Analysis of genetic relationships and evaluation of fruit quality traits in breeding forms of Persian walnut (Juglans regia L.)

Persian walnut is a valuable nut crop whose fruits are rich in unsaturated fatty acids, phenolic compounds, and trace elements, determining their high nutritional value and health benefits. The development of trait-specific collections and the preservation of their genetic and phenotypic diversity are relevant directions in breeding and genetic research aimed at improving the efficiency of breeding programs. This article presents the results of genetic diversity analysis using SSR markers, along with data on a set of fruit quality traits in promising walnut breeding forms. The study involved 43 hybrid forms of Persian walnut from the germplasm collection of the North Caucasian Federal Scientific Center of Horticulture, Viticulture, and Winemaking (NCFSCHVW). The Rodina cultivar was used as a control. During the study period (2022–2025), fruits were comprehensively evaluated for key quality traits, including fruit weight (ranging from 6.42 to 14.27 g in the studied sample), kernel percentage (41.14–61.83 %), shell thickness (0.92–1.83 mm), kernel color, kernel extraction ease, kernel filling, and total fat content (61–77 %). Overall, 11 promising forms that simultaneously possessed three or more valuable fruit quality traits were identified. Using 12 microsatellite DNA markers, the level of genetic diversity and the genetic relationships among the 43 hybrid forms, as well as with several domestic and foreign cultivars, were assessed. A total of 90 alleles were detected, with an average of 7.5 alleles per locus. Polymorphism indices (observed heterozygosity = 0.451; expected heterozygosity = 0.670) also indicated a relatively high level of genetic heterogeneity within the studied sample. Bayesian clustering analysis (STRUCTURE, K = 4) and Principal Coordinates Analysis (PCoA) were used to determine genetic relationships among the hybrid forms and domestic and foreign cultivars. Four major groups of samples were identified, and their distribution was consistent with the origin of the samples. Based on genetic distance estimates and cluster assignment, recommendations were developed for the selection of parental combinations in breeding programs aimed at developing cultivars with improved fruit characteristics while maintaining a high level of genetic diversity within the germplasm.