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

PLoS ONE ◽  
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.

scholarly journals Genetic diversity of natural populations of Taxus wallichiana var. mairei

2021 ◽  
Author(s):  
Qianqian Luo ◽  
Fengqing Li ◽  
Longhua Yu ◽  
Liyun Wang ◽  
Gangbiao Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Natural Populations ◽  
Mantel Test ◽  
Jiangxi Province ◽  
Timber Species ◽  
Endangered Tree ◽  
Endangered Tree Species ◽  
Taxus Wallichiana

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.

Species delimitation and population structure in three Onosma (Boraginaceae) species

Biologia ◽  
2015 ◽  
Vol 70 (10) ◽  
Author(s):  
Masoud Sheidai ◽  
Samira Sadeghi ◽  
Mahnaz-Arab Ameri ◽  
Ahmad-Reza Mehrabeian
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Species Delimitation ◽  
Genetic Difference ◽  
Morphological Variability ◽  
Morphological Diversity ◽  
Mantel Test ◽  
Geographical Distance ◽  
Nj Tree ◽  
Issr Molecular Markers

AbstractThe present study aimed to reveal genetic diversity and population structure in three Onosma species i.e., Onosma bulbotrichum DC., O. elwendicum Wettst. and O. sericeum Willd. (Boraginaceae) growing in Iran. This study was performed to check if the ISSR molecular markers could be used in the Onosma species delimitation. We also investigated the infra-specific morphological variability and if we can identify infra-species taxonomic forms. The present study revealed within species genetic and morphological diversity. ISSR data could delimit the studied species as they were separated from each other in NJ tree, maximum parsimony and STRUCTURE analysis. AMOVA and Hickory tests produced significant genetic difference among the studied species. The Mantel test showed no correlation between genetic distance and geographical distance of the populations for all three species. Reticulation analysis and Nm estimation showed gene flow among these populations. We could identify a few ISSR loci that are adaptive. Data obtained can be used in conservation of these medicinal plants in Iran.

scholarly journals Genetic Diversity and Population Structure of Brachiaria (syn. Urochloa) Ecotypes from Uganda

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1193
Author(s):  
Clementine Namazzi ◽  
Julius Pyton Sserumaga ◽  
Swidiq Mugerwa ◽  
Martina Kyalo ◽  
Collins Mutai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Crop Production ◽  
Clustering Algorithm ◽  
Principal Component ◽  
Model Based Clustering ◽  
High Gene ◽  
Nj Tree ◽  
Improvement Programs ◽  
The Tropics

Brachiaria (syn. Urochloa) grass is an important tropical forage of African origin that supports millions of livestock and wildlife in the tropics. Overgrazing, conversion of grasslands for crop production and non-agricultural uses, and the introduction of improved forages have threatened the natural diversity of Brachiaria grass in Uganda. This study established a national collection of Brachiaria ecotypes in Uganda and analyzed them for genetic diversity and population structure using 24 simple sequence repeats (SSR) markers. These markers had a high discriminating ability with an average polymorphism information content (PIC) of 0.89 and detected 584 alleles in 99 ecotypes. Analysis of molecular variance revealed a high within populations variance (98%) indicating a high gene exchange or low genetic differentiation (PhiPT = 00.016) among the ecotype populations. The Bayesian model based clustering algorithm showed three allelic pools in Ugandan ecotypes. The principal component analysis (PCA) of ecotypes, and Neighbor-joining (NJ) tree of ecotypes and six commercial cultivars showed three main groups with variable membership coefficients. About 95% of ecotype pairs had Rogers’ genetic distance above 0.75, suggesting most of them were distantly related. This study confirms the high value of these ecotypes in Brachiaria grass conservation and improvement programs in Uganda and elsewhere.

Genetic Diversity of Dalbergia monticola (Fabaceae) an Endangered Tree Species in the Fragmented Oriental Forest of Madagascar

2006 ◽  
Vol 15 (4) ◽  
pp. 1109-1128 ◽  
Author(s):  
Olivarimbola Andrianoelina ◽  
Hery Rakotondraoelina ◽  
Lolona Ramamonjisoa ◽  
Jean Maley ◽  
Pascal Danthu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tree Species ◽  
Endangered Tree ◽  
Endangered Tree Species

Genetic Diversity and Population Structure of Phyllosticta citriasiana in China

2020 ◽  
Author(s):  
Yibing Zeng ◽  
Tao Xiong ◽  
Bei Liu ◽  
Elma Carstens ◽  
Xiangling Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Mating Type ◽  
Tan Spot ◽  
Long Distance ◽  
High Genetic Diversity ◽  
Geographic Population ◽  
Sexual And Asexual Reproduction ◽  
Geographic Populations ◽  
Genetic Clusters

