Genetic diversity and relationships among populations of Camellia japonica, an endangered species in China

Camellia japonica, an evergreen ornamental plant in the Theaceae, its natural range is now shrinking. This is evidenced by the fact that the species is on the verge of extinction in Laoshan Mountain (Qingdao), the northernmost area of China for natural population of C. japonica. Little is known about the genetic diversity and relationships among cultivated and wild C. japonica populations. 180 samples of six C. japonica populations were tested for genetic diversity with SSR markers; these included three cultivated populations, two natural populations in Qingdao, and one natural population in Daqingshan. The average values of polymorphism information content (PIC), expected heterozygosity (He), and Shannon’s information index (I) were 0.5849, 0.6385 and 1.3170, respectively, indicating that C. japonica has a high genetic diversity. The genetic diversities of the six populations in rank order were as follows: Daqingshan > Zhongshan Park > Changmenyan Island > Daguan Island > Botanical Garden > May Fourth Square. The geographical isolation of the islands had no significant influence on the genetic diversity of C. japonica. Clustering results showed that the six C. japonica populations could be grouped into three categories, and most populations were clustered according to their geographical origin and genetic background. These results also reconfirmed that the C. japonica (Naidong) population in Qingdao originated from Changmenyan Island. Genetic variation was highest within populations (89%), indicating that C. japonica can be protected at the population level. These findings will prove useful for the genetic analysis, protection, and horticultural use of C. japonica.

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Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae)

Canadian Journal of Plant Science ◽

10.4141/cjps07015 ◽

2008 ◽

Vol 88 (1) ◽

pp. 179-186 ◽

Cited By ~ 2

Author(s):

Chu-Chuan Fan ◽

Nicola Pecchioni ◽

Long-Qing Chen

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Differentiation ◽

Genetic Distance ◽

Gene Diversity ◽

Genetic Relationships ◽

Natural Populations ◽

Population Level ◽

Conservation Strategy ◽

Information Index

Calycanthus chinensis Cheng et S.Y. Chang, a tertiary relic species in China, is a shade-loving and deciduous bush withan elegant shape and beautiful flower of high ornamental value. It was widely planted in gardens and miniature scapes in China.The objective of this study was to characterize the genetic variation and structure in the three extant populations of the species, in order to provide useful information for a future conservation strategy. Twenty-two of 120 RAPD primers were selected and a total of 257 stable and clear DNA fragments were scored. Calycanthus chinensis showed a lower level of genetic diversity. At the population level, the percentage of polymorphic loci, Nei's gene diversity and Shannon’s information index were 40.9%, 0.1641 and 0.2386, respectively; while at the species level, the corresponding values were 59.1%, 0.2097 and 0.3123, respectively. The estimates of genetic differentiation based on Shannon’s information index (0.2360), Nei’s gene diversity (0.2175) and AMOVA (24.94%) were very similar, and significantly higher than the average genetic differentiation reported in outcrossed spermatophyte. So it suggested high genetic differentiation emerged among populations of C. chinensis. Genetic relationships among populations were assessed by Nei’s standard genetic distance, which suggested that the Tiantai population was genetically distinct from the other two populations. Moreover, the genetic distance was significantly correlated with geographical distance among populations (r = 0.997, t > t0.05). The gene flow (Nm) was 0.8994, indicating that gene exchange among populations was restricted. A conservation strategy was proposed based on the low gene flow and habitat deterioration, which are contributing to the endangered status of this species. Key words: Genetic diversity, endangered plant, population genetics, RAPD

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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 Divergence among Populations of Invasive Alien Species Lantana camara L. from Selected Areas of Bangladesh

Plants and Ecosystem ◽

10.54479/pae.v1i01.6664 ◽

2021 ◽

Vol 1 (01) ◽

pp. 9-14

Author(s):

SAILA KABIR ◽

MD ABUL KASHEM ◽

MOHAMMAD ZABED HOSSAIN

Keyword(s):

