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. 2024 Feb 23;13(5):618.
doi: 10.3390/plants13050618.

Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu

Ziwei Zhou  1   2 , Fen Liu  2 , Yanqin Xu  1 , Weiming Hu  1
Affiliations

Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu

Ziwei Zhou et al. Plants (Basel). .

Abstract

Rubus chingii Hu is the only species that is used for both edible and medicinal purposes among the 194 species of the genus Rubus in China. It is well known for its sweet and sour fresh fruits that are rich in vitamins and for its dried immature fruits that are used to treat kidney-related ailments. This study aims to evaluate genetic diversity and population structure and build a core germplasm repository of 132 R. chingii accessions from the provinces of Jiangxi and Fujian, using Hyper-seq-derived single-nucleotide polymorphism (SNP) markers. This is the first genetic study of R. chingii based on SNP molecular markers, and a total of 1,303,850 SNPs and 433,159 insertions/deletions (InDels) were identified. Low values for observed heterozygosity, nucleotide diversity (Pi) and fixation indexes (Fis) indicated low genetic diversity within populations, and an analysis of molecular variance (AMOVA) showed that 37.4% and 62.6% of the variations were found between populations and within samples, respectively. Four main clusters were identified by means of neighbor-joining (NJ) trees, the ADMIXTURE program and principal component analysis (PCA). Based on the genetic diversity, we finally constructed 38 representative core collections, representing 50% of the total core germplasm samples and 95.3% of the genotypes. In summary, the results of our study can provide valuable information on the genetic structure of R. chingii germplasm resources, which is helpful for further explorations of potential high-quality genes and for formulating future breeding and conservation strategies.

Keywords: Rubus chingii Hu; SNP; core collection; genetic diversity; population structure.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
SNPs and InDels screening and in silico simulation. (A) Genome-wide variation distribution. Tracks toward the center: a, CG content (%); b, number of genes; c, number of SNPs; d, number of insertions; e, number of deletions. (B) Proportion of six variant types of SNPs in the whole population. (C) Distribution of InDel lengths.
Figure 2
Figure 2
Neighbor-joining phylogenetic tree of 132 R. chingii accessions using SNP data. Different inferred populations are distinguished by different colors.
Figure 3
Figure 3
Principal component analysis (PCA) on the 132 R. chingii accessions.
Figure 4
Figure 4
Population structure of 132 R. chingii accessions at K = 2–11. The square columns represent samples; the colors correspond to the origins of the ancestors, and the proportions of the colors represent the proportions of the ancestries in the sample.
Figure 5
Figure 5
Genotype coverage trend map. When the sample size is 50, the genotype coverage reaches 95.3%.
Figure 6
Figure 6
Geographic distribution map of 11 populations of R. chingii from Jiangxi and Fujian provinces of China.
See this image and copyright information in PMC

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