Genetic diversity of Simao pine in China revealed by SRAP markers

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 revealed 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 (Gst = 0.1701), and a slightly high level of gene flow (Nm = 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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Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

Canadian Journal of Forest Research ◽

10.1139/x26-162 ◽

1996 ◽

Vol 26 (8) ◽

pp. 1454-1462 ◽

Cited By ~ 31

Author(s):

Naoki Tani ◽

Nobuhiro Tomaru ◽

Masayuki Araki ◽

Kihachiro Ohba

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Phylogenetic Trees ◽

Genetic Relationships ◽

Natural Populations ◽

Group Method ◽

Stone Pine ◽

Arithmetic Means ◽

Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

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Genetic Diversity and Population Structure of Alnus cremastogyne as Revealed by Microsatellite Markers

Forests ◽

10.3390/f10030278 ◽

2019 ◽

Vol 10 (3) ◽

pp. 278 ◽

Cited By ~ 2

Author(s):

Hong-Ying Guo ◽

Ze-Liang Wang ◽

Zhen Huang ◽

Zhi Chen ◽

Han-Bo Yang ◽

...

Keyword(s):

Genetic Diversity ◽

Geographical Distribution ◽

Mantel Test ◽

Group Method ◽

Arithmetic Means ◽

Mountain Area ◽

Pair Group ◽

Hill Area ◽

Population Genetic Variation ◽

High Level

Alnus cremastogyne Burk. is a nonleguminous, nitrogen-fixing tree species. It is also the most important endemic species of Alnus Mill. in China, possessing important ecological functions. This study investigated population genetic variation in A. cremastogyne using 175 trees sampled from 14 populations native to Sichuan Province with 25 simple sequence repeat (SSR) markers. Our analysis showed that A. cremastogyne has an average of 5.83 alleles, 3.37 effective alleles, an expected heterozygosity of 0.63, and an observed heterozygosity of 0.739, indicating a relatively high level of genetic diversity. The A. cremastogyne populations in Liangshan Prefecture (Meigu, Mianning) showed the highest level of genetic diversity, whereas the Yanting population had the lowest. Our analysis also showed that the average genetic differentiation of 14 A. cremastogyne populations was 0.021. Analysis of molecular variance (AMOVA) revealed that 97% of the variation existed within populations; only 3% was among populations. Unweighted pair-group method with arithmetic means (UPGMA) clustering and genetic structure analysis showed that the 14 A. cremastogyne populations could be clearly divided into three clusters: Liangshan Prefecture population, Ganzi Prefecture population, the other population in the mountain area around the Sichuan Basin and central Sichuan hill area, indicating some geographical distribution. Further analysis using the Mantel test showed that this geographical distribution was significantly correlated with elevation.

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Genetic diversity of Juglans sigillata Dode germplasm in Yunnan Province, China, as revealed by SSRs

Plant Genetic Resources ◽

10.1017/s1479262120000441 ◽

2020 ◽

pp. 1-10

Author(s):

Shaoyu Chen ◽

Tao Wu ◽

Liangjun Xiao ◽

Delu Ning ◽

Li Pan

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Yunnan Province ◽

Allelic Richness ◽

Geographic Distance ◽

Group Method ◽

Pair Group ◽

Ssr Loci ◽

Juglans Sigillata ◽

High Level

Abstract Iron walnut, Juglans sigillata Dode, restricted to southwestern China, has its centre of distribution in Yunnan Province which has a varied climate, geography and rich plant diversity. Yunnan contains abundant J. sigillata germplasm. In this study, a provincial-scale set of walnut germplasm resources (14 populations comprising 1122 individuals) was evaluated for genetic diversity based on 20 simple sequence repeat (SSR) loci. The number of SSR alleles per locus ranged from 7 to 27, with an average of 17.55. Mean allelic richness and mean private allelic richness ranged from 3.40 to 4.62 and 0.11 to 0.36, with average of 3.93 and 0.30, respectively. Expected heterozygosity (He) varied from 0.26 to 0.78, with an average of 0.57. Polymorphism information content ranged from 0.22 to 0.79, with an average of 0.57. Genetic differentiation (FST) was 0.05, indicating that only 5% of total genetic variability was inter-populational, a finding supported by an analysis of molecular variance and STRUCTURE analysis. Relatively high gene flow (Nm = 6.70) was observed between populations. A unweighted pair-group method with arithmetic analysis classified the 14 populations into two major groups. Mantel testing uncovered a significant correlation between geographic distance and genetic distance (r = 0.33, P = 0.04). Overall, the research revealed a moderately high level of genetic diversity in the germplasm and low genetic differentiation among populations, which showed great potential for further development and exploitation of this resource.

