Genome wide association study uncovers significant SNPs and candidate genes for kernel grades in groundnut (Arachis hypogaea L.)

Kernel grade is a key market trait that significantly influences the market price of groundnut and is directly proportional to pod yield. A set of 574 multi-parent advanced generation inter-cross (MAGIC) lines including parents and checks was assessed for kernel grade, yield, and component traits in a partially replicated (p-rep) design for two seasons (rainy and post-rainy; 2021-22). A genome-wide association study (GWAS) was conducted to identify marker-trait associations (MTAs) and potential candidate genes for kernel grades and yield. MAGIC lines ICGR 171238 (79.45%) and ICGR 171206 (85.65%) showed highest percent net recovery of grade-I kernel (PNR_I) in rainy and post-rainy seasons respectively. Twenty-four high confidence SNPs were associated with kernel-grades and yield traits across 11 chromosomes. SNPs AX_147226917 (A07) and AX_177643480 (B08) showed consistent association with PNR_I and counts per ounce of grade-I kernel (CPO_I) across seasons. Key candidate genes for kernel grades include Aradu.6Z78F (RING-H2 finger protein), Aradu.993Q7 (ascorbate peroxidase 1), Araip.MKV8R (protein FAR1-RELATED SEQUENCE 3-like isoform X1) and Aradu.S3AS8 (Vacuolar protein-sorting protein BRO1). For yield traits, Aradu.Y7AIG (cytochrome P450), Aradu.BD60N (Glucose-1-phosphate adenylyltransferase) and Aradu.TW8M6 (LEA protein) were identified. Predominantly these genes are known to regulate growth and development, control cell functions, confer disease resistance and stress tolerance, and influence pod size in groundnuts. The validation studies of the identified MTAs would facilitate the development of molecular markers for use in marker-assisted selection (MAS), enabling efficient selection of progenies with higher percent recovery of grade-I kernels in the segregating populations.