ArticleMolecular genetics and genomics : MGG2026
Unravelling genetic diversity in grain amaranth (Amaranthus hypochondriacus L.) core accessions using genome-wide SNP markers.
Article in Molecular genetics and genomics : MGG, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Grain amaranth (Amaranthus hypochondriacus L.) is a gluten-free pseudocereal with high nutritional value and notable climate resilience; however, its genome-wide population structure and genetic diversity remain poorly characterized. Given the considerable diversity observed in its gene pool, comprehensive genome-scale characterization are required to understand the genetics of important traits for effective breeding and improvement. Here, we employed Whole-Genome Sequencing (WGS) approach to generate genome-wide SNPs in a core accessions of A. hypochondriacus, leveraging the available reference genome. A total of 248 accessions, comprising Indian and some exotic accessions, were sequenced through Illumina paired-end sequencing, yielding 285,236 high-quality SNPs, with an average of ~ 20 × genome coverage. Population structure analysis identified six sub-populations among the core accessions, consistent with kinship and phylogenetic analyses, reflecting substantial genetic diversity within the genetic material used. Linkage disequilibrium (LD) analysis indicated moderate genome-wide LD, with an average decay distance of 29.8 kb, although strong LD (r
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