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

生物 遗传学 联动装置(软件) 数量性状位点 关联映射 单核苷酸多态性 叶斑病 遗传连锁 全基因组关联研究 联想(心理学) 基因 基因组 遗传关联 计算生物学 植物 基因型 认识论 哲学
作者
Sunil S. Gangurde,Ethan Thompson,Yaduru Shasidhar,Hui Wang,Jake C. Fountain,Ye Chu,Peggy Ozias‐Akins,T. G. Isleib,C. Corley Holbrook,Bhabesh Dutta,A. K. Culbreath,Manish K. Pandey,Baozhu Guo
出处
期刊:Phytopathology [American Phytopathological Society]
卷期号:114 (6): 1346-1355 被引量:3
标识
DOI:10.1094/phyto-04-23-0143-r
摘要

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 population has been genotyped with the peanut 58K single-nucleotide polymorphism (SNP) array and phenotyped for LLS severity in the field for 3 years. Joint linkage-based quantitative trait locus (QTL) mapping identified nine QTLs for LLS resistance with significant phenotypic variance explained up to 47.7%. A genome-wide association study identified 13 SNPs consistently associated with LLS resistance. Two genomic regions harboring the consistent QTLs and SNPs were identified from 1,336 to 1,520 kb (184 kb) on chromosome B02 and from 1,026.9 to 1,793.2 kb (767 kb) on chromosome B03, designated as peanut LLS resistance loci, PLLSR-1 and PLLSR-2, respectively. PLLSR-1 contains 10 nucleotide-binding site leucine-rich repeat disease resistance genes. A nucleotide-binding site leucine-rich repeat 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, acyl-activating enzyme, and C2 GRAM domains-containing protein. This study highlights the power of multi-parent populations such as nested association mapping for genetic mapping and marker-trait association studies in peanuts. Validation of these two LLS resistance loci will be needed for marker-assisted breeding.
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