Unravelling Genetic Determinants of Shell Thickness in Groundnut: Insights from a Genome-Wide Association Study

Groundnut is an important oilseed crop with a high export value. Shell thickness is a key trait affecting shelling percentage, pest resistance, and processing efficiency. This study aimed to identify genomic regions and candidate genes associated with shell thickness in groundnut using a multi-parent advanced generation inter-cross (MAGIC) population. The MAGIC population, consisting of 574 lines, was evaluated for shell thickness at three pod positions (T₁, T₂, and T₃) during the rainy and post-rainy seasons of 2022-23. Statistical analysis revealed significant differences among genotypes and pod positions for shell thickness. A negative correlation was observed between shell thickness and shelling percentage. Genome-wide association studies (GWAS) using 13,937 high-quality SNP markers identified eight SNPs associated with shell thickness on chromosomes A02, A03, A10, B03, B04, and B08. The SNP AX_177642526 on chromosome B08 explained the highest phenotypic variance of 14.67%. Gene mining for shell thickness has identified 35 candidate genes within a 100 kb window of the associated SNPs, with functions related to secondary cell wall synthesis, pod size development, plant defence, abiotic stress tolerance, and nutrient availability. The identified genomic regions and candidate genes provide valuable insights for marker-assisted selection and genetic improvement of shell thickness and associated traits in groundnut breeding programs.