Genetic diversity and genome wide population structure analysis of a grain amaranth (Amaranthus hypochondriacus) diversity panel using Genotyping by Sequencing

Abstract

Abstract Amaranth, a gluten-free pseudo-cereal, is grown, cultivated, and adapted in diverse ecological zones all over the world. In recent years, increased attention has been paid on its nutritional eminence, particularly in terms of its seed protein, which specifically contains high levels of the essential amino acids. This important food and nutritional security crop's gene pool, which is diverse, needs to be characterized and genotyped in order to broaden its genetic base and to boost production. Genotyping by sequencing data of diverse germplasm serve useful tool for identification of important candidate genes associated with important traits of plants. In the present study, genotyping-by-sequencing (GBS) approach was used to characterize a genetically diverse collection of 192 Amaranth accessions. This resulted in an estimated 41,931 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the Amaranth accessions, which are in parallel with the results of phylogenetic analysis. A total of 1796 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. High-throughput genotyping and sequencing data generated, will be very useful not only for breeders for further enhancement of Amaranth but also for molecular biologists for isolation and identification of nutritionally important genes from Amaranth, which can be used for biofortification programs.