Research

13 pages, 3111 KiB

Open AccessArticle

Joint Identification and Application of Microsatellite Markers in Genetic Diversity Study of Closely Related Species Teucrium montanum, T. capitatum and Their Natural Hybrid

by Filip Varga, Zlatko Liber, Ante Turudić, Jernej Jakše, Lea Juzbašić, Nina Jeran, Martina Grdiša, Miloš Zbiljić and Zlatko Šatović

Diversity 2024, 16(4), 206; https://doi.org/10.3390/d16040206 - 28 Mar 2024

Viewed by 672

Abstract

Teucrium montanum L. and T. capitatum L. are two plant species with overlapping distribution in the Balkan Peninsula, especially in Croatia, where several occurrences of their putative hybrid species T. × rohlenae have been recorded. Next-generation sequencing of both species and de novo [...] Read more.

Teucrium montanum L. and T. capitatum L. are two plant species with overlapping distribution in the Balkan Peninsula, especially in Croatia, where several occurrences of their putative hybrid species T. × rohlenae have been recorded. Next-generation sequencing of both species and de novo assembly was carried out resulting in 120 contigs for T. montanum and 1685 contigs for T. capitatum assembled. The Dig-up primers pipeline was used for SSR mining of both assemblies, applying different criteria that resulted in 112 SSR candidates for testing. A subset of 41 SSRs was selected and after two rounds of testing, twelve SSRs were developed and characterized. A total of 232 alleles were detected with 5 to 29 alleles per locus, based on the test sample. The genetic diversity analysis of three Teucrium taxa from a single location revealed a higher level of diversity in T. montanum than in T. capitatum with intermediate values for the hybrid species. The NeighborNet diagram and genetic structure analysis grouped the taxa into two separate clusters, the first of which consisted exclusively of T. montanum, while the other was composed of intermixed T. capitatum and T. × rohlenae individuals. The availability of SSR markers for two Teucrium taxa will allow in-depth analysis of genetic diversity and structure, as well as molecular identification of their putative hybrids in the future. Full article

(This article belongs to the Special Issue Population Genetics of Animals and Plants)

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18 pages, 2343 KiB

Open AccessArticle

Genetic Variation among Aeluropus lagopoides Populations Growing in Different Saline Regions

by Basharat A. Dar, Abdullah A. Al-Doss, Abdulaziz M. Assaeed, Muhammad M. Javed, Abdelhalim I. Ghazy, Saud L. Al-Rowaily and Ahmed M. Abd-ElGawad

Diversity 2024, 16(1), 59; https://doi.org/10.3390/d16010059 - 16 Jan 2024

Viewed by 793

Abstract

Aeluropus lagopoides is a halophytic grass growing in different sabkhas of Saudi Arabia. In this study, 14 inter-simple sequence repeat (ISSR) and 15 sequence-related amplified polymorphism (SRAP) molecular markers were selected to investigate the genetic diversity within and among five natural populations of [...] Read more.

Aeluropus lagopoides is a halophytic grass growing in different sabkhas of Saudi Arabia. In this study, 14 inter-simple sequence repeat (ISSR) and 15 sequence-related amplified polymorphism (SRAP) molecular markers were selected to investigate the genetic diversity within and among five natural populations of A. Lagopiodes. The genetic diversity varied within and among populations. ISSR markers were slightly more efficient than SRAP markers in evaluating genetic diversity. Average polymorphism information content, effective number of alleles, Nei’s genetic diversity, and Shannon’s information index values of ISSR markers were higher than SRAP. Analysis of molecular variance revealed about 40% genetic variation among the population and 60% within the population. Overall, the genetic diversity was lowest in Jouf (40%), while the Qaseem populations were the highest (60%). Jizan populations were highly dissimilar to other regions. A Mantel test indicated a positive correlation between geographic and genetic distance. The cluster analysis showed three groups; the first group comprises Jouf and Salwa populations, the second group comprises Qareenah and Qaseem, and the third group comprises the Jizan population. This observation matched the geographic distribution of the species. These findings can help in the conservation of a diverse population of A. lagopoides in saline regions as well as rehabilitation of these degraded unique habitats. Full article

(This article belongs to the Special Issue Population Genetics of Animals and Plants)

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15 pages, 2399 KiB

Open AccessArticle

Exploring the Genetic Diversity and Population Structure of Daphnia cucullata Sars, 1862 in Boreal Lakes (Latvian Lakeland) Based on Microsatellites

by Aija Brakovska and Nataļja Škute

Diversity 2023, 15(11), 1128; https://doi.org/10.3390/d15111128 - 31 Oct 2023

Viewed by 880

Abstract

We have used Daphnia cucullata (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most [...] Read more.

