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

Gene. 2021 Feb 15:769:145215. doi: 10.1016/j.gene.2020.145215. Epub 2020 Oct 7.

Abstract

Cultivated peanut (Arachis hypogaea L.) 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 1 Mb 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.

Keywords: GWAS; Genetics; Peanuts; RNA-Seq; Seed composition traits.

MeSH terms

  • Arachis / genetics*
  • Arachis / metabolism
  • Fatty Acids / metabolism
  • Gene Expression Regulation, Developmental
  • Gene Expression Regulation, Plant
  • Genome-Wide Association Study*
  • Linkage Disequilibrium
  • Plant Proteins / metabolism
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci*
  • Seeds / genetics*
  • Seeds / metabolism
  • Sequence Analysis, RNA / methods*

Substances

  • Fatty Acids
  • Plant Proteins