High-Density Genetic Variation Map Reveals Key Candidate Loci and Genes Associated With Important Agronomic Traits in Peanut

Abstract

Peanut is one of the most important cash crops with high quality oil, high protein content, and many other nutritional elements, and grown globally. Cultivated peanut (Arachis hypogaea L.) is allotetraploid with a narrow genetic base, and its genetics and molecular mechanisms controlling the agronomic traits are poorly understood. Here, we report a comprehensive genome variation map based on the genotyping of a panel of 178 peanut cultivars using Axiom_Arachis2 SNP array, including 163 representative varieties of different provinces in China, and 15 cultivars from 9 other countries. According to principal component analysis (PCA) and phylogenetic analysis, the peanut varieties were divided into 7 groups, notable genetic divergences between the different areas were shaped by environment and domestication. Using genome-wide association study (GWAS) analysis, we identified several marker-trait associations (MTAs) and candidate genes potentially involved in regulating several agronomic traits of peanut, including one MTA related with hundred seed weight, one MTA related with total number of branches, and 14 MTAs related with pod shape. This study outlines the genetic basis of these peanut cultivars and provides 13,125 polymorphic SNP markers for further distinguishing and utility of these elite cultivars. In addition, the candidate loci and genes provide valuable information for further fine mapping of QTLs and improving the quality and yield of peanut using a genomic-assisted breeding method.

Keywords: GWAS; SNP array; agronomic traits; molecular markers; peanut.

FIGURE 1

Frequency distribution of 178 peanut cultivars for 20 traits. MSH, main stem height; LBL, lateral branch length; TNB, total number of branches; PBN, pod-bearing branches number; PNP, pod number per plant; LBA, lateral branch angle; HPW, hundred pod weight; HSW, hundred seed weight; PL, pod length; PW, pod width; SL, seed length; SW, seed width; PT, peel thickness; FPN, filled pods number; OAC, oleic acid content; LAC, linoleic acid content; BAC, behenic acid content; AAC, arachidic acid content; PAC, palmitic acid content; SAC, stearic acid content.

FIGURE 2

Distribution and types of SNPs. (A) Distribution and density of SNPs in 20 peanut chromosomes. The horizontal axis shows the length of the chromosome (Mb), and the vertical axis represents 20 chromosomes. The shades of assorted color represent the SNP density on corresponding loci. (B) Frequency of several types of SNPs.

FIGURE 3

Population structure and genetic diversity of the 178 peanut varieties. (A) Cross-validation value of each K ranging from 1 to 10. (B) The PCA analysis of the total accessions. Each dot represents one variety. (C) Population structure. Each variety is represented with a single vertical line, and the color represents ancestry. (D) Phylogenetic trees constructed by the maximum likelihood method. (E) Geographical distribution of total varieties.

FIGURE 4

GWAS signals for hundred seed weight (A) and total number of branches (B) of peanut. The significance level is log10 (0.05/13125) = 5.4 (the gray horizontal line). The characteristic analysis of functional genes in the screening intervals is shown below each Manhattan plot.

FIGURE 5

GWAS signals for oil patch (spots) of peanut. (A) Peanut cultivars without an oil patch (LH14) and with an oil patch (JH3). (B) Manhattan plot. The characteristic analysis for one gene encoding peroxidase superfamily protein is shown below.

FIGURE 6

GWAS signals for (A) pod shape, (B) peel thickness, and (C) main stem height, related to the appearance of peanut.

FIGURE 7

Manhattan plots showing significant marker-trait associations for testa color of peanut. (A) Peanuts with different testa color, and its (B) GWAS signal. The characteristic analysis for one gene encoding lysosomal cystine transporter is shown below.