Analysis of genetic diversity of ancient Ginkgo populations using SSR markers

Zhou, Qi; Mu, Kemin; Ni, Zhouxian; Liu, Xinhong; Li, Yingang; Li, Xu

doi:10.1016/j.indcrop.2019.111942

Cited by 46 publications

(31 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The evolutionary potential of a species and its ability to withstand adverse environments depend on both genetic diversity of the species and its population genetic structure (Stebbins, 1950). Different levels of genetic variation and genetic structure of populations can be attributed to multiple factors, such as distribution ranges, life forms, breeding systems, seed dispersal mechanisms, evolutionary history, natural selection, and human interference (Hamrick and Godt, 1996;Sarin et al, 2015;Zhou et al, 2020). In general, the genetic diversity of widespread plant species is higher than that of narrowly distributed species (Hamrick and Godt, 1996), and compared to annual and perennial herbaceous plants, perennial woody plants tend to have higher genetic diversity at the species level and within Alt, altitude as environmental distance measured as Euclidean distance; Geo, geographic distance; Pre, precipitation as environmental distance measured as Euclidean distance using seven precipitation-related bioclimatic variables shown in Figure 3; Na, average number of alleles; He, expected heterozygosity; I, Shannon's information index.…”

Section: High Genetic Diversity Within Populations and Low Genetic DImentioning

confidence: 99%

“…Therefore, the protection and maintenance of genetic diversity has important theoretical and practical implications for the protection and utilization of plant resources and genetic improvement of forest tree species. The genetic diversity and structure of populations or species can be attributed to multiple factors, such as distribution ranges, life forms, breeding systems, seed dispersal mechanisms, evolutionary history, climate factors, and human interference (overexploitation, overgrazing, landslides, and fragmentation) (Hamrick and Godt, 1996;Sarin et al, 2015;Gaisberger et al, 2020;Zhou et al, 2020). Identifying climatic factors affecting genetic diversity may provide insights into genetic conservation of species in the context of rapid global climate change.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas

Liu

Wan

et al. 2020

Front. Plant Sci.

View full text Add to dashboard Cite

Phyllanthus emblica L. is a well-known medicinal and edible plant species. Various medicinal compounds in the fruit make it an important medicinal and promising economic material. The plant is widely distributed in Southwestern and Southern China. However, due to massive deforestation and land reclamation as well as deterioration of its natural habitat in recent years, the wild resources of this species have been sharply reduced, and it is rare to see large-scale wild P. emblica forests so far. In order to effectively protect and rationally utilize this species, we investigated the genetic diversity, genetic structure, and population dynamics of 260 individuals from 10 populations of P. emblica sampled from the dry climate area in Yunnan and wet climate area in Guangxi using 20 polymorphic EST-SSR markers. We found high genetic diversity at the species level (He = 0.796) and within populations (He = 0.792), but low genetic differentiation among populations (FST = 0.084). In addition, most genetic variation existed within populations (92.44%) compared with variation among the populations (7.56%). Meanwhile, the NJ tree, STRUCTURE, and hierarchical analysis suggested that the sampled individuals were clustered into two distinct genetic groups. In contrast, the genetic diversity of the dry climate group (He = 0.786, Na = 11.790, I = 1.962) was higher than that of the wet climate group (He = 0.673, Na = 9.060, I = 1.555), which might be attributed to the combined effects of altitude, precipitation, and geographic distance. Interestingly, only altitude and precipitation had significant pure effects on the genetic diversity, and the former was slightly stronger. In addition, DIYABC analysis suggested the effective population size of P. emblica might have contracted in the beginning of the Last Glacial Maximum. These genetic features provided vital information for the conservation and sustainable development of genetic resources of P. emblica, and they also provided new insights and guidelines for ecological restoration and economic development in dry-hot valleys of Yunnan and karst areas in Guangxi.

show abstract

Section: High Genetic Diversity Within Populations and Low Genetic DImentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas

Liu

Wan

et al. 2020

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…These effects could also be confirmed for the population genetic structure, which was investigated by STRUCTURE. Arthofer et al demonstrate that the population structure was still retained, though about a quarter of a individuals cannot be correctly assigned, when using only two loci with the Arwere 12.94 and 13.54, , respectively 5 , which were much larger than the average Ar of microsatellite sites in the other study 25 – 27 . Thus, it is difficult to de novo develop microsatellite primers with such high polymorphism.…”

Section: Discussionmentioning

confidence: 92%

Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species

Wang

Yang

Wang

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Microsatellites (simple sequence repeats, SSRs) are co-dominant nuclear markers that are widely used in population genetic studies. Population genetic parameters from different studies might be significantly influenced by differences in marker number. In our study, 265 sequences with polymorphic microsatellites were obtained from SLAF-seq data. Then, subpopulations containing different numbers (5, 6, 7,…, 15, 20, 25, 30, 35, 40) of markers were genotyped 10 times to investigate the impact of marker numbers on population genetic diversity results. Our results show that genotyping with less than 11 or 12 microsatellite markers lead to significant deviations in the population genetic diversity or genetic structure results. In order to provide markers for population genetic and conservation studies for Rhododendron, 26 SSR primers were designed and validated in three species.

show abstract

“…var. jujuba) (Jin et al 2016;Duan et al 2017;Xu et al 2016;Zhou et al 2020) including R. pseudoacacia L. (Fabaceae; black locust) (Guo et al 2017(Guo et al , 2018Dong et al 2019a, b).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of Robinia pseudoacacia from six improved variety bases in China as revealed by simple sequence repeat markers

et al. 2021

View full text Add to dashboard Cite

Robinia pseudoacacia is an important afforestation tree introduced to China in 1878. In the present study, we examined the genetic diversity among 687 strains representing four improved varieties and two secondary provenances, comprising 641 clones and 46 seedlings. Ninety-one simple sequence repeats (SSRs) were selected through segregation analysis and polymorphism characterization, and all sampled individuals were genotyped using well-characterized SSR markers. After excluding loci with non-neutral equilibrium, missing locus data and null alleles, we used 36 primer pairs to assess the genetic diversity of these germplasm resources, revealing vast genetic differentiation among the samples, with an average of 8.352 alleles per locus and a mean Shannon′s index of 1.302. At the population level, the partitioning of variability was assessed using analysis of molecular variance, which revealed 93% and 7% variation within and among collection sites, respectively. Four clusters were detected using structure analysis, indicating a degree of genetic differentiation among the six populations. Insights into the genetic diversity and structure of R. pseudoacacia provide a theoretical basis for the conservation, breeding and sustainable development in China.

show abstract

Analysis of genetic diversity of ancient Ginkgo populations using SSR markers

Cited by 46 publications

References 32 publications

Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas

Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas

Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species

Genetic diversity and population structure of Robinia pseudoacacia from six improved variety bases in China as revealed by simple sequence repeat markers

Contact Info

Product

Resources

About