Phyllosticta citriasiana is the causal agent of citrus tan spot, an important pomelo disease in Asia. At present, there is little or no information on the epidemiology or population structure of P. citriasiana. Using simple sequence repeat (SSR) markers, 94 isolates obtained from three pomelo production regions in southern/southeastern China were analyzed. The analyses showed high genetic diversity in each of the three geographic populations. A STRUCTURE analysis revealed two genetic clusters among the 94 isolates, one geographic population was dominated by genotypes in one cluster while the other two geographic populations were dominated by genotypes of the second cluster. P. citriasiana has a heterothallic mating system with two idiomorphs, MAT1-1 and MAT1-2. Analyses using mating type-specific primers revealed that both mating types were present in all three geographic populations, and in all three populations the mating type ratios were in equilibrium. Although the sexual stage of the fungus has not been discovered yet, analyses of allelic associations indicated evidence for sexual and asexual reproduction within and among populations. Despite the observed genetic differentiation among the three geographic populations, evidence for long-distance gene flow was found.

scholarly journals Pollen-mediated gene flow ensures connectivity among spatially discrete sub-populations of Phalaenopsis pulcherrima, a tropical food-deceptive orchid

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhe Zhang ◽  
Stephan W. Gale ◽  
Ji-Hong Li ◽  
Gunter A. Fischer ◽  
Ming-Xun Ren ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Polynomial Regression ◽  
Genetic Erosion ◽  
Population Level ◽  
Hainan Island ◽  
Paternity Analysis ◽  
Genetic Structuring ◽  
Long Distance ◽  
High Genetic Diversity

Abstract Background Gene flow in plants via pollen and seeds is asymmetrical at different geographic scales. Orchid seeds are adapted to long-distance wind dispersal but pollinium transfer is often influenced by pollinator behavior. We combined field studies with an analysis of genetic diversity among 155 physically mapped adults and 1105 F1 seedlings to evaluate the relative contribution of pollen and seed dispersal to overall gene flow among three sub-populations of the food-deceptive orchid Phalaenopsis pulcherrima on Hainan Island, China. Results Phalaenopsis pulcherrima is self-sterile and predominantly outcrossing, resulting in high population-level genetic diversity, but plants are clumped and exhibit fine-scale genetic structuring. Even so, we detected low differentiation among sub-populations, with polynomial regression analysis suggesting gene flow via seed to be more restricted than that via pollen. Paternity analysis confirmed capsules of P. pulcherrima to each be sired by a single pollen donor, probably in part facilitated by post-pollination stigma obfuscation, with a mean pollen flow distance of 272.7 m. Despite limited sampling, we detected no loss of genetic diversity from one generation to the next. Conclusions Outcrossing mediated by deceptive pollination and self-sterility promote high genetic diversity in P. pulcherrima. Long-range pollinia transfer ensures connectivity among sub-populations, offsetting the risk of genetic erosion at local scales.

Genetic diversity, population structure and association analysis in coconut (Cocos nucifera L.) germplasm using SSR markers

2017 ◽  
Vol 16 (2) ◽  
pp. 156-168 ◽  
Author(s):  
S. Geethanjali ◽  
J. Anitha Rukmani ◽  
D. Rajakumar ◽  
P. Kadirvel ◽  
P.L. Viswanathan
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Association Analysis ◽  
Gene Diversity ◽  
Cocos Nucifera ◽  
Germplasm Collection ◽  
Yield Component ◽  
Chromosome 1 ◽  
Genetic Structuring ◽  
Model Based Clustering

AbstractA world-wide coconut germplasm collection (79 genotypes) was analyzed for genetic diversity and population structure based on 48 simple sequence repeat (SSR) loci. The genotypes displayed moderately high amount of genetic diversity, which was strongly structured according to geographical origins. Number of SSR alleles ranged from 2 to 7 with an average of 4.1 per locus. Gene diversity (expected heterozygosity) estimates ranged from 0.162 to 0.811 with a mean of 0.573. Polymorphism information content values ranged from 0.149 to 0.785 with an average of 0.522. Hierarchical clustering analysis grouped the genotypes into two major clusters with two sub-groups in each, which corresponded with the geographic origins. The first cluster comprised of ‘Tall’ genotypes originated from Indo-Atlantic and South Asia regions. The second cluster comprised mostly of ‘Dwarf’ genotypes and some Tall genotypes which originated from Indo-Pacific and South-East Asia regions. Model-based clustering by STRUCTURE analysis also supported the presence of clear genetic structuring in the collection with two major populations (K = 2) and four sub-populations (K = 4). The proportion of SSR locus-pairs in linkage disequilibrium was low (2.4%). Association analysis in a subset of 44 genotypes detected a single SSR locus, CnCir73 (chromosome 1) putatively associated with fruit yield component traits, which corresponded with a previously mapped quantitative trait locus in coconut.