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Genetic diversity and structure among natural populations of Mytilaria laosensis (Hamamelidaceae) revealed by microsatellite markers

Silvae Genetica ◽

10.2478/sg-2018-0013 ◽

2018 ◽

Vol 67 (1) ◽

pp. 93-98 ◽

Cited By ~ 1

Author(s):

Niu Yu ◽

Jie Yuan ◽

Guangtian Yin ◽

Jinchang Yang ◽

Rongsheng Li ◽

...

Keyword(s):

Genetic Diversity ◽

Geographic Distance ◽

Natural Populations ◽

Magnetic Bead ◽

Mantel Test ◽

High Genetic Diversity ◽

Information Index ◽

Genetic Diversity And Structure ◽

High Level ◽

Mytilaria Laosensis

Abstract Mytilaria laosensis is a fast-growing tropical broadleaf tree that is extensively used for wood production and has significant ecological benefits. To investigate the genetic diversity and population structure of M. laosensis, eight major natural populations in China were analyzed by using simple sequence repeat (SSR) markers. A total of 88 microsatellite-containing fragments were obtained by the method of magnetic bead enrichment, among which 26 pairs of SSR primers were screened out and used to generate a total of 190 alleles among 152 individuals. The average of observed number of alleles, Shannon’s information index and polymorphism information content per locus were 18.3, 1.1577 and 0.7759, respectively, implying a high level of genetic diversity in M. laosensis populations. The variation within populations accounted for 81.74 % of total variation based on analysis of molecular variance. Cluster analysis divided the eight populations into four groups, among which five populations from the southern parts of Guangxi province were classified as one major group. Mantel test showed that there was highly significant correlation between Euclidean genetic distance and geographic distance, suggesting that geographic isolation contribute to the high genetic diversity of M. laosensis. Together, these could provide support for the feasibility of exploration and utilization of M. laosensis in subtropical areas of East Asia including Jiangxi, Hunan and Fujian province of China.

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Genetic Diversity and Differentiation among Natural, Production, and Introduced Populations of the Narrowly Endemic Species Coreopsis leavenworthii (Asteraceae)

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.133.2.234 ◽

2008 ◽

Vol 133 (2) ◽

pp. 234-241 ◽

Cited By ~ 3

Author(s):

David M. Czarnecki ◽

Madhugiri Nageswara Rao ◽

Jeffrey G. Norcini ◽

Frederick G. Gmitter ◽

Zhanao Deng

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Natural Populations ◽

Seed Collection ◽

Central Florida ◽

Natural Production ◽

Introduced Populations ◽

Total Genetic Diversity ◽

High Level ◽

Introduced Population

Seeds of Coreopsis leavenworthii Torr. & Gray (Asteraceae) are being commercially produced but the lack of genetic diversity information has hindered growers and end users from addressing several critical issues affecting wild collection, commercial production, distribution, and the use of seeds. In this study, the genetic diversity and differentiation among natural, production, and introduced populations were analyzed at the molecular level using 320 amplified fragment length polymorphism (AFLP) markers. A high level of diversity [68.6% average polymorphism; total genetic diversity (H t ) = 0.309] and a moderate level of genetic differentiation [total genetic diversity residing among populations (G st ) = 0.226; Φ st = 0.244; Bayesian analog of Nei's G st (G st -B) = 0.197] was detected among six natural populations—two each from northern, central, and southern Florida. Two distance-based clustering analyses, based on an individual's AFLP phenotypes or a population's allele frequencies, grouped natural populations into three clusters, concordant with our previous results from a common garden study of phenotypic variation. Clustering of populations was mostly according to their respective geographical origin within Florida. The correlation between geographical distances and pairwise F st values between populations was very significant (r = 0.855, P < 0.0001). Two central Florida natural populations were divergent and grouped into separate clusters, indicating that the existence of factors other than physical distance alone were contributing to genetic isolation. Three production populations maintained a level of genetic diversity comparable to that in the natural populations and were grouped with the natural populations from which the production populations were derived, suggesting that the genetic identity of the seed origin was maintained under production practices. The genetic diversity of the introduced population was comparable to that of the source populations (central Florida natural populations), but genetic shift seems to have occurred, causing the introduced population to cluster with local (northern Florida) populations where planted. The observed genetic differentiation among natural populations may indicate a need to develop appropriate zones within Florida for preservation of genetic diversity during seed collection, increase, and distribution. This high level of population differentiation also suggests a need to collect and analyze more natural populations across Florida and from Alabama for a better understanding of the species' genetic diversity and population structure across its distribution range.

