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Xiang X.-Y.,Anhui Normal University | Zhang Z.-X.,Anhui Normal University | Duan R.-Y.,Anhui Normal University | Zhang X.-P.,Anhui Normal University | And 2 more authors.
Biochemical Systematics and Ecology | Year: 2015

Assessing patterns of genetic variation in rare endangered species is critical for developing both in situ and ex situ conservation strategies. Pinus dabeshanensis Cheng et Law is an endangered species endemic to the Dabieshan Mountains of eastern China. To obtain fundamental information of genetic diversity, population history, effective population size, and gene flow in this species, we explored patterns of genetic variation of natural populations, in addition to an ex situ conserved population, using expressed sequence tag-simple sequence repeats (EST-SSR) markers. Our results revealed moderate levels of genetic diversity (e.g., HE=0.458 vs. HE=0.423) and a low level of genetic differentiation (FST=0.028) among natural and conserved populations relative to other conifers. Both contemporary and historical migration rates among populations were high. Bayesian coalescent-based analyses suggested that 3 populations underwent reductions in population size ca. 10,000yr ago, and that two populations may have experienced recent genetic bottlenecks under the TPM. Bayesian clustering revealed that individuals from the ex situ population were largely assigned to the 'red' cluster. Additionally, our results identified private alleles in the natural populations but not in the ex situ population, suggesting that the ex situ conserved population insufficiently represents the genetic diversity present in the species. Past decline in population size is likely to be due to Holocene climate change. Based on the genetic information obtained for P. dabeshanensis, we propose some suggestions for the conservation and efficient management of this endangered species. © 2015 Elsevier Ltd. Source


Xiang X.,Anhui Normal University | Zhang Z.,Anhui Normal University | Wang Z.,Anhui Normal University | Zhang X.,Anhui Normal University | And 2 more authors.
Molecular Breeding | Year: 2015

Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the present study, a cDNA library of P. dabeshanensis needles was sequenced using Illumina HiSeq™ 2000 paired-end sequencing technology. By mining 42,248 non-redundant unigenes, 1966 expressed sequence tag–simple sequence repeats (EST-SSRs) derived from 1835 unigenes were identified. The most abundant repeat motif was trinucleotide (41.6 %), followed by dinucleotide (23.25 %), mononucleotide (21.41 %), hexanucleotide (7.83 %), pentanucleotide (4.43 %) and tetranucleotide repeats (1.53 %). The top tri- and dinucleotide motifs included AGC/CTG and AT/AT, respectively. A total of 20,194 unigenes were assigned to three main GO categories with 153,373 GO terms. A KOG classification showed that 11,604 unigenes and 732 SSR-containing unigenes were assigned to 25 and 23 possible functional categories, respectively. Among the 1966 EST-SSRs, 431 primer pairs were successfully designed. After selecting 82 of these pairs at random for further validation, 44 pairs amplified unambiguous bands, 19 of which were polymorphic among 24 individuals of P. dabeshanensis. A total of 57 alleles were identified, varying from 2 to 5 alleles per locus with an average of 3.0. The observed and expected heterozygosity per locus ranged from 0 to 0.958 and from 0.082 to 0.759, respectively. The PIC values ranged from 0.077 to 0.707 with an average of 0.380. The generation of such large-scale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development. Such markers will be robust tools for genomic research and breeding of P. dabeshanensis. © 2015, Springer Science+Business Media Dordrecht. Source


Li X.H.,Anhui Normal University | Zhang X.P.,Anhui Normal University | Zhang X.P.,The Key Laboratory of Conservation and Employment of Biological Resources of Anhui | Zhang X.P.,The Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province | And 4 more authors.
Genetics and Molecular Research | Year: 2015

Pteroceltis tatarinowii (Ulmaceae) is a scientifically and economically important temperate deciduous tree that is endemic to China. In the present study, 12 P. tatarinowii polymorphic microsatellite loci were developed using the tailed primer-M13-simple sequence repeats (TP-M13-SSR) biotin-capture method. The number of alleles per locus ranged from 2 to 10, with an average of 6.58. The observed and expected heterozygosity ranged from 0.208 to 0.958 and from 0.198 to 0.858, with average values of 0.703 and 0.710, respectively. The markers isolated in this study represent a favorable tool for further analyses of the population genetic structure and evolutionary history of this relic tree. © FUNPEC-RP. Source


Wang D.-Y.,Anhui Normal University | Chen Y.-J.,Anhui Normal University | Zhu H.-M.,Anhui Normal University | Lv G.-S.,Anhui Normal University | And 4 more authors.
Biochemical Systematics and Ecology | Year: 2014

The perennial herb Primula cicutariifolia Pax is an endangered and endemic species with narrow distribution in eastern Anhui and Zhejiang provinces of China. In this study, the levels of genetic variation and the pattern of genetic structure in five natural populations of P. cicutariifolia were assessed by inter-simple sequence repeats (ISSR) and simple sequence repeat (SSR) markers. Both markers revealed that there was remarkably low genetic variation within populations (e.g., He=0.19 and 0.18, for ISSR and SSR respectively) and high differentiation among populations (GST=0.714 and 0.611; ΦST=0.698 and 0.599, for ISSR and SSR respectively). The level of population genetic diversity was correlated to population size only detected by ISSR markers. The genetic structure of P. cicutariifolia may be explained by limited gene flow that was caused by habitat fragmentation and limited seeds and pollen dispersal ability, self breeding system and biennial life form. To protect and avoid disappearance of P. cicutariifolia, much more attentions should be paid to protect all the remnant populations and their habitats, and three management units, i.e. Tianmushan, Damodao, and Panan units, were proposed. © 2014 Elsevier Ltd. Source

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