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 FST 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.
Highlights
Peanut, known as groundnut (Arachis hypogaea L.), is one of the most important edible oil crops in the world
Two restriction enzymes (RsaI and HaeIII) were selected based on uniqueness and uniformity of simulated fragment alignments to the reference genome sequence of two diploids, A. ipaensis and A. duranensis
The candidate gene for seed coat color, located ∼12 kb from the peak single nucleotide polymorphisms (SNPs) B03-22076736, which explained 21.94% of the phenotypic variation), represented a bHLH transcription factor previously found to influence seed coat color in rice (Sweeney et al, 2006). These results suggest that Genome-wide association studies (GWAS) was effective in clarifying candidate genes related to major domestication-related traits in peanut
Summary
Known as groundnut (Arachis hypogaea L.), is one of the most important edible oil crops in the world. Based on the presence or absence of floral axes on the main stem, cultivated peanut is classified into two subspecies: hypogaea and fastigiata. Subspecies hypogaea is generally described as having a prostrate growth habit with no floral axes on the main stem, while in subspecies fastigiata flowers arise on leaf axils on branches as well as the main stem (Krapovickas and Gregory, 1994). As the only cultivated species of Arachis, peanut has been grown for hundreds of years in more than 100 countries worldwide (Huang et al, 2012). The evolution of Arachis is closely related to the domestication of cultivated peanut, with a vast number of morphological forms having evolved under cultivation.
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