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Genetic Analyses of Saprolegnia Strains Isolated from Salmonid Fish of Different Geographic Origin Document the Connection Between Pathogenicity and Molecular Diversity

Journal of Fungi ◽

10.3390/jof7090713 ◽

2021 ◽

Vol 7 (9) ◽

pp. 713

Author(s):

Abdelhameed Elameen ◽

Svein Stueland ◽

Ralf Kristensen ◽

Rosa F. Fristad ◽

Trude Vrålstad ◽

...

Keyword(s):

Genetic Diversity ◽

Sequence Data ◽

Genetic Relationships ◽

Geographic Origin ◽

Mantel Test ◽

Group Method ◽

Aflp Analysis ◽

Its Sequencing ◽

Sequencing Data ◽

Pair Group

Saprolegnia parasitica is recognized as one of the most important oomycetes pests of salmon and trout species. The amplified fragment length polymorphism (AFLP) and method sequence data of the internal transcribed spacer (ITS) were used to study the genetic diversity and relationships of Saprolegnia spp. collected from Canada, Chile, Japan, Norway and Scotland. AFLP analysis of 37 Saprolegnia spp. isolates using six primer combinations gave a total of 163 clear polymorphic bands. Bayesian cluster analysis using genetic similarity divided the isolates into three main groups, suggesting that there are genetic relationships among the isolates. The unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCO) confirmed the pattern of the cluster analyses. ITS analyses of 48 Saprolegnia sequences resulted in five well-defined clades. Analysis of molecular variance (AMOVA) revealed greater variation within countries (91.01%) than among countries (8.99%). We were able to distinguish the Saprolegnia isolates according to their species, ability to produce oogonia with and without long spines on the cysts and their ability to or not to cause mortality in salmonids. AFLP markers and ITS sequencing data obtained in the study, were found to be an efficient tool to characterize the genetic diversity and relationships of Saprolegnia spp. The comparison of AFLP analysis and ITS sequence data using the Mantel test showed a very high and significant correlation (r2 = 0.8317).

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Estimation of Genetic Diversity in Genus Mentha Collected From Azad Jammu And Kashmir, Pakistan

10.1101/866111 ◽

2019 ◽

Author(s):

Fozia Abasi ◽

Israr Ahmad ◽

Sami Ullah khan ◽

Khawaja Shafique Ahmad ◽

Aneela Ulfat ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Molecular Data ◽

Group Method ◽

Similarity Coefficients ◽

Arithmetic Means ◽

Jammu And Kashmir ◽

Pair Group ◽

High Level

ABSTRACTMints are perennial aromatic herbs used both for medicinal and aromatic purposes. Flora of Pakistan has reported six species of genus Mentha. Taxonomy of genus Mentha is more complex and confusing due to inter specific hybridization. The present research is the first documented report from Pakistan for the purpose to dissect Mentha specimens using molecular tools. A total of 17 SCoT and SSR markers used to dissect genetic diversity among 41 Mentha specimens. The results revealed substantial variation among Mentha specimens. The molecular data analyzed through NTSYS and Power marker software’s. Dendrogram constructed on the base of similarity coefficients generated using weighted pair group method of arithmetic means (UPGMA) recorded high level of polymorphism. Polymorphic Information Content (PIC) for molecular markers recorded in the range of 5-8. Mean genetic distance (GD) was estimated in the range from 0.35% to 100%. The minimum and maximum GD recorded in one combination each as P2-P4 and M41-P10. The present study was explored the efficiency of SCoT and SSR markers for evaluating the genetic diversity of medicinal plants. The present research was concluded that both morphological and molecular dendrogram determined considerable level of diversity among Mentha species. Furthermore, specific primers and DNA chloroplast technology could be needed for further molecular analysis to refine the data more up to varietal level.

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Population Genetic Survey of Populus cathayana Originating From Southeastern Qinghai-Tibetan Plateau of China Based on SSR Markers

Silvae Genetica ◽

10.1515/sg-2005-0018 ◽

2005 ◽

Vol 54 (1-6) ◽

pp. 116-122 ◽

Cited By ~ 9

Author(s):

Y. H. Peng ◽

Z. X. Lu ◽

K. Chen ◽

O. Luukkanen ◽

H. Korpelainen ◽

...

