Genetic diversity and population structure of Taxus cuspidata in the Changbai Mountains assessed by chloroplast DNA sequences and microsatellite markers

B, Cheng; Zheng, Yongqi; Qi-zhong, Sun

doi:10.1016/j.bse.2015.10.009

Cited by 26 publications

(16 citation statements)

References 38 publications

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“…The results of UPGMA and PCoA also showed that the assignment of populations was not completely consistent with their geographic origin, a result that has been observed in previous studies (Liu et al, 2013;Cheng et al, 2015). This finding indicated that geographical distance had no obvious effect on genetic differentiation of Simao pine populations.…”

Section: Discussionsupporting

confidence: 61%

Peer Review #1 of "Genetic diversity of Simao pine in China revealed by SRAP markers (v0.1)"

2019

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Background. Simao pine (Pinus kesiya Royle ex Gordon var. langbianensis (A. Chev.) Gaussen), is one of the most important tree species in the production of timber and resin in China. However, the genetic diversity of the natural populations has not been assessed to date. In this study, sequence related amplified polymorphism (SRAP) markers were used to investigate the genetic composition of natural Simao pine populations. Method. The SRAP markers were applied and their efficiency was compared using various statistical multivariate methods, including analysis molecular of variance (AMOVA), the unweighted pair group method with arithmetic mean (UPGMA), and Principal coordinate analysis (PCoA). Results. The 11 populations reveal ed a high level of genetic diversity (PPB = 95.45%, H = 0.4567, I = 0.6484) at the species level. A moderately low level of genetic differentiation (G st = 0.1701), and a slightly high level of gene flow (N m = 2.4403) were observed among populations using AMOVA. Eleven populations of Simao pine were gathered into four distinct clusters based on molecular data, and the results of UPGMA and PCoA also illustrated that assignment of populations is not completely consistent with geographic origin. The Mantel test revealed there was no significant correlation between geographic and genetic distance (r = 0.241, p = 0.090). Discussion. The SRAP markers were very effective in the assessment of genetic diversity in Simao pine. Simao pine populations display high levels of genetic diversity and low or moderate levels of genetic differentiation due to frequent gene exchange among populations. The low genetic differentiation among populations implied that conservation efforts should aim to preserve all remaining natural populations of this species. The information derived from this study is useful when identifying populations and categorizing their population origins, making possible the design of long term management program such as genetic improvement by selective breeding.

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Section: Discussionsupporting

confidence: 61%

Peer Review #1 of "Genetic diversity of Simao pine in China revealed by SRAP markers (v0.1)"

2019

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“…Moreover, in a previous study of DNA barcoding for Eurasian Taxus species based on five DNA regions (rbcL, matK, trnL-trnF, trnH-psbA and ITS), eleven species were clearly identified (Liu et al 2011). Population genetic study of several Taxus species were also recorded using trnL-trnF and petA-psbE showed significant genetic variation (Gao et al 2007;Liu et al 2013;Poudel et al 2012;Cheng et al 2015). This observation suggests that the extremely no genetic variation in the cpDNA regions examined here is specific for T. sumatrana since those loci yielded some extent of genetic variation when assessed to other Taxus and non Taxus species.…”

Section: Resultsmentioning

confidence: 92%

Short Communication: Genetic diversity and conservation strategy considerations for highly valuable medicinal tree of Taxus sumatrana in Indonesia

Rachmat¹,

Subiakto

Kamiya

2016

Biodiversitas

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Genetic variation is considered to be the key factor for longterm survival of the species. The recognition of the existing genetic diversity is the preliminary phase in development of an effective strategy for conservation of forest tree species. Taxus sumatrana or is confined to grow naturally only in Asia, it is a rare and endangered species that in several Asian countries needs both ex situ and in situ protection program. In its natural distribution, T. sumatrana is the only Taxus species that reached its southernmost distribution to Sumatran forest-Indonesia and locally named as Sumatran Yew. The objective of this research was to determine the genetic variation of T. sumatrana as baseline information for designing conservation strategy of the species. Leaves samples were collected from two natural population of T. sumatrana in Mt. Kerinci (Sungai Penuh, Jambi) and Mt. Dempo (Pagaralam, South Sumatra), both sites are located along Bukit Barisan Mountain Ranges of Sumatra. We sequenced two non-coding chloroplast DNA (cpDNA) regions of trnL-trnF and psbC-trnS that each yielded 808 bp and 1092 bp, and rbcL gene of 523 bp, in which the total length covered 2423 bp. Surprisingly, we found no variation for all individuals and population, which means that the species is similar and both populations are not genetically structured. This study also revealed on how a proper conservation strategy should be practiced for the species as we know that without a sufficient amount of genetic variation, a population cannot evolve in response to changing environmental conditions. In situ conservation program is a must that can maintain the existence of the species while at the same time keeping the sustainability of the entire systems; in other side ex situ conservation strategy can take place as an additional effort to secure the genetic resources in case of the catastrophic events that might diminish their limited natural habitat.

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“…Meanwhile, this different consequence might be related to the type and evolutionary rates of different genome sequences [76]. In general, the evolutionary rate of nuclear genomes transmitted by parents was higher than that of maternally inherited chloroplast genomes [77]. Therefore, cpDNA variations reflected a past change, whereas nSSR variations inferred recent events in the population demographics of R. rex subsp.…”

Section: Genetic Differentiation and Structure Among R Rex Subsp Rementioning

confidence: 99%

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Zhang

Liu

Wang

et al. 2020

Plants

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Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (H E = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: F ST = 0.165***; cpDNA: F ST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000-100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex. Plants 2020, 9, 338 2 of 16 potential genetic resources for the development of new cultivars that can adapt to diverse environmental conditions [4]. In addition, plants in the genus Rhododendron L. produce numerous chemical constituents and are recognized as an important source of bioactive phytochemicals [5]. Some Rhododendron species are used as traditional medicine in China, India, Europe, and North America against various diseases, such as inflammation, pain, skin ailments, common cold, and gastrointestinal disorders [5]. However, as an important natural resource for human daily life and ecosystem composition, most Rhododendron species are facing risk of extinction due to the high frequency of anthropogenic disturbance [6]. Thus, research on the population genetic information of Rhododendron species is undoubtedly beneficial for germplasm protection and sustainable utilization [6][7][8][9].Inferring genetic information is recognized as the undisputed basis for the sustainable exploitation and conservation of plant diversity [10,11]. Different molecular markers are used in assessing genetic information and identifying distinct plant populations for management and conservation [12][13][14]. Microsatellite markers (SSRs) are used in revealing the genetic characteristics and related influence factors of plant species at individual and population levels due to their desirable advantages [13,15]. Chloroplast DNA (cpDNA), whic...

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Genetic diversity and population structure of Taxus cuspidata in the Changbai Mountains assessed by chloroplast DNA sequences and microsatellite markers

Cited by 26 publications

References 38 publications

Peer Review #1 of "Genetic diversity of Simao pine in China revealed by SRAP markers (v0.1)"

Peer Review #1 of "Genetic diversity of Simao pine in China revealed by SRAP markers (v0.1)"

Short Communication: Genetic diversity and conservation strategy considerations for highly valuable medicinal tree of Taxus sumatrana in Indonesia

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

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