Genetic diversity and construction of core collection provides new insight for the conservation of edible Allium galanthum in Xinjiang

Abstract

Allium galanthum Kar. et Kir. is a significant wild edible plant species that plays an important role in food security and the breeding of onion (Allium cepa L.). In this study, we investigated the genetic diversity, population structure, and core collection construction of 129 A. galanthum individuals from six different populations in Xinjiang, China, using 58,993 high-quality single nucleotide polymorphism (SNP) sites through the genotyping-by-sequencing (GBS) method. The minor allele frequency (MAF), inbreeding coefficient (Fis), observed heterozygosity (Ho), expected heterozygosity (He), and nucleotide diversity (Pi) were calculated as 0.1054, -0.0940, 0.1709, 0.1586, and 0.1594, respectively. Phylogenetic tree and population structure analyses divided A. galanthum individuals into two subgroups: POP1, which included 85 individuals (65.9 % of the total), and POP2, which comprised 44 individuals (34.1 %). The linkage disequilibrium (LD) analysis indicated that the genetic diversity of POP1 was greater than that of POP2. Subsequently, a core collection of 21 samples was constructed, which retained over 98 % of the genetic diversity of the entire collection. Phylogenetic tree and analysis of molecular variance (AMOVA) results showed that the diversity parameters of the core collection were not significantly different from those of the original collection. These findings reveal the genetic diversity and population structure of A. galanthum, which are crucial for the conservation and management of A. galanthum germplasm.