Identification of potential QTLs and genes associated with seed composition traits in peanut (Arachis hypogaea L.) using GWAS and RNA-Seq analysis

Authors: ZHANG, HUI - Auburn University; Wang, Ming; Dang, Phat; JIANG, TAO - Auburn University; ZHAO, SHUZHEN - Shandong Academy Of Agricultural Sciences; Lamb, Marshall; CHEN, CHARLES - Auburn University

Submitted to: Gene
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2020
Publication Date: 10/7/2020
Citation: Zhang, H., Wang, M.L., Dang, P.M., Jiang, T., Zhao, S., Lamb, M.C., Chen, C.Y. 2020. Identification of potential QTLs and genes associated with seed composition traits in peanut (Arachis hypogaea L.) using GWAS and RNA-Seq analysis. Gene. 769:145215. https://doi.org/10.1016/j.gene.2020.145215.
DOI: https://doi.org/10.1016/j.gene.2020.145215

Interpretive Summary: Cultivated peanut (Arachis hypogaea) is a major oilseed crop providing edible oil and protein. Oil quality is determined by fatty acid composition including the ratio of oleic acid (monosaturated fat) and linoleic acid (polysaturated fat). A study was conducted evaluating nucleotide differences of the peanut genome focusing on 13,382 nucleotide locations to investigate the genetics basis of oil, protein, eight fatty acid concentrations using a diverse panel of 120 peanut lines mainly selected from a subset of the U.S. peanut germplasm collection in two years field study. A total of 178 significant regions of the DNA associated with specific seed composition traits were identified with high probability ranging from 18.35% to 27.56%. From sequencing ribonucleotide plant molecular messages, 282 candidate genes were identified to be within a specific range of these significant DNA regions. Among these genes, sixteen genes were related to seed fatty acid metabolism and protein synthesis. Identification and association of the genes associated with specific seed traits will facilitate the selection of peanut plants with the desired seed profiles for human food consumption.

Technical Abstract: Cultivated peanut (Arachis hypogaea) is a major oilseed crop providing edible oil and protein. Oil quality is determined by fatty acid composition including the ratio of oleic acid (C18:1) and linoleic acid (C18:2). A genome-wide association study with 13,382 single nucleotide polymorphisms (SNPs) was conducted to investigate the genetics basis of oil, protein, eight fatty acid concentrations, and O/L ratio (ratio of oleic and linoleic acid) using a diverse panel of 120 genotypes mainly selected from the U.S. peanut mini core collection grown in two years. A total of 178 significant quantitative trait loci (QTLs) associated with those seed composition traits were identified with phenotypic variation explained (PVE) from 18.35% to 27.56%. RNA-Seq analysis identified 282 DEGs (differentially expressed genes) within the 1Mb of the significant QTLs for seed composition traits. Among those 282 genes, sixteen candidate genes for seed fatty acid metabolism and protein synthesis were screened according to the gene functions.