scholarly journals Genetic Diversity and Population Structure of Chinese Corylus heterophylla and Corylus kweichowensis Using Simple Sequence Repeat Markers

2020 ◽  
Vol 145 (5) ◽  
pp. 289-298
Author(s):  
Tiantian Zhao ◽  
Wenxu Ma ◽  
Qinghua Ma ◽  
Zhen Yang ◽  
Lisong Liang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
In Situ Conservation ◽  
Geographic Distance ◽  
Natural Populations ◽  
Distinct Species ◽  
Mantel Test ◽  
Conservation Of Genetic Resources ◽  
Genetic Clusters

Corylus heterophylla and Corylus kweichowensis are economically and ecologically important nut-producing woody shrubs that are distributed across northern and southern regions of China. However, few studies have examined the genetic diversity and genetic relationships between C. heterophylla and C. kweichowensis, and their taxonomic relationships have been questioned. In this study, 796 individuals collected from 34 natural populations (21 C. heterophylla and 13 C. kweichowensis populations) were investigated to assess the genetic diversity and population structure using 11 microsatellite loci. Analysis of molecular variance revealed that genetic differentiation of C. heterophylla and C. kweichowensis within populations accounted for 93.57% and 88.91% of total variation, respectively. The C. heterophylla and C. kweichowensis populations as a whole group were analyzed by multiple programs, which showed that the 34 populations were divided into two genetic clusters. One cluster included 21 C. heterophylla populations, and the second cluster contained 13 C. kweichowensis populations. We conclude from these results that C. heterophylla and C. kweichowensis are distinct species. The Mantel test showed that the genetic distance was significantly correlated with the geographic distance (r = 0.580, P < 0.001). The populations of C. heterophylla [e.g., populations WC (Weichang), MS (Mishan), and WA (Wu’an)] and C. kweichowensis [e.g., populations YX (Yuexi), ZP (Zhenping), LA (Lin’an), and TB (Taibai)] with high allelic richness are considered suitable for in situ conservation. Our study provides valuable information for breeding and conservation of genetic resources of C. heterophylla, C. kweichowensis, and related species.

Genetic diversity and population structure of Vigna exilis and Vigna grandiflora (Phaseoleae, Fabaceae) from Thailand based on microsatellite variation

Botany ◽  
2013 ◽  
Vol 91 (10) ◽  
pp. 653-661 ◽  
Author(s):  
Anochar Kaewwongwal ◽  
Arunee Jetsadu ◽  
Prakit Somta ◽  
Sompong Chankaew ◽  
Peerasak Srinives
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Allelic Richness ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Natural Populations ◽  
Microsatellite Variation ◽  
Genetic Clusters ◽  
Simple Sequence

The objective of this research was to determine the genetic diversity and population structure of natural populations of two rare wild species of Asian Vigna (Phaseoleae, Fabaceae), Vigna exilis Tateishi & Maxted and Vigna grandiflora (Prain) Tateishi & Maxted, from Thailand. Employing 21 simple sequence repeat markers, 107 and 85 individuals from seven and five natural populations of V. exilis and V. grandiflora, respectively, were analyzed. In total, the markers detected 196 alleles for V. exilis and 219 alleles for V. grandiflora. Vigna exilis populations showed lower average values in number of alleles, allelic richness, observed heterozygosity, gene diversity, and outcrossing rate than V. grandiflora populations, namely 58.00% versus 114.60%, 51.96% versus 74.80%, 0.02% versus 0.18%, 0.40% versus 0.66%, and 3.24% versus 17.41%, respectively. Pairwise FST among populations demonstrated that V. exilis was much more differentiated than V. grandiflora. Analysis of molecular variance revealed that 41.83% and 15.06% of total variation resided among the populations of V. exilis and V. grandiflora, respectively. Seven and two genetic clusters were detected for V. grandiflora and V. exilis by STRUCTURE analysis. Our findings suggest that different strategies are required for in situ conservation of the two species. All V. exilis populations, or as many as possible, should be conserved to protect genetic resources of this species, while a few V. grandiflora populations can capture the majority of its genetic variation.

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

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1082 ◽  
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.

scholarly journals Detection of Genetic Variation and Genetic Diversity in Two Indian Mudskipper Species (Boleophthalmus boddarti, B. dussumieri) using RAPD Marker

2013 ◽  
Vol 5 (2) ◽  
pp. 139-143
Author(s):  
Vellaichamy RAMANADEVI ◽  
Muthusamy THANGARAJ ◽  
Anbazhagan SURESHKUMAR ◽  
Jayachandran SUBBURAJ
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Environmental Changes ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Distinct Species ◽  
Fish Population ◽  
Habitat Destruction ◽  
Arbitrary Primers ◽  
Vellar Estuary

Due to the environmental changes and habitat destruction the mudskipper fish population is decreasing in recent years. To predict the fish population structure, frequent manual survey and molecular methods are widely used. Molecular markers such as RAPD, microsatellite, allozyme, D-loop haplotype are frequently adopted to assess the population structure of an organism. In this study ten- arbitrary primers were screened to estimate the genetic relationships and diversity of two mudskipper species (Boleophthalmus boddarti and B. dussumieri) in Vellar estuary, Tamilnadu, India. By this RAPD marker study, the genetic diversity (H) in B. boddarti was more (0.0116 ± 0.0066) than in B. dussumieri (0.0056 ± 0.0024) in Vellar estuary (India). The genetic distance between B. boddarti and B. dussumieri was 1.7943. By observing the species specific bands and the phylogenetic analysis it is revealed that these two species clearly deviated into separate clusters emphasizing the distinct species status.

