Genetic diversity of natural populations of Taxus wallichiana var. mairei

Abstract Maire yew (Taxus wallichiana var. mairei (Lemée H. Léveillé.) L. K. Fu et Nan Li) is a rare and endangered tree species, and it is also a precious timber species in China. We used 13 microsatellites to assess the genetic diversity and differentiation of 665 Maire yew samples from 18 natural populations. A total of 291 alleles were detected. The average number of alleles (Na=22.39), expected heterozygosity (He=0.74), polymorphic information content (PIC = 0.86) and Shannon diversity index (I = 1.66) of the loci indicated a high level of genetic diversity in natural Maire yew populations. Moreover, gene flow was more active among populations (Nm=1.62) than within populations. Among the 18 populations, the Xinfeng population in Jiangxi Province has the highest genetic diversity. Although each of the studied populations should be protected from further deforestation and agricultural expansion, the Xinfeng population deserves the highest conservation priority. The results based on analysis of molecular variance showed that genetic variation occurred mainly within populations (84.90%; P < 0.001), which indicated that the degree of genetic differentiation of the natural populations of Maire yew was low. Based on UPGMA, the 18 populations were categorized into 4 groups. A Mantel test showed that there was no significant correlation between standard genetic distance and geographical distance or altitude differences among the populations. The genetic clustering results also indicated that the genetic relationship followed a north to south clustered trend. The information presented here forms the basis for the development of genetic guidelines for appropriate conservation programs.

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Low Divergence Among Natural Populations of Cornus kousa subsp. chinensis Revealed by ISSR Markers

Forests ◽

10.3390/f10121082 ◽

2019 ◽

Vol 10 (12) ◽

pp. 1082 ◽

Cited By ~ 1

Author(s):

Jia-Qiu Yuan ◽

Qin Fang ◽

Guo-Hua Liu ◽

Xiang-Xiang Fu

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

In Situ Conservation ◽

Geographic Distance ◽

Natural Populations ◽

Issr Markers ◽

Mantel Test ◽

Distribution Area ◽

Genetic Characteristics ◽

Cornus Kousa

Research Highlights: Taking Chinese dogwood (Cornus kousa subsp. chinensis) as an example, the genetic characteristics of natural populations collected from main a distribution area were evaluated using intersimple sequence repeat (ISSR) markers to reveal the genetic basis for further selection and breeding. Background and Objectives: Chinese dogwood is a small understory tree that is widely distributed in China. Chinese dogwood has attracted interest for its potential horticultural and ornamental values, and its natural resource potential urgently needs to be estimated. Materials and Methods: In this study, the genetic diversity of 12 natural populations collected from six provinces containing 223 individuals was evaluated based on ISSR markers. Results: Relatively high levels of genetic diversity were found at both the population and individual levels. The Shannon’s diversity index (I) among individuals (0.504) was higher than that among populations (0.338). Analysis of molecular variance (AMOVA) revealed that genetic variation mainly existed within populations (61.55%) rather than among populations (38.45%). According to the STRUCTURE analysis, 12 populations were assigned to two groups, i.e., the northern and southern ecological regions, which are separated by the Yangtze River. A Mantel test analysis showed that there was no significant correlation between genetic distance and geographic distance. Conclusions: Considering the breeding system of dogwoods, we speculated that the genetic characteristics of the natural populations of this species would be affected by the dispersal mode of its pollens and seeds; additionally, genetic drift could play an important role in its genetic differentiation. In conclusion, in situ conservation is recommended for Chinese dogwood based on our results.

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Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

Agronomy ◽

10.3390/agronomy11061121 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1121

Author(s):

Hela Chikh-Rouhou ◽

Najla Mezghani ◽

Sameh Mnasri ◽

Neila Mezghani ◽

Ana Garcés-Claver

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Phenotypic Diversity ◽

Diversity Index ◽

Polymorphic Information Content ◽

Crop Improvement ◽

Molecular Data ◽

Mantel Test ◽

Phenotypic Traits ◽

Genetic Diversity And Structure

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into fivegroups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.

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Genetic diversity and population structure in the endangered tree Hopea hainanensis (Dipterocarpaceae) on Hainan Island, China

PLoS ONE ◽

10.1371/journal.pone.0241452 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0241452

Author(s):

Chen Wang ◽

Xiang Ma ◽

Mingxun Ren ◽

Liang Tang

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Population Decline ◽

Hainan Island ◽

Mantel Test ◽

Long Distance ◽

Endangered Tree ◽

Important Indicator ◽

Endangered Tree Species ◽

Model Based Clustering

Hopea hainanensis Merrill & Chun (Dipterocarpaceae) is an endangered tree species restricted to Hainan Island, China and a small part of Northern Vietnam. On Hainan Island, it is an important indicator species for tropical forests. However, because of its highly valued timber, H. hainanensis has suffered from overexploitation, leading to a sharp population decline. To facilitate the conservation of this species, genetic diversity and population structure were assessed using 12 SSR markers for 10 populations sampled across Hainan Island. Compared to non-threatened Hopea species, H. hainanensis exhibited reduced overall genetic diversity and increased population differentiation (AMOVA: FST = 0.23). Bayesian model-based clustering and principal coordinate analysis consistently assigned H. hainanensis individuals into three genetic groups, which were found to be widespread and overlapping geographically. A Mantel test found no correlation between genetic and geographical distances (r = 0.040, p = 0.418). The observed genetic structure suggests that long-distance gene flow occurred among H. hainanensis populations prior to habitat fragmentation. A recent population bottleneck was revealed, which may cause rapid loss of genetic diversity and increased differentiation across populations. Based on these findings, appropriate strategies for the long-term conservation of the endangered species H. hainanensis are proposed.

