Genetic Diversity and Population Structure Analysis of Castanopsis hystrix and Construction of a Core Collection Using Phenotypic Traits and Molecular Markers

Abstract

Castanopsis hystrix is a valuable native, broad-leaved, and fast-growing tree in South China. In this study, 15 phenotypic traits and 32 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of a natural population of C. hystrix and to construct a core germplasm collection by a set of 232 accessions. The results showed that the original population of C. hystrix had relatively high genetic diversity, with the number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), Shannon's information index (I), and polymorphism information content (PIC) averaging at 26.188, 11.565, 0.863, 0.897, 2.660, and 0.889, respectively. Three sub-populations were identified based on a STRUCTURE analysis, indicating a strong genetic structure. The results from the phylogenetic and population structures showed a high level of agreement, with 232 germplasms being classified into three main groups. The analysis of molecular variance (AMOVA) test indicated that 96% of the total variance was derived from within populations, which revealed a low differentiation among populations. A core collection composed of 157 germplasms was firstly constructed thereafter, of which the diversity parameters non-significantly differed from the original population. These results revealed the genetic diversity and population structure of C. hystrix germplasms, which have implications for germplasm management and genome-wide association studies on C. hystrix, as well as for core collection establishment applications in other wood-producing hardwood species.

Keywords: Castanopsis hystrix; core collection; genetic diversity; molecular markers; phenotypic traits; population genetics.

Figure 1

Maps showing the geographic location of the collection site of the 17 C. hystrix populations sampled. The red dot in the figure represents 17 sampling sites The Chinese letters in the picture represent six provinces. The lower right corner represents the South China Sea Islands, which are an integral part of China.

Figure 2

The STRUCTURE estimation of the number of populations for K values ranging from 1 to 10. The K value with the highest delta K represents the suggested cluster number.

Figure 3

Phylogenetic tree of the accession with three different colors indicating three groups obtained from the STRUCTURE analysis result. Red, green and blue represent Q1, Q2 and Q3 respectively. The vertical coordinate of each subgroup indicates the membership coefficients for each C. hystrix accession.

Figure 4

Principal component analysis (PCA) of 232 C. hystrix elite germplasms by https://www.bioladder.cn/web/#/chart/62. PCA plot of the first three components (PC1, PC2, and PC3) of the 232 germplasms.

Figure 5

Phylogenetic tree of all 232 C. hystrix elite germplasms based on the SSRs built by the neighbor-joining method in PowerMarker 3.25 software. I, II and III represent the three categories of clustering, respectively.

Figure 6

Percentage of trait differences between the core collections and the initial collection obtained by different combinations. B1 and B2 represent Euclidean distance and Mahalanobis distance, respectively; C1, C2, and C3 represent the unweighted pair-group average method, Ward’s method, and mediate distance method in the systematic clustering, respectively. D1, D2, and D3 represent the random sampling, deviation sampling, and preferred sampling methods, respectively. Seven sampling ratios of 10%, 15%, 20%, 25%, 30%, 35%, and 40% were set. The percentage of the mean difference (MD), percentage of the variance difference (VD), coincidence rate of the range (CR) and rate of variation in the coefficient of variation (VR). * represents the maximum for each sampling ratio in the figure.

Figure 7

Principal coordinate distribution of the C. hystrix core collection and original collection.