Isolation and characterization of polymorphic microsatellite markers in the endangered species Bretschneidera sinensis Hemsl.

Li, M; Chen, H F; Wang, Z F; Zhang, S

doi:10.4238/gmr.15038234

Cited by 3 publications

(6 citation statements)

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“…Using the same RAD-seq method, we obtained 63 polymorphic loci from 170 candidate loci (37.1%) in an endangered species, Bretschneidera sinensis, in a previous study (Li et al, 2016), but we could obtain only 11 polymorphic loci among the 49 loci (29.7%) identified in this study. In addition, the highest number of alleles per locus was three in D. duperreanum and 16 in B. sinensis with 30 samples from one population.…”

Section: Resultsmentioning

confidence: 66%

A set of novel microsatellite markers developed for an economically important tree, Dracontomelon duperreanum, in China

Wang

Cao

et al. 2017

Genet. Mol. Res.

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ABSTRACT. Dracontomelon duperreanum, the most representative species of the family Anacardiaceae, is an important multipurpose tree in China and Vietnam. However, no genetic diversity studies have been reported on this species. In this study, we identified 11 microsatellite markers for D. duperreanum by using the restriction-site-associated DNA sequencing (RAD-seq) method and examined their polymorphisms in 22 samples obtained from the South China Botanical Garden, South China. We could detect only two or three alleles for each microsatellite marker. The mean observed and expected heterozygosities were 0.41 and 0.39, respectively, which were lower than those reported for the species with similar life history forms. These relatively low genetic diversities in this common plant species are unexpected and might have resulted from its extensive cultivation. To our knowledge, this is the first report of microsatellite markers in the genus Dracontomelon. These microsatellite markers will be valuable for studying the genetic

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Section: Resultsmentioning

confidence: 66%

A set of novel microsatellite markers developed for an economically important tree, Dracontomelon duperreanum, in China

Wang

Cao

et al. 2017

Genet. Mol. Res.

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“…Bretschneidera sinensis Hemsl., a deciduous tree species of montotypic genera belongs to the family Akaniaceae, is a relic species of the Tertiary tropical ora mainly occurring in evergreen broad-leaved or mixed evergreen and deciduous forests in mountainous areas at altitudes of 300-1,700 m above sea level in Southern China (Dong et al 2019;Li et al 2016;Wang et al 2018). The species is listed as endangered on the IUCN Red List of Threatened Species (IUCN 2020, http://www.iucnredlist.org).…”

Section: Plant Species and Collectionsmentioning

confidence: 99%

“…According to recent studies, most of the populations are seriously threatened (Hu et al 2014) and the species also suffers from reproductive failure due to low seed productivity and seed germination rates (Qiao et al 2012). Geographical range of the endangered species extents from Southern China to India, Indo China, Vietnam, and Taiwan (Dong et al 2019;Hu et al 2014;Kumar et al 2017;Li et al 2016;Wang et al 2018). Taiwan is a continental island possessed isolated population of B. sinenis at geographical margin of the Eurasia continent.…”

Section: Plant Species and Collectionsmentioning

confidence: 99%

“…In this study, the WorldClim and local climate datasets were applied for RF and PCA to project potential distribution range and to construct climate space of the endangered plant species, Bretschneidera sinensis Hemsl. The endangered plant species is majorly distributed in Southern China and marginal populations of the species extend to Indo China, India and Taiwan (Dong et al 2019;Hu et al 2014;Kumar et al 2017;Li et al 2016;Wang et al 2018). Populations of the species are quiet small and have suffered from isolation and fragmentation of habitats (Dong et al 2019).…”

Section: Introductionmentioning

confidence: 99%

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Advantage and Disadvantage of Global and Local Climate Datasets on Modeling Species Distribution at Continental and Landscape Scales

Liao

Chang

Chen

2021

Preprint

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Species distribution model based on global and local climate datasets were hypothesized to have advantages on projecting distribution range at continental and landscape scales, respectively. Random Forest (RF) and principle components analysis (PCA) aimed to project potential distribution range and to construct climate space of Bretschneidera sinensis in continental East Asia (CEA) and northern Taiwan (NTWN) based on the WorldClim and local climate datasets. Geographical extent of the endangered species at continental scale was available to be projected by RF based on the WorldClim dataset, whereas RF had projected bias map that presented gridded squares at edges of the potential distribution range. At landscape scale, projection map of RF in NTWN based on the WorldClim dataset presented gridded distribution far from empirical distribution pattern, while that based on local climate dataset presented a distribution pattern relevant to elevation and topography. PCA had revealed climate differentiation between continental and island populations. Evidently, local climate dataset had reflected climate heterogeneity at landscape scale and is essential for identifying local adaptation of island population at geographical margin of the endangered species. However, huge number of gridded cells generated from local climate interpolation method for projecting potential distribution range at landscape scale is not available to expand geographical extent to continental region. Global climate dataset has the advantage on modeling geographical extent of plant species at continental scale, while local climate dataset used for modelling species distribution enables conservationists to delineate reliable conservation areas in fragmented natural habitats at landscape scale.

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“…Previously, several markers have been used to evaluate the genetic diversity of B. sinensis, including amplified fragment length polymorphism (AFLP) (Hu et al, 2017), random amplified polymorphic DNA (RAPD) (Wang et al, 2008), inter-simple sequence repeats (ISSRs) (Liang et al, 2012;Xu et al, 2013;Hu et al, 2014), microsatellite (SSR) (Guan et al, 2012;Li et al, 2016), and several chloroplast sequence markers (Wang et al, 2018). These results showed that the genetic diversity of B. sinensis was low within populations but relatively high at the species level (Hu et al, 2014(Hu et al, , 2017Wang et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae)

Shang

et al. 2022

Front. Ecol. Evol.

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Bretschneidera sinensis is an endangered woody species found in East and South China. Comprehensive intraspecies chloroplast genome studies have demonstrated novel genetic resources to assess the genetic variation and diversity of this species. Using genome skimming method, we assembled the whole chloroplast genome of 12 genotypes of B. sinensis from different geographical locations, covering most wild populations. The B. sinensis chloroplast genome size ranged from 158,959 to 159,045 base pairs (bp) and displayed a typical circular quadripartite structure. Comparative analyses of 12 B. sinensis chloroplast genome revealed 33 polymorphic simple sequence repeats (SSRs), 105 polymorphic single nucleotide polymorphisms (SNPs), and 55 indels. Phylogenetic analysis showed that the 12 genotypes were grouped into 2 branches, which is consistent with the geographical distribution (Eastern clade and Western clade). Divergence time estimates showed that the two clades were divergent from 0.6 Ma in the late Pleistocene. Ex situ conservation is essential for this species. In this study, we identified SNPs, indels, and microsatellites of B. sinensis by comparative analyses of chloroplast genomes and determined genetic variation between populations using these genomic markers. Chloroplast genomic resources are also important for further domestication, population genetic, and phylogenetic analysis, possibly in combination with molecular markers of mitochondrial and/or nuclear genomes.

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Isolation and characterization of polymorphic microsatellite markers in the endangered species Bretschneidera sinensis Hemsl.

Cited by 3 publications

References 6 publications

A set of novel microsatellite markers developed for an economically important tree, Dracontomelon duperreanum, in China

A set of novel microsatellite markers developed for an economically important tree, Dracontomelon duperreanum, in China

Advantage and Disadvantage of Global and Local Climate Datasets on Modeling Species Distribution at Continental and Landscape Scales

Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae)

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