Genetic Diversity ◽

Alien Species ◽

Invasive Alien Species ◽

Gene Diversity ◽

Lantana Camara ◽

Native Plant ◽

High Genetic Diversity ◽

Native Plant Species ◽

Information Index ◽

Genetic Clustering

Lantana camara L., a well-known invasive alien species causing invasion and posing threat to native plant species community in different regions of Bangladesh. The present study aimed to investigate the genetic diversity of L. camara populations in different regions of Bangladesh. Eight RAPD markers were used in order to probe into its genetic variability. Total number of bands (202), polymorphic loci (104), per-centage of polymorphism (97.20%), average Shanon’s information index (0.3051±0.115), Nei’s gene diversity (0.4733±0.144) was found and in different populations and multiple divergent genetic clustering along with presence of unique alleles (4) for RAPD revealed high genetic diversity among the populations of L. camara in different regions of Bangladesh.

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There Is No Evidence of Geographical Patterning among Invasive Kentucky Bluegrass (Poa pratensis) Populations in the Northern Great Plains

Weed Science ◽

10.1614/ws-d-15-00169.1 ◽

2016 ◽

Vol 64 (3) ◽

pp. 409-420 ◽

Cited By ~ 2

Author(s):

Lauren A. Dennhardt ◽

Edward S. DeKeyser ◽

Sarah A. Tennefos ◽

Steven E. Travers

Keyword(s):

Genetic Diversity ◽

Great Plains ◽

Propagule Pressure ◽

Poa Pratensis ◽

Natural Populations ◽

Kentucky Bluegrass ◽

Grass Species ◽

Northern Great Plains ◽

Wild Populations ◽

High Genetic Diversity

The study of colonizing and of dominant grass species is essential for prairie conservation efforts. We sought to answer how naturalized Kentucky bluegrass in the northern Great Plains has become successful in the last 20 yr despite its long history in the northern Great Plains. We tested for evidence of geographical differentiation using flow cytometry and microsatellite markers to ascertain the population genetics of Kentucky bluegrass. Across all tested wild populations, high levels of genetic diversity were detected along with moderate levels of structure. Mantel tests of geographical patterns were not significant. Using clonal assignment, we found two major clones that made up the majority of the tested wild populations. When we compared the wild individuals to pedigree cultivars, we found virtually no genetic overlap across all tests, which did not support our hypothesis of developed cultivars contributing to high genetic diversity in natural populations. Furthermore, DNA content tests indicated a narrow range in ploidy in wild populations compared with lawn cultivars, further supporting a hypothesis of divergence between wild and pedigree cultivars. These results indicate the recent invasion of Kentucky bluegrass in the northern Great Plains is not because of adaptation or propagule pressure, but rather likely an environmental or land use shift.

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

BMC Plant Biology ◽

10.1186/s12870-019-2179-y ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

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.

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Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of EndangeredPolyporus umbellatus

BioMed Research International ◽

10.1155/2015/941357 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 2

Author(s):

Yuejin Zhang ◽

Yuanyuan Chen ◽

Ruihong Wang ◽

Ailin Zeng ◽

Michael K. Deyholos ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Large Scale ◽

Gene Diversity ◽

High Genetic Diversity ◽

Information Index ◽

Polyporus Umbellatus ◽

Ssr Primers ◽

Expressed Sequence

A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences inGanoderma lucidumobtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 naturalPolyporus umbellatusaccessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13P.umbellatusaccessions showed relatively high genetic diversity. The expected heterozygosity, Nei’s gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups.

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Using Random Amplified Polymorphic DNA to Assess Genetic Diversity and Structure of NaturalCalophyllum brasiliense(Clusiaceae) Populations in Riparian Forests

International Journal of Forestry Research ◽

10.1155/2014/305286 ◽

2014 ◽

Vol 2014 ◽

pp. 1-8

Author(s):

Evânia Galvão Mendonça ◽

Anderson Marcos de Souza ◽

Fábio de Almeida Vieira ◽

Regiane Abjaud Estopa ◽

Cristiane Aparecida Fioravante Reis ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Random Amplified Polymorphic Dna ◽

