Identification of Candidate Genes and Markers for Kernel Iron, Zinc and Protein Content in Groundnut (Arachis hypogaea L.)

Groundnut, a nutrient rich legume crop popularly known as “poor person almond”, is grown mainly in the semi-arid tropic (SAT) regions of the world. It contains several mineral nutrients, essential amino-acids and vitamins that are essential for good health and aid in overcoming the issues like malnutrition or hidden hunger, particularly in the Asian and African countries. In this study, GWAS analysis was conducted using whole genome re-sequencing based genotyping data combined with multi-season phenotyping data of a mini-core collection of 184 accessions. Studies on phenotypic variability showed a large variation in the iron (Fe) content (7.6 – 42.8 ppm), zinc (Zn) content (10.9 – 62.4 ppm) and protein content (12.7 – 33.6 %). Genome-wide association study (GWAS) identified a total of 59 marker-trait associations (MTAs), of which 15 MTAs associated with 28 candidate genes and 44 MTAs associated with 62 candidate genes were identified for pooled and individual seasons, respectively. The key candidate genes such as 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 associated with the Fe and Zn homeostasis pathway, and the other genes like protein kinase family protein (Arahy.4D7KBI), and E3 ubiquitin-protein ligase (Arahy.PE3CF6), were linked with the protein homeostasis. SNP-based Kompetitive Allele Specific Polymerase Chain Reaction (KASP) markers have been designed and validated for 9 MTAs of Fe and Zn contents. Of these markers, 3 KASP markers (snpAH00636, snpAH00641 and snpAH00644) were successfully validated and showed polymorphism between high and low content lines. These KASP markers could be used in the genomics-assisted breeding to develop nutrient-rich groundnut varieties.