Genetic diversity analysis and core collection construction of 259 garlic germplasm resources based on SSR molecular markers

Abstract

This study utilized 23 SSR primer pairs for amplification and capillary electrophoresis detection across 259 garlic germplasm accessions. Genetic diversity and clustering were assessed through locus-based statistical methods. A core collection was identified using Powercore software, based on allele maximization, and representativeness was evaluated through genetic parameters calculated with GenAlex software, along with principal coordinate analysis (PCoA). Results indicated the presence of 171 polymorphic loci across the 23 SSR primers, with an average of 7.43 alleles per primer pair. The polymorphism information content (PIC) ranged from 0.081 to 0.669, with a mean of 0.407. The effective number of alleles ( Ne ) varied from 1.04 to 3.79. The average Shannon’s diversity index ( I ), observed heterozygosity ( Ho ), expected heterozygosity ( He ), and Nei’s diversity index ( H ) were recorded at 0.938, 0.488, 0.517, and 0.482, respectively. Cluster analysis categorized the 259 accessions into five clusters, some of which exhibited identical amplification profiles. After excluding accessions with identical loci, 100 distinct accessions were identified using the 23 primer pairs. A total of 50 core collections were selected, representing 19.31% of the original collection. Compared to the original collection, the core collection retained 100% of the alleles, 155.20% of Ne , and 137.15% of I . Additionally, the core collection displayed an even distribution on the PCoA plot, confirming its representativeness. Thirteen core primers were identified from the 23 SSR primer pairs based on the number of unique alleles and distinguishable accessions, enabling the construction of a fingerprint map for the 50 core collections. These findings will enhance the efficient screening, conservation, and utilization of garlic germplasm resources, support the protection of genetic diversity, and contribute to the breeding of new varieties.