Genetic variation and population structure of a threatened timber tree Dalbergia cochinchinensis in Cambodia

Moritsuka, Etsuko; Chhang, Phourin; Tagane, Shuichiro; Toyama, Hironori; Sokh, Heng; Yahara, Tetsukazu; Tachida, Hidenori

doi:10.1007/s11295-017-1199-8

Cited by 10 publications

(19 citation statements)

References 40 publications

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“…These characters are consistent with a predominantly outcrossing mating system that includes at least some extent of inbreeding. Alternatively, it is due to the small populations in which mating between relatives occurred more frequently than in large populations [61].…”

Section: Genetic Diversity Of D Odoriferamentioning

confidence: 99%

Genetic Diversity of the Endangered Dalbergia odorifera Revealed by SSR Markers

Liu

Hong

et al. 2019

Forests

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Dalbergia odorifera T. Chen (Fabaceae) is a semi-deciduous tree species indigenous to Hainan Island in China. Due to its precious heartwood “Hualimu (Chinese)” and Chinese medicinal components “Jiangxiang”, D. odorifera is seriously threatened of long-term overexploitation and has been listed on the IUCN (International Union for Conservation of Nature’s) red list since 1998. Therefore, the elucidation of its genetic diversity is imperative for conservation and breeding purposes. In this study, we evaluated the genetic diversity of 42 wild D. odorifera trees from seven populations covering its whole native distribution. In total, 19 SSR (simple sequence repeat) markers harbored 54 alleles across the 42 samples, and the medium genetic diversity level was inferred by Nei’s gene diversity (0.36), observed (0.28) and expected heterozygosity (0.37). Among the seven wild populations, the expected heterozygosity (He) varied from 0.31 (HNQS) to 0.40 (HNCJ). The analysis of molecular variance (AMOVA) showed that only 3% genetic variation existed among populations. Moderate population differentiations among the investigated populations were indicated by pairwise Fst (0.042–0.115). Structure analysis suggested two clusters for the 42 samples. Moreover, the seven populations were clearly distinguished into two clusters from both the principal coordinate analysis (PCoA) and neighbor-joining (NJ) analysis. Populations from Haikou city (HNHK), Baisha autonomous county (HNBS), Ledong autonomous county (HNLD), and Dongfang city (HNDF) comprised cluster I, while cluster II comprised the populations from Wenchang city and Sansha city (HNQS), Changjiang autonomous county (HNCJ), and Wuzhisan city (HNWZS). The findings of this study provide a preliminary genetic basis for the conservation, management, and restoration of this endemic species.

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Section: Genetic Diversity Of D Odoriferamentioning

confidence: 99%

Genetic Diversity of the Endangered Dalbergia odorifera Revealed by SSR Markers

Liu

Hong

et al. 2019

Forests

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“…Although nuclear gene markers are useful for investigating the genetic variation in non-model species, it cannot be ignored that natural selection may influence estimates of the levels of genetic diversity and population differentiation (e.g., Adh in Drosophila; see Kreitman and Hudson, 1991). Indeed, in our previous study we found a few candidate loci under natural selection in this species (Moritsuka et al, 2017); therefore, it was worthwhile to now examine the genetic variation in the noncoding regions using the MIG-seq method, which is considered to experience less pressure from natural selection, and to compare the results with those obtained for the coding genes. Additionally, the accuracy of the estimates obtained using a small number of loci (~10 loci) may not be adequate to evaluate the population structure or to measure the genetic variation and levels of differentiation because the coefficient of variation for the estimate of nucleotide diversity is of the order of one (Tajima, 1983).…”

Section: Introductionmentioning

confidence: 86%

“…Previously, we analyzed the genetic variation of D. cochinchinensis by resequencing nuclear coding genes (Moritsuka et al, 2017). That study revealed that the level of silent nucleotide diversity within populations of D. cochinchinensis ranged from 0.0027 to 0.0050, and the populations were strongly differentiated.…”

Section: Introductionmentioning

confidence: 99%

“…In this paper, we analyzed the genetic variation in D. cochinchinensis and D. nigrescens using MIG-seq. The aims of this study were threefold: 1) to assess the basic features of the genetic variation at the loci surveyed by MIG-seq (MIG loci) in the two species to infer the population structure and the levels of nucleotide diversity and differentiation in these two species; 2) to compare the results for D. cochinchinensis with those of the nuclear coding genes obtained by the conventional sequencing method for this species (Moritsuka et al, 2017), focusing on the accuracy of the estimates and differences in genetic variation between the coding regions and those surveyed by MIG-seq; and 3) to compare the features of the genetic variation between the two species, relating them to their ecological features.…”

