Linkage-Mapping and Genome-wide Association Study Identified Two Peanut Late Leaf Spot Resistance Loci, PLLSR-1 and PLLSR-2, Using a Nested Association Mapping

Identification of candidate genes and molecular markers for late leaf spot (LLS) disease resistance in peanut (Arachis hypogaea) has been a focus of molecular breeding for the U.S. industry funded peanut genome project. Efforts have been hindered by limited mapping resolution due to low levels of genetic recombination and marker density available in traditional biparental mapping populations. To address this, a multi-parental nested association mapping (NAM) population has been genotyped with the peanut 58 K SNP array and phenotyped for LLS severity in the field for three years. Joint linkage-based QTL mapping identified nine QTLs for LLS resistance with significant phenotypic variance explained (PVE) up to 47.7%. A genome-wide association study (GWAS) identified 13 SNPs consistently associated with LLS resistance. Two genomic regions harboring the consistent QTLs and SNPs were identified from 1,336 Kb to 1,520 Kb (184 Kb) on chromosome B02 and from 1,026.9 Kb to 1,793.2 Kb (767 Kb) on chromosome B03, designated as peanut late leaf spot resistance loci, PLLSR-1 and PLLSR-2, respectively. PLLSR-1 contains 10 NBS-LRR disease resistant genes. An NBS-LRR disease resistance gene Arahy.VKVT6A was also identified on homoeologous chromosome A02. PLLSR-2 contains five significant SNPs associated with five different genes encoding callose synthase, pollen defective in guidance protein, pentatricopeptide repeat (PPR), acyl-activating enzyme, and C2 GRAM domains-containing protein. This study highlights the power of multi-parent populations such as NAM for genetic mapping and marker-trait association studies in peanuts. Validation of these two LLS resistance loci will be needed for marker-assisted breeding.