Genetic evolution analysis of Chinese bayberry germplasm resources in Southern Zhejiang with single nucleotide polymorphism (SNP) and insertion deletion (InDel) markers

It is of great significance for the development of the Chinese bayberry industry to deeply understand the genetic evolutionary relationship of Chinese bayberry germplasm resources in Southern Zhejiang, fully tap into excellent local germplasm resources, and improve its breeding efficiency. Hence, this study conducted high-throughput whole genome resequencing on 47 Chinese bayberry germplasm resources in Southern Zhejiang with single nucleotide polymorphism (SNP) and Insertion Deletion (InDel) markers used to analyze the population genetic structure, evolutionary relationships, phylogenetic relationships, and genetic diversity. The results revealed that the quantity of clean reads mapped to the reference genome accounted for 96.53% of the total, and a total of 5,380,296 variant sites were detected, including 4,667,304 SNP variant sites and 712,992 InDel variant sites. According to the genetic structure and principal component analysis, the 47 Chinese bayberry samples were clustered into 3 groups, among which, group1(G1) included 10 resources, mainly consisting of large-fruited and late-maturing Chinese bayberry introduced from external regions. It was closely aggregated with each other and had small genetic difference in G1. Group2(G2) included 17 resources, mainly consisting of local cultivars with early maturity and medium-sized fruits, with large genetic differences and rich diversity. Group3(G3) included 20 resources which grew from direct germination of seeds to adult fruiting trees, exhibiting complex genetic backgrounds and significant differences. The genetic distance of the 47 Chinese bayberry samples ranged from 0.024 to 0.332, with an average genetic distance of 0.241. The average value of the diversity index (He) was 0.3, and the average value of the polymorphism information content (PIC) was 0.244. In the genetic evolution analysis, G2 and G3 were further divided into 5 subgroups and 6 subgroups, respectively, both demonstrating a relatively high genetic diversity. In summary, the genetic background of the 47 Chinese bayberry resources is rich, their genetic evolutionary relationship is relatively independent and complex, and their genetic diversity is high. This conclusion could further broaden the genetic distance between parents, and provide materials and theoretical guidance for the subsequent selection of parents and screening of excellent cultivars in Chinese bayberry breeding.