Natural Populations ◽

Rio Grande ◽

Shannon Index ◽

High Genetic Diversity ◽

Family Structures ◽

Genetic Diversity And Structure ◽

Kinship Coefficients

The objective of this study was to assess the genetic variability in two natural populations ofCalophyllum brasilienselocated along two different rivers in the state of Minas Gerais, Brazil, using RAPD molecular markers. Eighty-two polymorphic fragments were amplified using 27 primers. The values obtained for Shannon index (I) were 0.513 and 0.530 for the populations located on the margins of the Rio Grande and Rio das Mortes, respectively, demonstrating the high genetic diversity in the studied populations. Nei’s genetic diversity (He) was 0.341 for the Rio Grande population and 0.357 for the Rio das Mortes population. These results were not significantly different between populations and suggest a large proportion of heterozygote individuals within both populations. AMOVA showed that 70.42% of the genetic variability is found within populations and 29.58% is found among populations (ФST=0.2958). The analysis of kinship coefficients detected the existence of family structures in both populations. Average kinship coefficients between neighboring individuals were 0.053 (P<0.001) in Rio das Mortes and 0.040 (P<0.001) in Rio Grande. This could be due to restricted pollen and seed dispersal and the history of anthropogenic disturbance in the area. These factors are likely to contribute to the relatedness observed among these genotypes.

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The Genetic Diversity and Geographic Differentiation of the Wild Soybean in Northeast China Based on Nuclear Microsatellite Variation

International Journal of Genomics ◽

10.1155/2018/8561458 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9

Author(s):

Hongkun Zhao ◽

Yumin Wang ◽

Fu Xing ◽

Xiaodong Liu ◽

Cuiping Yuan ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Northeast China ◽

Wild Soybean ◽

Population Level ◽

Mantel Test ◽

Microsatellite Variation ◽

Information Index ◽

Ssr Loci ◽

The Mean

In this study, the genetic diversity and population structure of 205 wild soybean core collections in Northeast China from nine latitude populations and nine longitude populations were evaluated using SSR markers. A total of 973 alleles were detected by 43 SSR loci, and the average number of alleles per locus was 22.628. The mean Shannon information index (I) and the mean expected heterozygosity were 2.528 and 0.879, respectively. At the population level, the regions of 42°N and 124°E had the highest genetic diversity among all latitudes and longitudes. The greater the difference in latitude was, the greater the genetic distance was, whereas a similar trend was not found in longitude populations. Three main clusters (1N, <41°N-42°N; 2N, 43°N-44°N; and 3N, 45°N–>49°N) were assigned to populations. AMOVA analysis showed that the genetic differentiation among latitude and longitude populations was 0.088 and 0.058, respectively, and the majority of genetic variation occurred within populations. The Mantel test revealed that genetic distance was significantly correlated with geographical distance (r=0.207, p<0.05). Furthermore, spatial autocorrelation analysis showed that there was a spatial structure (ω=119.58, p<0.01) and the correlation coefficient (r) decreased as distance increased within a radius of 250 km.

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Environmental and genetic influences on phenology and plant size in a perennial herb, Senecio integrifolius

Canadian Journal of Botany ◽

10.1139/b91-029 ◽

1991 ◽

Vol 69 (1) ◽

pp. 209-217 ◽

Cited By ~ 18

Author(s):

Björn Widén

Keyword(s):

Natural Population ◽

Rank Order ◽

Natural Populations ◽

Flowering Phenology ◽

Plant Size ◽

Genetic Influences ◽

Perennial Herb ◽

Cultivated Plants ◽

Mother Plants ◽

Progeny Size

Individual plants of the perennial herb Senecio integrifolius showed a highly significant correlation between rank order of the dates of first flowering and of first fruiting in a natural population and in cultivation. Plants exposed to full sunshine were smaller and flowered earlier than shaded plants both in a natural population and in cultivation. Within the two groups, plants with large inflorescences started to flower first. Duration of flowering was regulated by the size of the inflorescence; plants with many heads flowered longer than plants with few heads. There was a significant correlation between phenological rank order of mother plants in natural populations and their progenies in cultivation, but no consistent relationship between mother size and progeny size was found. Cultivated plants were consistent in rank order of flowering and in size over the years. Key words: flowering phenology, plant size, genetic variation, Senecio.

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

PeerJ ◽

10.7717/peerj.10327 ◽

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.

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