Genotyping and Genetic Diversity Analysis of 47 Flowering Cherry (<I>Cerasus</i>) Germplasms

Abstract

In order to provide a theoretical basis for conservation and utilization of excellent flowering cherry germplasms, genetic diversity and genotype were analyzed based on single nucleotide polymorphism (SNP) molecular markers. A total of 47 germplasms were sequenced using restriction site-associated DNA sequencing (RAD-Seq) method, and highly consistent SNP sites have been identified for genetic diversity analysis and genotyping. The RAxML program was used for phylogenetic tree construction, based on the maximum likelihood (ML) method. The ADMIXTURE software was used to analyze genetic structure. The GCTA software was used for principal component analysis. Genetic diversity parameters, includes nucleotide diversity (π value), expected heterozygosity (exp  He ) and genetic differentiation index ( F ST ), were carried out using the PopGenome and Arlequin 3.0 software. A total of 79 667 highly consistent SNPs were obtained, after genotype integrity filtering and closely linked sites screening. According to the phylogenetic, principal components and population structure analysis results, the 47 germplasms could be divided into eight genetic clusters. The π and exp  He  value of each cluster was as follows: I: 0.128 19, 0.119 94; II: 0.139 64, 0.130 55; III: 0.21 55, 0.164 73; IV: 0.086 82, 0.061 22; V: 0.095 49, 0.069 73; VI: 0.191 22, 0.10 61; VII: 0.16 85, 0.158 78; VIII: 0.290 98, 0.183 43. The cluster IV and V presented the largest genetic differentiation, with an  F ST value of 0.4612 89, followed by IV and VI, with an  F ST  value of 0.456 958; the lowest genetic differentiation existed between the cluster VII and VIII, with an  F ST  value of 0.0976 13. Except for cluster VII and VIII, the genetic differentiation among the other clusters was at or above the medium level. The results of genotyping showed that there were 29 individuals (61.70 %) with single genetic component, and 18 individuals (38.30 %) with two or three genetic components. Based on the results of genetic components analysis, there were four potential interspecific hybridizations. There was a high genetic diversity among 47 flowering cherry germplasms, obvious genetic differentiation among the eight clusters. The genetic components of natural hybrid individuals and artificial hybrid cultivars were revealed, and their parents were inferred, based on the genotyping results.&nbsp