GENOME-WIDE ASSOCIATION MAPPING OF EARLY LEAF SPOT RESISTANCE AND YIELD TRAITS IN GROUNDNUT (ARACHIS HYPOGAEA L.) REVEALS NOVEL SNP MARKERS FOR MARKER-ASSISTED BREEDING
DOI:
https://doi.org/10.33003/jaat.2025.1104.18Keywords:
Groundnut,, Marker-trait association,, Population structure,, genome wide association study,, foliar diseaseAbstract
Groundnut, an important food and oilseed crop globally, but its productivity is constrained by early leaf spot (ELS) disease and limited genetic diversity. This study aimed to assess the genetic diversity, population structure, linkage disequilibrium (LD), and identify marker-trait associations (MTAs) for ELS resistance and pod weight sing 3,592 SNP markers in a mini core collection of groundnut accessions. After quality filtering, 964 SNPs were retained for downstream analyses. Population structure analysis using STRUCTURE software revealed two subpopulations, consistent with cluster analysis based on geographic origin. LD decay was moderate, dropping to r² = 0.1 at approximately 2 Mb, which is suitable for genome-wide association studies (GWAS). Nineteen significant MTAs (p < 0.001) were identified across environments and conditions. SNP marker SM01 on chromosomes A05 and B05 showed a remarkably high phenotypic variance explained (PVE) of 63.56% for ELS at 65 days after sowing (DAS), indicating a strong potential for marker-assisted selection (MAS). Other moderate-effect SNPs such as SM02 and SM07 demonstrated stable associations across locations and conditions, particularly for ELS at 90 DAS and pod weight. The findings confirm the feasibility of using SNP-based GWAS for dissecting complex traits in groundnut and highlight genomic regions of interest for breeding ELS-resistant and high-yielding cultivars. The identified markers provide a valuable genomic resource for accelerating genetic improvement in groundnut through MAS and genomic selection. Future work should focus on validating these markers across diverse germplasm and environments to ensure robust application in breeding programs.
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