Section: Introductionmentioning

confidence: 99%

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Evaluating the genetic diversity in two tropical leguminous trees, <i>Dalbergia cochinchinensis</i> and <i>D. nigrescens</i>, in lowland forests in Cambodia and Thailand using MIG-seq

et al. 2021

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It is vital to measure the levels of genetic diversity and differentiation between populations in a species to understand the current genetic structure and evolution of the species. Here, MIG-seq (multiplexed inter-simple sequence repeat genotyping by sequencing) was employed to assess the genetic variation in two tropical leguminous tree species, Dalbergia cochinchinensis and D. nigrescens, in Cambodia and Thailand. Sequence data for 255-618 loci, each with an approximate length of 100 bp, were obtained, and the nucleotide diversity, Tajima's D and F ST were computed. The estimates calculated from the data obtained by MIG-seq were compared to those obtained by Sanger sequencing of nine nuclear coding genes in D. cochinchinensis in our previous study. The nucleotide diversity at the MIGseq loci was slightly higher than that at silent sites in the coding loci, whereas the F ST values at the MIG-seq loci were generally lower than those at the coding loci, although the differences were not significant. Moreover, nucleotide diversities within populations of the two species were similar to each other, at approximately 0.005. Three and four population clusters were genetically recognized in D. cochinchinensis and D. nigrescens, respectively. Although the populations were differentiated from each other, the levels of differentiation among them, as measured by F ST , were higher in D. cochinchinensis than in D. nigrescens. This indicates higher levels of gene flow between the populations in the latter species. We recommend using MIG-seq for quick surveys of genetic variation because it is costeffective and results in smaller variance in the estimates of population genetic parameters.

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“…(1219 bp, 793 bp) [36], Millettia pinnata Forst. (699 bp, 534 bp) [37], Quercus kerrii Craib (1166 bp, 720 bp), and Quercus austrocochinchinensis Currently, scarce genome information has been published for a few Dalbergia species [32][33][34], and to date, there is no de novo assembly data for the D. odorifera yet. Therefore, high-quality transcriptome resources, particularly those covering full-length sequences and have been filtered for redundancy, remain essential for D. odorifera.…”

Section: Transcriptome Sequencing De Novo Assembly and Annotation Fmentioning

confidence: 99%

De Novo Transcriptome Analysis of Dalbergia odorifera T. Chen (Fabaceae) and Transferability of SSR Markers Developed from the Transcriptome

Liu

Hong

Yang

et al. 2019

Forests

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Dalbergia odorifera T. Chen (Fabaceae), indigenous to Hainan Island, is a precious rosewood (Hainan hualimu) in China. However, only limited genomic information is available which has resulted in a lack of molecular markers, limiting the development and utilization of the germplasm resources. In this study, we aim to enrich genomic information of D. odorifera, and develop a series of transferable simple sequence repeat (SSR) markers for Dalbergia species. Therefore, we performed transcriptome sequencing for D. odorifera by pooling leaf tissues from three trees. A dataset of 138,516,418 reads was identified and assembled into 115,292 unigenes. Moreover, 35,774 simple sequence repeats (SSRs) were identified as potential SSR markers. A set of 19 SSR markers was successfully transferred across species of Dalbergia odorifera T. Chen, Dalbergia tonkinensis Prain, and Dalbergia cochinchinensis Pierre ex Laness. In total, 112 alleles (3-13 alleles/locus) were presented among 60 Dalbergia trees, and polymorphic information content ranged from 0.38 to 0.75. The mean observed and mean expected heterozygosity was 0.34 and 0.40 in D. odorifera, 0.27 and 0.32 in D. tonkinensis, and 0.29 and 0.33 in D. cochinchinensis, respectively. The cluster analysis classified these 60 trees into three major groups according to the three Dalbergia species based on the genetic similarity coefficients, indicating these newly developed transferable markers can be used to explore the relationships among Dalbergia species and assist genetic research. All these unigenes and SSR markers will be useful for breeding programs in the future.

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Genetic variation and population structure of a threatened timber tree Dalbergia cochinchinensis in Cambodia

Cited by 10 publications

References 40 publications

Genetic Diversity of the Endangered Dalbergia odorifera Revealed by SSR Markers

Genetic Diversity of the Endangered Dalbergia odorifera Revealed by SSR Markers

Evaluating the genetic diversity in two tropical leguminous trees, <i>Dalbergia cochinchinensis</i> and <i>D. nigrescens</i>, in lowland forests in Cambodia and Thailand using MIG-seq

De Novo Transcriptome Analysis of Dalbergia odorifera T. Chen (Fabaceae) and Transferability of SSR Markers Developed from the Transcriptome

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