Genetic diversity analysis and core collection construction for Amaranthus tricolor germplasm based on genome-wide single-nucleotide polymorphisms

Abstract

• Genetic diversity among Amaranthus tricolor accessions was evaluated using genome-wide SNPs. • A set of 5638 SNPs without missing data in accessions was identified. • The population structure was analyzed among accessions. • A core collection of 105 accessions was created. The genus Amaranthus includes 60 to 70 species, some used as grain or leafy vegetable crops, others as ornamental crops. A. tricolor is used as a traditional leafy vegetable in Asia. It has a remarkably valuable nutrient composition and a high tolerance to environmental stresses but has been neglected in modern breeding. Detecting DNA polymorphisms among accessions helps in understanding the genetic diversity and population structure of germplasm collections. The genetic diversity and population structure were analysed among 465 A. tricolor accessions held by the World Vegetable Center genebank with genome-wide single-nucleotide polymorphisms (SNPs) developed by the double-digest restriction-site-associated DNA sequencing method. We found a total of 10 509 SNPs among the accessions and identified a set of 5638 SNPs without missing data in 440 accessions. This marker set was used to verify the species attribution of the germplasm, to analyse genetic diversity and population structure of the collection, and to create a core collection of 105 accessions representing the genetic diversity of 377 source accessions. This core collection is available for research and breeding (World Vegetable Center: info@worldveg.org). The SNP data generated here will contribute to exploring genetic loci related to economically and agronomically important traits in this species.