was 0.47): subsp. hypogaea (group I) and subsp. fastigiata (group II).

Figure 3

Genome-wide association studies (GWAS) of traits associated with peanut domestication. Manhattan plots with corresponding small QQ plots are shown in each figure of each trait. Associated significant SNPs are marked by arrows with reported candidate genes. The Bonferroni multiple test threshold is shown by a dotted blue line. MD: Malate dehydrogenase; P450: Cytochrome P450 superfamily protein; bHLH: bHLH transcription factor; ARF: Auxin response factor; MAP: Microtubule-associated protein.

Figure 4

Selective sweeps and population differentiation analyses of subsp. hypogaea (group I) and subsp. fastigiata (group II). (A) Regional plot of 15 SNPs in the 200-kb selective sweep region on chromosome A03. The bottom panel indicates the extent of LD in the region based on pairwise r2-values which are shown in the LD triangles. (B) Distributions of selective sweeps in subsp. hypogaea (group I) and subsp. fastigiata (group II). (C) Manhattan plots of FST values of peanut chromosome.