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

Forests ◽  
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.

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.

scholarly journals DIVERSITY AND GENETIC STRUCTURE OF NATURAL POPULATIONS OF ARAÇÁ (Psidium guineense Sw.)

2016 ◽  
Vol 29 (1) ◽  
pp. 37-44 ◽  
Author(s):  
EDSON FERREIRA DA SILVA ◽  
RAFAELA LIMA DE ARAÚJO ◽  
CRISTINA DOS SANTOS RIBEIRO MARTINS ◽  
LUIZA SUELY SEMEN MARTINS ◽  
ELIZABETH ANN VEASEY
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Natural Populations ◽  
Fruit Tree ◽  
Northeastern Brazil ◽  
Economic Resource ◽  
Expected Heterozygosity ◽  
Isozyme Loci ◽  
Differentiation Index

ABSTRAT: Psidium guineense Sw, popularly known as araçá, is a fruit tree there is widely distributed in Brazil and belongs to the Myrtaceae family. In northeastern Brazil, araçá occurs along coast and in the Zona da Mata; its fruit looks like guava but is more acidic and has a stronger smell. There is a little information about this species, which increases the difficulty of conserving its genetic resources and exploiting araçá as an economic resource. The objective of this research was the evaluation of the genetic diversity and genetic structure of P. guineense from Pernambuco's Zona da Mata. One hundred and fourteen individuals and 18 isozyme loci were evaluated, showing 28 alleles. The percentage of polymorphic loci () and the average number of alleles per locus () were 0.5 and 1.5, respectively, in this population. The expected heterozygosity, which corresponds to the genetic diversity, ranged from 0.22 to 0.23, a high value when considering that isozymes mark access from the functional genome. The differentiation index among the population was () = 0.015; therefore, the populations were not different among the sampled places. The inbreeding values () ranged from -0.549 to -0.794, indicating an absence of inbreeding and a greater-than-expected heterozygosity in all the studied populations. The estimated gene flow (Nm) for a pair of this population ranged from 3.23 to 20.77, sufficient to avoid genetic differentiation among the population and in accordance with the values of genetic divergence found in this study.

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

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.

scholarly journals GENOMIC DETERMINATION OF THE MOST IMPORTANT FATHER LINES OF SLOVAK PINZGAU COWS

AGROFOR ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Veronika KUKUČKOVÁ ◽  
Nina MORAVČÍKOVÁ ◽  
Radovan KASARDA
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
The State ◽  
Most Probable Number ◽  
Pedigree Data ◽  
Probable Number ◽  
Expected Heterozygosity ◽  
High Level ◽  
The Bayesian Approach

The aim of this study was to assess genetic structure of Slovak Pinzgau populationbased on polymorphism at molecular markers using statistical methods. Femaleoffspring of 12 most frequently used bulls in Slovak Pinzgau breeding programmewere investigated. Pinzgau cattle were found to have a high level of diversity,supported by the number of alleles observed across loci (average 5.31, range 2-11)and by the high within-breed expected heterozygosity (average 0.66, range 0.64-0.73). The state of genetic diversity is satisfying and standard for local populations.Detection of 12 possible subpopulation structures provided us with detailedinformation of the genetic structure. The Bayesian approach was applied, detectingthree, as the most probable number of clusters. The similarity of eachsubpopulation using microsatellites was confirmed also by high-throughputmolecular data. The observed inbreeding (FROH=2.3%) was higher than thatexpected based on pedigree data (FPED=0.4%) due to the limited number ofavailable generations in pedigree data. One of the most important steps indevelopment of efficient autochthonous breed protection programs ischaracterization of genetic variability and assessment of the population structure.The chosen set of microsatellites confirmed the suitability in determination of thesubpopulations of Pinzgau cattle in Slovakia. The state of genetic diversity at moredetailed level was successfully performed using bovineSNP50 BeadChip.

Genetic Diversity and Genetic Structure Analysis of the Natural Populations of Lilium brownii from Guangdong, China

2009 ◽  
Vol 47 (7-8) ◽  
pp. 503-510 ◽  
Author(s):  
Yong-fang Huang ◽  
Mao-xun Yang ◽  
Hao Zhang ◽  
Xue-ying Zhuang ◽  
Xue-hui Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Structure Analysis ◽  
Natural Populations

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

scholarly journals Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10327
Author(s):  
Ricardo M. Landínez-García ◽  
Juan Carlos Narváez ◽  
Edna J. Márquez
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Freshwater Fish ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
Genetic Stock ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Genetic Stocks ◽  
Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

scholarly journals Population Genetic Structure of Asclepias Tuberosa In Northwest Iowa: A Comparison Within and Between Remnant Prairies and Commercially Available Seed

2015 ◽  
Vol 122 (1-4) ◽  
pp. 1-6
Author(s):  
Jeffrey T Ploegstra ◽  
Brittany de Ruyter ◽  
Tony Jelsma
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Tallgrass Prairie ◽  
Microsatellite Analysis ◽  
Outbreeding Depression ◽  
Moderate Degree ◽  
Asclepias Syriaca ◽  
Minimal Impact ◽  
Low Degree ◽  
Degree Of Differentiation

Isolated in scattered remnants, less than 0.1% of Iowa's original tallgrass prairie remains. The small populations remaining are at risk for reduced genetic diversity, inbreeding depression, and outbreeding depression. In light of these concerns, we used microsatellite analysis to assess the genetic structure of butterfly milkweed (Asclepias tuberosa) populations on prairie remnants in northwest Iowa. We compared remnant populations with a restoration population at Dordt College in Sioux Center, Iowa, and with an Oklahoma seed source. Microsatellites identified for use in common milkweed (Asclepias syriaca) had sufficient polymorphism information content (PIC) across the butterfly milkweed (A. tuberosa) populations sampled (mean PIC = 0.624). The FIS values indicated a lack of inbreeding (mean FIS = −0.1455) even in the commercially expanded seed. The pairwise FST values showed a low degree of differentiation among the remnants (mean FST = 0.0453) but a moderate degree (mean FST = 0.105) of differentiation when comparing the remnants to the Dordt restoration or to seed from Oklahoma. Despite massive loss and fragmentation of the tallgrass prairie, our microsatellite analysis revealed no evidence of inbreeding in A. tuberosa. However, evidence of genetic differentiation suggests that effort should be made to preserve the diversity still present. Seed expansion efforts appear to have had minimal impact on overall genetic diversity, although the diversity in particular selectable traits may be reduced. The differences between the genetics of the propagated seed at the Dordt restoration and the Oklahoma seed when compared to native remnants support the usefulness of source-identified seed.

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