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Study on the Genetic Structure Based on Geographic Populations of the Endangered Tree Species: Liriodendron chinense

Forests ◽

10.3390/f12070917 ◽

2021 ◽

Vol 12 (7) ◽

pp. 917

Author(s):

Peng-Yan Zhou ◽

Li-Xing Hui ◽

Shu-Jing Huang ◽

Zhou-Xian Ni ◽

Fa-Xin Yu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Natural Populations ◽

Systematic Research ◽

Endangered Tree ◽

Endangered Tree Species ◽

Expected Heterozygosity ◽

Liriodendron Chinense ◽

Geographic Populations ◽

Degree Of Differentiation

Liriodendron chinense (Hemsley) Sargent is a Class II protected plant in China as natural populations are on the verge of extinction. There is still a lack of systematic research on the genetic resources of its geographic populations. In this study, we used 20 pairs of SSR markers with high polymorphism to analyze a total of 808 L. chinense samples from 22 regions, and 63 Liriodendron tulipifera Linn samples from 2 regions were used as a comparison group. The results revealed a total of 78 alleles in L. chinense, and the average expected heterozygosity (He) was 0.558, showing a low level of genetic diversity. The degree of differentiation of L. chinense was high, with the differentiation coefficient (Fst) as high as 0.302, which is related to the low gene flow (Nm = 0.578). Based on the genetic structure, principal coordinate analysis (PCoA) and phylogenetic analysis of 24 Liriodendron spp. populations, L. chinense and L. tulipifera had obvious differentiation, while the differentiation between L. chinense geographic populations was very large and irregular. Inbreeding appears within the geographic populations, and the level of genetic diversity is very low. In order to protect the genetic diversity of L. chinense, in addition to protecting the existing population as much as possible, artificial cultivation should introduce materials from multiple populations.

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Genetic diversity of natural populations of Machilus thunbergii, an endangered tree species in eastern China, determined with ISSR analysis

Genetics and Molecular Research ◽

10.4238/2013.march.11.10 ◽

2013 ◽

Vol 12 (3) ◽

pp. 3689-3697 ◽

Cited By ~ 1

Author(s):

J. Liu ◽

H.G. Sun ◽

J.M. Jiang ◽

W.H. Shao ◽

Q.F. Luan

Keyword(s):

Genetic Diversity ◽

Tree Species ◽

Eastern China ◽

Natural Populations ◽

Endangered Tree ◽

Issr Analysis ◽

Endangered Tree Species ◽

Machilus Thunbergii

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Floristic Variation of Tree Communities and Their Association with Soil Properties in Pulau Jerejak, Penang, Peninsular Malaysia

Science Letters ◽

10.24191/sl.v14i1.7899 ◽

2020 ◽

Vol 14 (1) ◽

pp. 34

Author(s):

Faezah Pardi

Keyword(s):

Tree Species ◽

Diversity Index ◽

Basal Area ◽

Peninsular Malaysia ◽

Importance Value ◽

Conservation Action ◽

Endangered Tree ◽

Endangered Tree Species ◽

Tree Communities ◽

Floristic Variation

This study was conducted at Pulau Jerejak, Penang to determine the floristic variation of its tree communities. A 0.5-hectare study plot was established and divided into 11 subplots. A total of 587 trees with diameter at breast height (DBH) of 5 cm and above were measured, identified and recorded. The tree communities comprised of 84 species, 63 genera and 32 families. The Myrtaceae was the most speciose family with 10 recorded species while Syzgium glaucum (Myrtaceae) was the most frequent species. The Myrtaceae recorded the highest density of 306 individuals while Syzgium glaucum (Myrtaceae) had the highest species density of 182 individuals. Total tree basal area (BA) was 21.47 m2/ha and family with the highest BA was Myrtaceae with 5.81 m2/ha while at species level, Syzgium glaucum (Myrtaceae) was the species with the highest total BA in the plot with value of 4.95 m2/ha. The Shannon˗Weiner Diversity Index of tree communities showed a value of 3.60 (H'max = 4.43) and Evenness Index of 0.81 which indicates high uniformity of tree species. The Margalef Richness Index (R') revealed that the tree species richness was 13.02. Myrtaceae had the highest Importance Value of 20.4%. The Canonical Correspondence Analysis (CCA) showed that Diospyros buxifolia (Ebenaceae) and Pouteria malaccensis (Sapotaceae) were strongly correlated to low pH. Dysoxylum cauliflorum (Meliaceae) and Eriobotrya bengalensis (Rosaceae) were correlated to phosphorus (P) and calcium ion (Ca2+), respectively. Therefore, the trees species composition at Pulau Jerejak showed that the biodiversity is high and conservation action should be implemented to protect endangered tree species. Keywords: Floristic variation; Tree communities; Trees composition; Pulau Jerejak; Species diversity