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

2018 ◽  
Vol 67 (1) ◽  
pp. 93-98 ◽  
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.

scholarly journals Population Genetic Structure of Aphis gossypii Glover (Hemiptera: Aphididae) in Korea

Insects ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 319
Author(s):  
Nam ◽  
Park ◽  
Lee
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Isolation By Distance ◽  
Aphis Gossypii ◽  
Geographic Distance ◽  
Mantel Test ◽  
Low Genetic Diversity ◽  
Study Results ◽  
Aphis Gossypii Glover ◽  
Genetic Clusters

Aphis gossypii Glover (Hemiptera: Aphididae) is a serious polyphagous agricultural pest worldwide. In the present study, we used eight microsatellite markers to investigate the genetic structure and diversity of A. gossypii populations in Korea. Samples were collected from 37 locations in Korea (18 populations in 2016, 14 populations in 2017, and five populations in 2018) from pepper plants. A. gossypii had low to moderate genetic diversity, and expected heterozygosity (HE) ranged from 0.354 to 0.719. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2 = 0.0004, p = 0.370), suggesting high gene flow among populations in Korea. Populations of A. gossypii in Korea were divided into two distinct genetic clusters (ΔK = 2). In 2016 and 2017, the genetic clusters changed into opposite genetic structures within one year mostly in northwest and southeast parts of Korea. Possible relevance of study results was discussed. Chemical control, cyclical parthenogenesis, and immigrants from the exterior might have resulted in this low genetic diversity and opposite genetic clusters.

Genetic diversity in Anatolian wild grapes (Vitis vinifera subsp. sylvestris) estimated by SSR markers

2011 ◽  
Vol 9 (3) ◽  
pp. 375-383 ◽  
Author(s):  
Ali Ergül ◽  
Gemma Perez-Rivera ◽  
Gökhan Söylemezoğlu ◽  
Kemal Kazan ◽  
Rosa Arroyo-Garcia
Keyword(s):  
Genetic Diversity ◽  
Vitis Vinifera ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Peripheral Populations ◽  
Pair Group ◽  
Wild Grape ◽  
Anatolian Peninsula ◽  
Genetic Clusters

Anatolia (Asia Minor) is considered to be the cradle of viticulture, but wild grape accessions from this region have not been subjected to any genetic analysis. We present the first genetic characterization of wild grapes (Vitis vinifera subsp. sylvestris) from this region. Using 15 nuclear microsatellites, we genotyped 84 wild grape accessions collected from three Anatolian locations. The unweighted pair group method with arithmetic mean analysis revealed four genetic clusters that partially separated Anatolian wild grape populations. In general, accessions from geographically closer locations showed higher genetic similarities than those from more distant locations. In some cases, accessions from one population showed close genetic relationships to accessions from a different population. The genetic diversity between natural populations from both ends of the Mediterranean basin has shown higher genetic diversity in the Anatolian Peninsula than peripheral populations, suggesting that this area could be one centre of diversity of the species. The genetic relationship between wild and cultivated grapevine from Anatolian Peninsula indicated a clear separation between them. However, we cannot discarded a local genetic contribution. Overall, this study reveals useful information for management and potential utilization of Anatolian wild grape germplasm.

Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed Science ◽  
2007 ◽  
Vol 55 (2) ◽  
pp. 95-101 ◽  
Author(s):  
Runzhi Li ◽  
Shiwen Wang ◽  
Liusheng Duan ◽  
Zhaohu Li ◽  
Michael J. Christoffers ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
The United States ◽  
Mantel Test ◽  
Wild Oat ◽  
Chinese Populations ◽  
Nei's Distance ◽  
The Impact

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

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 Evaluation of a Diverse, Worldwide Collection of Wild, Cultivated, and Landrace Pepper (Capsicum annuum) for Resistance to Phytophthora Fruit Rot, Genetic Diversity, and Population Structure

2015 ◽  
Vol 105 (1) ◽  
pp. 110-118 ◽  
Author(s):  
R. P. Naegele ◽  
A. J. Tomlinson ◽  
M. K. Hausbeck
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phytophthora Capsici ◽  
The United States ◽  
Fruit Rot ◽  
Sources Of Resistance ◽  
Plant Introductions ◽  
Genetic Clusters ◽  
Commercial Breeding ◽  
Moderately Resistant

Pepper is the third most important solanaceous crop in the United States and fourth most important worldwide. To identify sources of resistance for commercial breeding, 170 pepper genotypes from five continents and 45 countries were evaluated for Phytophthora fruit rot resistance using two isolates of Phytophthora capsici. Genetic diversity and population structure were assessed on a subset of 157 genotypes using 23 polymorphic simple sequence repeats. Partial resistance and isolate-specific interactions were identified in the population at both 3 and 5 days postinoculation (dpi). Plant introductions (PIs) 640833 and 566811 were the most resistant lines evaluated at 5 dpi to isolates 12889 and OP97, with mean lesion areas less than Criollo de Morelos. Genetic diversity was moderate (0.44) in the population. The program STRUCTURE inferred four genetic clusters with moderate to very great differentiation among clusters. Most lines evaluated were susceptible or moderately susceptible at 5 dpi, and no lines evaluated were completely resistant to Phytophthora fruit rot. Significant population structure was detected when pepper varieties were grouped by predefined categories of disease resistance, continent, and country of origin. Moderately resistant or resistant PIs to both isolates of P. capsici at 5 dpi were in genetic clusters one and two.

scholarly journals Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

2021 ◽  
Author(s):  
Varun Hiremath ◽  
Kanwar Pal Singh ◽  
Neelu Jain ◽  
Kishan Swaroop ◽  
Pradeep Kumar Jain ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Test Analysis ◽  
Average Value ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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