Variations in genetic diversity in cultivated Pistacia chinensis

Abstract

Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39 P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.

Keywords: Pistacia chinensis; discordance; genetic diversity; nuclear SNPs; plastome.

Figure 1

Circos plot showing the indel and nucleotide diversity of the Pistacia chinensis plastome. The concentric circles (inner to outer) indicate the following: quadripartite structure (represented by different colors); location of genes in the plastome; nucleotide diversity; and the number of indels. Nucleotide diversity and number of indels were computed for windows of 500 bp.

Figure 2

Genetic diversity of Pistacia chinensis assessed using complete plastome sequences. (A) Principal component analysis, (B) Phylogenetic tree. ML bootstrap support values/Bayesian posterior probabilities are shown at each node. (C) Population structure analysis with K = 6, 7 and 8.

Figure 3

TCS network of 12 haplotypes from the plastome sequences. The colored circles represent plastid haplotypes; the black circles are extinct haplotypes; the number of mutational steps is shown on the lines. The size of the pie chart represents the number of the accessions. The haplotype for each sample is listed in Table S1 .

Figure 4

Genetic diversity of Pistacia chinensis based on nuclear SNPs. (A) Signal of introgression among different groups detected using the TreeMix program. According to the structure results (K = 2), we defined three groups, stu01, stu02 and the crossed (hybrid) samples. (B) Phylogenetic tree. ML bootstrap support values are shown at each node. (C) Population structure analysis with K = 2, 3 and 4.

Figure 5

Discordance between phylogenetic trees reconstructed using plastomes (left) and nuclear SNPs (right). The trees included all the samples from the stu01 and stu02 clades from Figure 4B .

Figure 6

Divergence time of Anacardiaceae. The mean divergence time of the nodes is shown next to the nodes, and the blue bars correspond to the 95% highest posterior density (HPD).