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Genetic diversity of central and peripheral populations of Toona ciliata var. pubescens, an endangered tree species endemic to China

Chinese Journal of Plant Ecology ◽

10.3724/sp.j.1258.2013.00006 ◽

2013 ◽

Vol 37 (1) ◽

pp. 52-60 ◽

Cited By ~ 2

Author(s):

Jun LIU ◽

Jing-Min JIANG ◽

Jun ZOU ◽

Jin-Liang XU ◽

Han SHEN ◽

...

Keyword(s):

Genetic Diversity ◽

Tree Species ◽

Peripheral Populations ◽

Endangered Tree ◽

Endangered Tree Species ◽

Toona Ciliata

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Assessment of Genetic Diversity of Promising Castor Been (Ricinus communis L.) Genotypes in Nigeria

Notulae Scientia Biologicae ◽

10.15835/nsb11310346 ◽

2019 ◽

Vol 11 (3) ◽

pp. 467-474

Author(s):

Bolaji Zuluqurineen SALIHU ◽

Olamide Ahmed FALUSI ◽

Adeyinka Olufemi ADEPOJU ◽

Ibrahim Wasiu AROLU ◽

Oladipupo Yusuf DAUDU ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

Gene Diversity ◽

Ricinus Communis ◽

Polymorphic Information Content ◽

Block Design ◽

Genetic Material ◽

Morphological Data ◽

Research Attention ◽

Ricinus Communis L

Castor oil plant (Ricinus communis L.) is an important oil crop with little research attention in Nigeria. In the present research, extent of genetic diversity among 20 Nigerian castor genotypes was determined using morphological descriptors and molecular markers. The genotypes were laid out on a randomized complete block design with three replicated plots. Molecular genotyping of the genotypes was carried out using genomic Simple Sequence Repeats (SSR). The genotypes revealed high divergence in seed colour, seed shape, seed mottle, seed caruncle and seed sizes. Seedling establishment varied from 70.18% (in Acc. 006) to 93.25% (Acc. 001) with average mean of 81.53%. Raceme length ranged from 15.90 cm to 29.54 cm with population mean of 20.80 cm. The highest seed yield (1222.98 kg/ha) was recorded in Acc. 001 and the least (611.46 kg/ha) was observed in Acc. 006. Seed oil content varied between 32.15% in Acc. 042 and 54.03% in Acc. 006. Agglomerative cluster dendrogram constructed from morphological data showed random distribution of the genotypes into three cluster groups irrespective of the sources/collection points. The genetic diversity based on SSR Marker Analysis revealed high average expected heterozygosity (0.74), Polymorphic information content (0.68), Nei’s gene diversity index (0.72) and Shannon's Information index (1.43). The dendrogram constructed from molecular data grouped the twenty genotypes into three groups at coefficient of 0.34. From these findings, it showed that the twenty genotypes evaluated are divergent in nature and they could serve as good genetic material for castor breeding in Nigeria.

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Enrichment of chickpea genetic resources collection monitored by microsatellites

Czech Journal of Genetics and Plant Breeding ◽

10.17221/49/2008-cjgpb ◽

2009 ◽

Vol 45 (No. 1) ◽

pp. 11-17 ◽

Cited By ~ 4

Author(s):

K. Jomová ◽

M. Benková ◽

J. Kraic

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Slovak Republic ◽

Diversity Index ◽

Polymorphic Information Content ◽

Microsatellite Analysis ◽

Entire Collection ◽

Single Fragment ◽

New Germplasm ◽

New Alleles

A set of 49 chickpea accessions maintained in the collection of the Genebank of the Slovak Republic was analyzed using microsatellite markers. The level of genetic diversity and the effectivity of new germplasm acquisition for the collection enrichment were evaluated. Five primer pairs used generated 50 different amplified alleles. Four of them, TA2, TA5, TR1, and TR7, containing a long TAA-tandem repeat, were polymorphic with 11–13 alleles per locus. A single fragment was obtained from all the accessions with the primer pair CATPER flanking a small microsatellite repetition in the mRNA sequence of chickpea cationic peroxidase. The genetic diversity was expressed as a diversity index (DI) and polymorphic information content (PIC) with values in the range from 0.885 to 0.904 and from 0.972 to 0.991, respectively. Recently acquired new germplasm contributed 13 new alleles to the entire collection, i.e. almost 70% of microsatellite diversity originated from the recently acquired accessions. Remarkable is also, that one accession carries a unique allel, not present in the remaining collection. Microsatellite analysis revealed the importance of collecting missions for the enrichment of collections of genetic resources.

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