Whole genome sequencing-based multi-locus association mapping for kernel iron, zinc and protein content in groundnut

Abstract

Abstract Malnutrition is a major global challenge, especially in the developing regions, where improving the nutritional content of staple crops is an important step towards alleviating hidden hunger. Groundnut, a nutrient rich legume, contains several essential nutrients, high protein, essential amino-acids and vitamins required for human health. In this study, multi-season phenotyping data for kernel iron (Fe), zinc (Zn) and protein content (PC), along with whole genome re-sequencing (WGRS) data from a mini-core collection, were used to perform genome-wide association study (GWAS) analysis. Phenotypic variability analysis revealed a large variation in Fe (7.6 – 42.8 ppm), Zn (10.9 – 62.4 ppm) and PC (12.7 – 33.6%). GWAS analysis identified a total of 15 marker-trait associations (MTAs) and 28 candidate genes for pooled season data, and 44 MTAs and 62 candidate genes for individual seasons. Key candidate genes like MYB transcription factor ( Arahy.QI0PHV , Arahy.1I6ZSS ), Zn finger MYM type protein , RING finger MYM type protein ( Arahy.7P97F6 , Arahy.9R964H , Arahy.I3B88T ) and NAC domain protein ( Arahy.LV3APC ), were found to be associated with the Fe and Zn homeostasis pathway. In addition, genes related to protein homeostasis, such as Protein kinase family protein ( Arahy.4D7KBI ), and E3 ubiquitin-protein ligase ( Arahy.PE3CF6 ), were identified within significant MTA regions. These findings provide basis for the detection and characterization of potential candidate genes associated with nutritional quality traits. Haplo-pheno analysis revealed that accessions with superior haplotypes for kernel Fe and Zn content were predominantly found in the Spanish Bunch/Valencia Bunch types, whereas the accessions with inferior haplotypes were more common in the Virginia Bunch/Virginia Runner types. Single nucleotide polymorphism (SNP)-based KASP (Kompetitive Allele Specific Polymerase Chain Reaction) markers for 9 MTAs were designed and validated for Fe and Zn. Among these, three markers (snpAH00636 and snpAH00641 for Fe, and snpAH00644 for Zn) showed polymorphism, and could be utilized in genomics-assisted breeding to develop nutrient-rich groundnut varieties.