Keyword(s):

Genetic Diversity ◽

Tibetan Plateau ◽

Genetic Differentiation ◽

Natural Populations ◽

Habitat Characteristics ◽

Southeastern Part ◽

Population Mixing ◽

Populus Cathayana ◽

Divergence Pattern ◽

High Level

Abstract In this study, the genetic diversity of Populus cathayana Rehd was investigated using microsatellite markers. In a total of 150 individuals collected from six natural populations in the southeastern part of the Qinghai-Tibetan Plateau in China, a high level of microsatellite polymorphism was detected. At the seven investigated microsatellite loci, the number of alleles per locus ranged from 5 to 16, with a mean of 11.3, the observed heterozygosities across populations ranged from 0.408 to 0.986, with a mean of 0.792, and the expected heterozygosities across populations ranged from 0.511 to 0.891, with a mean of 0.802. The proportion of genetic differentiation among populations accounted for 37.3% of the whole genetic diversity. The presence of such a high level of genetic diversity could be attributed to the features of the species and the habitats where the sampled populations occur: The southeastern part of the Qinghai-Tibetan Plateau is regarded as the natural distribution and variation center of the genus Populus in China. Variation in environmental conditions and selection pressures in different populations, and topographic dispersal barriers could be factors associated with the high level of genetic differentiation found among populations. The populations possessed significant heterozygosity excesses, which may be due to extensive population mixing at the local scale. The cluster analysis showed that the populations are not strictly grouped according to their geographic distances but the habitat characteristics also influence the divergence pattern. In addition, we suggest that population SHY should be regarded as an ecologically divergent species of P. cathayana.

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Genetic Structure and Diversity among Species of Salacia: An Endangered Medicinal Herb of Western Ghats, India

South Asian Journal of Experimental Biology ◽

10.38150/sajeb.9(1).p23-33 ◽

2019 ◽

Vol 9 (1) ◽

pp. 23-33

Author(s):

Chandrashekhar G Patil ◽

Sheetal Ganapati Kamat ◽

R Vasudeva

Keyword(s):

Genetic Diversity ◽

Southern China ◽

Issr Marker ◽

Group Method ◽

Population Genetic Differentiation ◽

Expected Heterozygosity ◽

Marker Analysis ◽

Endangered Medicinal Herb ◽

High Level ◽

Genetic Structure And Diversity

Salacia is one of the medicinally valuable genus, distributed throughout tropical areas which include India, Sri Lanka, Southern China and other Southern Asian Countries. The genus Salacia is represented by 21 species in India, among them eight species are recorded from the state of Karnataka in the Southern part of India. Despite its pharmaceutical importance, very little information exists about the genetic diversity of Salacia at molecular level. Hence the present study was carried out to evaluate the genetic among six species of Salacia namely S. chinensis, S. malabarica, S. oblonga, S. macrosperma, S. reticulata and S. gambleana with the help of ISSR marker analysis. Dendrogram and genetic distance were generated adopting Unweighted Paired Group Method with Arithmetic mean (UPGMA) in the NTSYS-pc software. Basic genetic parameters were calculated by analysing the genetic data with Pop gene 1.32 and GenAlEx 6.2 software. The overall polymorphism across the ten primers screened revealed 26 % polymorphism. A 60% polymorphism was scored for the primer UBC 841, whereas, no polymorphism was observed for primer UBC 840 and ISSR 6. The average observed heterozygosity was more than expected heterozygosity. Observed heterozygosity (Ho) ranged from 0.15 (UBC 841) to 0.38 (ISSR 6) with an average of 0.25, whereas expected heterozygosity (He) ranged from 0.10 (UBC 843) to 0.35 (ISSR 6) with an average of 0.23 for Salacia species. The higher heterozygosity pointed towards increased genetic diversity amongst the species. ISSR marker analysis showed high level of inter and intra population genetic differentiation.

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Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

10.21203/rs.3.rs-779119/v1 ◽

2021 ◽

Author(s):

Guai-qiang Chai ◽

Yizhong Duan ◽

Peipei Jiao ◽

Zhongyu Du ◽

Furen Kang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Association Studies ◽

Natural Populations ◽

Principal Component ◽

Nucleotide Polymorphisms ◽

Future Design ◽

Ammopiptanthus Nanus ◽

Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

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