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ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Crop and Product Physiology
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1559621
This article is part of the Research Topic Pseudocereals as Sustainable Alternative Crops for Food Production Amid Ongoing Climate Change View all articles
Genome-wide identification and association analysis of informative SNPs of various Nutri-Nutraceutical traits in Buckwheat (Fagopyrum spp.)
Provisionally accepted
Madhiya Manzoor 1
Jebi Sudan 1
Adil Nath 1
Basharat Bhat 1
Parvaze A Sofi 1
M Ashraf Bhat 1
P. V. Vara Prasad 2
Sajad Majeed Zargar 1*- 1 Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
- 2 Kansas State University, Manhattan, Kansas, United States
Buckwheat (Fagopyrum spp.) is a pseudocereal with nutraceutical properties that offer several nutritional and health benefits. Buckwheat proteins are gluten-free and have balanced quantities of amino acid and micronutrients, with higher content of health-promoting bioactive flavonoids that make it a golden crop of the future. In the present study, we conducted a genome-wide association study (GWAS) to investigate the genetic basis of nutraceutical traits in buckwheat. Using 132 diverse genotypes, we evaluated ten key nutritional and nutraceutical traits: phenol, flavonoids, antioxidants, methionine, lysine, protein content, nitrogen, Iron, Zinc and ascorbic acid. Fagopyrum tartaricum displayed higher levels of phenols, flavonoids, antioxidants, iron, zinc, and nitrogen, while Fagopyrum esculentum exhibited elevated methionine, lysine, protein, and ascorbic acid. Genotyping by sequencing identified 3,728,028 SNPs, with the highest density on chromosome 1. GWAS detected 46 significant SNPs associated with the studied traits, including a SNP on chromosome 6 linked to lysine with a phenotypic contribution of 49.62%. Candidate gene analysis identified 138 genes within 100 kb of significant QTLs, involved in metabolic and biosynthetic pathways such as amino acid and carbohydrate metabolism. Population structure analysis grouped the genotypes into three populations, enhancing the reliability of markertrait associations. Gene ontology analysis highlighted key biological processes, including lipid transport, tryptophan metabolism, and protein phosphorylation, providing insights into the molecular mechanisms governing these traits. The present study emphasizes the potential of molecular breeding to enhance the nutritional quality of buckwheat and its role in addressing global malnutrition. The identified SNP markers and candidate genes offer a valuable foundation for developing high-yield, nutrient-rich buckwheat varieties through genome editing and marker-assisted selection.
Keywords: Buckwheat, nutraceutical, Single nucleotide polymorphisms, Genotyping by sequencing, genome wide association studies, Quantitative Trait Loci
Received: 13 Jan 2025; Accepted: 25 Mar 2025.
Copyright: © 2025 Manzoor, Sudan, Nath, Bhat, Sofi, Bhat, Prasad and Zargar. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Sajad Majeed Zargar, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
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