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ARS Home » Plains Area » El Reno, Oklahoma » Oklahoma and Central Plains Agricultural Research Center » Peanut and Small Grains Research Unit » Research » Publications at this Location » Publication #430048
Research Project: High Oleic Peanut Cultivars and Germplasm with Improved Disease Resistance for the Southwestern United States

Location: Peanut and Small Grains Research Unit

Title: Whole genome-wide association study reveals genetic insights into leaf spot disease resistances and seed germination/dormancy in peanut

Author
item ZHANG, JIE - Auburn University
item Chamberlin, Kelly
item Wang, Ming
item CLEVENGER, JOSH - Hudsonalpha Institute For Biotechnology
item Dang, Phat
item CHU, YE - University Of Georgia
item Holbrook Jr, C
item OZIAS-AKINS, PEGGY - University Of Georgia
item CHEN, CHARLES - Auburn University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2026
Publication Date: 6/10/2026
Citation: Zhang, J., Chamberlin, K.D., Wang, M.L., Clevenger, J.P., Dang, P.M., Chu, Y., Holbrook Jr, C.C., Ozias-Akins, P., Chen, C. 2026. Whole genome-wide association study reveals genetic insights into leaf spot disease resistances and seed germination/dormancy in peanut. Frontiers in Plant Science. 17. Article 1838203. https://doi.org/10.3389/fpls.2026.1838203.
DOI: https://doi.org/10.3389/fpls.2026.1838203

Interpretive Summary: Genomic studies were conducted to identify genes associated with leaf spot resistance, germination, and dormancy in peanut. Accessions from the USDA ARS peanut mini core were sequenced and the results were analyzed and correlated with phenotypic data to identify three candidate genes for leaf spot resistance and one gene regulating both seed germination and dormancy. These results provide targets for marker-assisted selection that peanut breeders can use to enhance leaf spot resistance and seed quality.

Technical Abstract: Peanut (Arachis hypogaea L.) is an important crop in the world, serving as a key source of edible oil and protein. Comprehensive genomic and phenotypic analyses were conducted on 87 accessions from the U.S. peanut mini-core collection using 217 Gb of high-quality resequencing data to identify the candidate genes and markers that underlie the leaf spot resistance and seed dormancy in peanuts. A total of 87,726 SNPs were identified and mapped across 20 chromosomes, revealing a higher SNP density in the B subgenome (35.55 SNPs/Mb) compared to the A subgenome (33.26 SNPs/Mb). Phylogenetic, population structure, and principal component analyses consistently partitioned the accessions into three distinct gene pools designated as Group 1, 2, and 3. Group 1, comprising primarily Arachis hypogaea, included 28 genotypes; Group 2, mainly fastigiate types, comprised 18 accessions; while Group 3, displaying the highest diversity, contained mixed genotypes from the other groups. Linkage disequilibrium analysis indicated an LD decay distance of approximately 63.1 kb, confirming that the marker density was sufficient for GWAS. Significant SNP associations at a threshold of p < 1.14 × 10'5 (Bonferroni-adjusted) were identified for leaf spot, seed germination and dormancy agronomic traits. As a result, three candidate genes were identified: Ah11g381400, homologous to Arabidopsis ATE1, was associated with early leaf spot resistance; Ah16g445600, a homolog of ERF34, was linked to late leaf spot resistance; and Ah19g214100, homologous to ICE1, emerged as a central regulator affecting both germination and dormancy. These findings provide actionable targets for marker-assisted selection to enhance disease resilience and seed quality in breeding programs.