Assessment of genetic diversity and population structure of common walnut (Juglans regia) germplasm with simple sequence repeat (SSR) markers

The aim of this study was to assess the genetic diversity and population structure of 94 common walnut germplasm resources from different provinces in China using simple sequence repeat (SSR) markers. The 10 pairs of simple sequence repeat (SSR) primers amplified a total of 137 clearly identifiable loci, with an average of 13.7 loci per marker. The mean values of observed number of alleles (Na), effective number of alleles (Ne), Nei’s diversity index (H), Shannon’s information index (I), and polymorphism information content (PIC) of the primers were 1.997, 1.295, 0.197, 0.327, and 0.504, respectively. Genetic relationship analysis was performed by principal coordinate analysis (PCoA) and neighbour-joining cluster analysis (NJ) to classify germplasm into 3 and 11 groups. Germplasm from different regions was interspersed in the groups, suggesting that there was also a certain degree of kinship between germplasm resources from different regions. All germplasms were divided into two populations by structural analysis, and there was low genetic differentiation between them, suggesting relatively narrow resource utilization and a relatively low genetic base of cultivars in breeding units over time. The above results indicated that the DNA clustering of walnut germplasm is not related to its geographical origin but rather to its genetic relationship, suggesting the complexity of the genetic background of walnut germplasm. These findings provide a theoretical basis for further rational use of walnut germplasm resources and for breeding new walnut cultivars with exceptional traits.