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

Sagar, U. N.; Parmar, S.; Gangurde, S. S.; Sharma, V.; Pandey, A. K.; Mohinuddin, D. K.; Dube, N.; Bhat, R. S.; John, K.; Sreevalli, M. D.; Rani, P. S.; Singh, K.; Varshney, R. K.; Pandey, M. K.

doi:10.1101/2025.08.04.668427

bioRxiv · 10.1101/2025.08.04.668427

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

Sagar, U. N.·Parmar, S.·Gangurde, S. S.·Sharma, V.·Pandey, A. K.·Mohinuddin, D. K.·Dube, N.·Bhat, R. S.·John, K.·Sreevalli, M. D.·Rani, P. S.·Singh, K.·Varshney, R. K.·Pandey, M. K.

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Abstract

Malnutrition is a major global challenge, especially in the developing regions, where improving the nutritional content of staple crops is a significant step towards alleviating hidden hunger. Groundnut, a nutrient rich legume contains several mineral nutrients, high protein, essential amino-acids and vitamins that are required for human health. In this study, multi-season phenotyping data for kernel iron (Fe), zinc (Zn) content and protein content (PC) and whole genome re-sequencing (WGRS) data on mini-core collection, were used to perform genome-wide association study (GWAS) analysis. Phenotypic variability analysis revealed a large variation in the 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, as well as 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), associated with the Fe and Zn homeostasis pathway, genes related to protein homeostasis, such as protein kinase family protein (Arahy.4D7KBI), and E3 ubiquitin-protein ligase (Arahy.PE3CF6), were also identified within significant MTA regions. These findings provide basis for the detection and characterization of the possible candidate genes related to the nutritional quality traits. Single nucleotide polymorphism (SNP)-based KASP (Kompetitive Allele Specific Polymerase Chain Reaction) markers for 9 SNPs were designed and validated. Of these, three markers (snpAH00636, snpAH00641 and snpAH00644) showed polymorphism which could be deployed in the genomics-assisted breeding for the development of nutrient-rich groundnut varieties.

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Sagar, U. N., Parmar, S., Gangurde, S. S., Sharma, V., Pandey, A. K., Mohinuddin, D. K., Dube, N., Bhat, R. S., John, K., Sreevalli, M. D., Rani, P. S., Singh, K., Varshney, R. K., Pandey, M. K.. 2025-08-05. Whole genome sequencing-based multi-locus association mapping for kernel iron, zinc and protein content in groundnut. https://doi.org/10.1101/2025.08.04.668427

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