Genetic diversity analysis and core collection construction of Phyllanthus emblica based on SSR markers

【Objective】The genetic diversity and core collection construction of Phyllanthus emblica were investigated using SSR molecular markers, in order to provide a scientific basis for preservation, genetic breeding and efficient utilization of the germplasm resources.【Methods】The experimental materials were collected from P. emblica Germplasm Resource Sub-Center, National Tropical Plants Germplasm Resource Center. The genetic diversity and genetic relationship among 192 accessions of P. emblica and a related species P. reticulatus were analyzed using the previously developed SSR molecular markers. The primers used were 10 pairs of highly polymorphic primers screened in the previous study. Subsequently, based on the SSR molecular marker data, the best scheme for constructing the core collection of P. emblica was selected. The SM genetic distance, Jaccard genetic distance, and Nei & Li genetic distance were used to select the appropriate clustering method. The priority sampling strategy and random sampling strategy were evaluated. The core collection was constructed based on the sampling ratios of 10%, 15%, 20%, 25%, 30%, 35% and 40%, and the optimal sampling ratio was screened. After the core collection was constructed, the differences of the genetic diversity parameters between the core collection and original collection were analyzed. Additionally, the principal component analysis was car-ried out to evaluate the representativeness and heterogeneity of the core collection.【Results】A total of 85 polymorphic bands were detected in 193 samples by 10 pairs of SSR primers. The effective number of alleles (Ne) was 1.321 6, the heterozygosity (h) was 0.194 6, the Shannon's information index (I) was 0.325 7, the polymorphic information content (PIC) was 0.77, and the genetic distance of P. emblica ranged from 0 to 0.958 3, indicating a high level of genetic differentiation among P. emblica germplasm resources, significant genetic differences, and substantial genetic diversity. The genetic distance between No. 107 and No. 108 was 0, while the distances between No. 116 and No. 115 was 0.001, and the distance between No. 20 and No. 19 was 0.006, indicating that the genetic relationships among these groups were very similar, and the genetic variation were small. They might represent the same or similar germplasm, which could be further judged by the phenotypic analysis. The cluster analysis revealed that the 192 accessions of P. emblica were categorized into three groups. The first group, comprising 170 resources, was primarily sourced from Fujian, Guangdong and Guangxi. The second group included 21 resources from Yunnan and abroad, indicating that the germplasms in different ecological distribution areas were separated from each other, and the germplasms in the same ecological distribution area had relatively close genetic relationships. The third group was No. 158, a wild resource from Fujian, which was far from other resources. It could be used as a potential experimental material for the study of the origin and genetic evolution of P. emblica. The results of the PCA principal component analysis and UPGMA cluster analysis were consistent. The resources from different ecological distribution areas were separated from each other, and the genetic relationship of the resources in the same ecological distribution area was relatively close. The core collection of P. emblica was constructed using the optimal scheme of Jaccard genetic distance, class average method, and priority sampling strategy. The effective alleles (1.339 6), Nei's gene diversity index (0.2238) and Shannon's information index (0.363 7) of the core collection were the highest at a sampling ratio of 10 %, indicating that the genetic diversity of the core collection was well preserved at this ratio. The primary core collection containing 20 resources was constructed. The retention rates of polymorphic loci, percentage of polymorphic loci, alleles, effective alleles, Nei's gene diversity index and Shannon's information index were 95.25%, 95.29%, 97.65%, 102.70%, 112.41% and 110.48%, respectively, shown by inspecting the primary core collection. The effective alleles, Nei's gene diversity index and Shannon’s information index were higher than those of the original germplasms and the reserved germplasms. The PCA score scatter plot, performed on the SSR molecular data of 20 core germplasms and 192 original germplasms of P. emblica, showed that the scatter distribution area and shape of the core germplasm had a high degree of coincidence with the scatter distribution area and shape of the original germplasms. The peripheral individuals were also selected into the core germplasms. This finding indicated that the core germplasm effectively eliminated genetic redundancy, thereby ensuring the representativeness and heterogeneity of the original germplasms. 【Conclusion】The level of genetic differentiation among P. emblica germplasm resources was high, exhibiting a wide range of genetic variation and rich genetic diversity. The developed SSR molecular marker technology effectively captured the genetic differences and relationships within P. emblica, which would offer reliable tools and foundational data for the identification of P. emblica germplasm resources, core germplasm construction, and genetic breeding. The optimal scheme for constructing the core collection of P. emblica was determined to be the combination of Jaccard genetic distance, UPGMA clustering, a priority sampling strategy, and a 10% sampling ratio. Consequently, a core collection of 20 P. emblica was constructed to provide scientific basis for the collection, preservation and innovative utilization of germplasm resources.