Morpho-phenological diversity among Tunisian natural populations of Brachypodium hybridum

2014 ◽  
Vol 153 (6) ◽  
pp. 1006-1016 ◽  
Author(s):  
M. NEJI ◽  
F. GEUNA ◽  
W. TAAMALLI ◽  
Y. IBRAHIM ◽  
M. SMIDA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographic Distribution ◽  
Phenotypic Diversity ◽  
Average Length ◽  
Natural Populations ◽  
Negative Relationship ◽  
Mantel Test ◽  
Population Variation ◽  
Long Distance ◽  
Temperate Cereal

SUMMARYBrachypodium hybridum belongs to the Poaceae grass subfamily. It has a close genetic relationship with temperate cereal crops, which means that it can be used as a model for temperate cereal and grass crops. In order to improve knowledge on the genetic diversity of this species, 145 lines of B. hybridum representative of nine populations and all the ecoregions of Tunisia were characterized on the basis of 18 morpho-phenologic features. The results show a considerable variation between populations and ecoregions in all traits studied. Variation was relatively higher for reproductive than vegetative traits. The majority of traits showed very low to high heritability with low border value for average length of spikelet (ALS) and an average value of 0·64. It is noticeable that high values of heritability were observed for most vegetative descriptors, with low values for reproductive ones. Differentiation between populations (QST) varied from 0·02 for ALS to 0·78 for average length of leaves with a mean value across traits of 0·4, which confirms the wide intra-population variation in Tunisian natural population of B. hybridum. Pairwise QST showed that the greatest differentiation among populations was registered between Ain Drahem and Jbel Zaghouan and the smallest between Haouria and Raoued. Overall, the Ain Draham population showed the largest differentiation from the rest of the populations. To infer the effect of geographic distribution of the species, a Mantel test was applied between observed pairwise differentiation and geographic distance between populations and between ecoregions: the results show a positive, but not significant, relationship. In addition a significant negative relationship was found between phenotypic diversity and altitude, indicating that genetic diversity decreased with increasing altitude. Taken together, the high levels of intra-population variation and the lack of correlation between genetic differentiation and geographic distribution suggest a potentially important rate of long-distance seed dispersal and confirm the role played by natural selection in the population structure of Tunisian natural populations of B. hybridum.

scholarly journals Genetic Diversity and Population Structure Revealed by SSR Markers on Endemic Species Osmanthus serrulatus Rehder from Southwestern Sichuan Basin, China

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1365
Author(s):  
Lin Chen ◽  
Tingting Pan ◽  
Huirong Qian ◽  
Min Zhang ◽  
Guodong Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Sichuan Basin ◽  
Polymorphic Information Content ◽  
Population Decline ◽  
Natural Populations ◽  
Genetic Population ◽  
Endangered Status ◽  
High Level

Osmanthus serrulatus Rehder (Oleaceae) is an endemic spring-flowering species in China. It is narrowly distributed in the southwestern Sichuan Basin, and is facing the unprecedented threat of extinction due to problems associated with natural regeneration, habitat fragmentation and persistent and serious human interference. Here, the genetic diversity and population structure of 262 individuals from ten natural populations were analyzed using 18 microsatellites (SSR) markers. In total, 465 alleles were detected across 262 individuals, with a high polymorphic information content (PIC = 0.893). A high level of genetic diversity was inferred from the genetic diversity parameters (He = 0.694, I = 1.492 and PPL = 98.33%). AMOVA showed that a 21.55% genetic variation existed among populations and the mean pairwise Fst (0.215) indicated moderate genetic population differentiation. The ten populations were basically divided into three groups, including two obviously independent groups. Our results indicate that multiple factors were responsible for the complicated genetic relationship and endangered status of O. serrulatus. The concentrated distribution seems to be the key factor causing endangerment, and poor regeneration, human-induced habitat loss and fragmentation seem to be the primary factors in the population decline and further genetic diversity loss. These findings will assist in future conservation management and the scientific breeding of O. serrulatus.

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