We have used Daphnia cucullata (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most appropriate microsatellite markers for future genetic studies of Daphnia cucullata populations of lakes Svente, Riča, Dridzis and Geraņimovas-Ilzas in the Boreal biogeographical region. Based on these microsatellite markers, we determined the genetic diversity of these populations. The loci Dgm105 and Dgm101 had the maximum number of alleles and the maximum number of private alleles. The specific locus Dgm105 had five private alleles (62% of all detected alleles), and locus Dgm101 had four private alleles (57% of all detected alleles) in these loci. We determined the observed heterozygosity (H_obs) and the expected heterozygosity (H_exp) level (via Hardy–Weinberg equilibrium), the number of polymorphic loci, the number of detected alleles in each analyzed microsatellite locus, the average number of alleles at the locus (N_a), the average effective number of alleles at the locus (N_e), the F_ST of the population’s genetic differentiation, the genetic distance (D) (following Nei) and the significance (χ²-test) of differences between the levels of observed and expected heterozygosity. It was shown that Daphnia cucullata populations from lakes with a low number of zooplankton taxa (Riča and Geraņimovas-Ilzas) have a higher genetic diversity compared to lakes with a high number of zooplankton taxa (Dridzis and Svente). It was found that Daphnia cucullata populations from lakes Dridzis and Svente have the least genetic distance, and these populations form a single genetic group, as confirmed via clustering. Full article

(This article belongs to the Special Issue Population Genetics of Animals and Plants)

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16 pages, 2808 KiB

Open AccessArticle

Assessment of Anthropogenic Impacts on the Genetic Diversity of Phragmites australis in Small-River Habitats

by Jolanta Patamsytė, Carla Lambertini, Jurgita Butkuvienė, Donatas Naugžemys and Donatas Žvingila

Diversity 2023, 15(11), 1116; https://doi.org/10.3390/d15111116 - 26 Oct 2023

Viewed by 873

Abstract

Common reed is often used as a model plant to study the anthropogenic impacts on ecosystems at local and global scales. As a community-forming species, it is directly exposed to the impacts of human activities on the ecosystem. The aim of our study [...] Read more.

Common reed is often used as a model plant to study the anthropogenic impacts on ecosystems at local and global scales. As a community-forming species, it is directly exposed to the impacts of human activities on the ecosystem. The aim of our study was to evaluate the patterns of genetic diversity in common reed stands located in habitats that are differently affected by anthropogenic factors. We studied whether riverbed modifications, land cover in the neighborhood of the stand and the chemical and physical parameters of the river water affect the genetic diversity of P. australis at the studied sites. Using DNA fingerprinting, we genotyped 747 plants from 42 sites located in 16 small Lithuanian rivers. Bayesian clustering and principal coordinate analysis revealed two main gene pools at the population (river) level. At the site level (i.e., considering all sites independently of their rivers), polymorphism was high even between sites in the same river. Our study revealed a negative relationship between the concentration of nitrogen compounds and the genotypic richness of P. australis populations. We did not find any correlations between the other chemical parameters of the water and the parameters of the genetic diversity. Additionally, there were no genetic differences between sites in modified and unmodified river sections or between sites that differed in land cover type in the neighborhood of the stand. Full article

(This article belongs to the Special Issue Population Genetics of Animals and Plants)

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13 pages, 1681 KiB

Open AccessArticle

Temporal Variation of Genetic Diversity in Rutilus rutilus Populations from Lithuania Using mtDNA Markers in the Context of Anthropogenic Activities

by Dalius Butkauskas, Ieva Ignatavičienė, Adomas Ragauskas and Vytautas Rakauskas

Diversity 2023, 15(11), 1113; https://doi.org/10.3390/d15111113 - 26 Oct 2023

Viewed by 868

Abstract

One of the most abundant fish species, Rutilus rutilus, is widely distributed in Lithuania and its potential to adapt to environmental changes attracted our interest. Unfortunately, it is not properly understood how anthropogenic activities can affect the genetic diversity within this species. [...] Read more.

One of the most abundant fish species, Rutilus rutilus, is widely distributed in Lithuania and its potential to adapt to environmental changes attracted our interest. Unfortunately, it is not properly understood how anthropogenic activities can affect the genetic diversity within this species. We studied three populations of roaches (samples collected in the Neris and Žeimena rivers, and Lake Drūkšiai) over a period of five years (from 2017 to 2022) to determine genetic diversity using mtDNA D-loop and ATP6 genetic markers. Genetic diversity parameters, AMOVA analysis, haplotype network, and PCoA analysis revealed a greater genetic variability in roach samples collected in 2017, and the greatest differences were noticed in the population inhabiting Lake Drūkšiai, as compared with other samples studied over a five-year period. Differences in genetic diversity detected after a five-year period led us to the assumption that roach populations may be related to the effects of natural (changing climatic conditions) and anthropogenic (operating nuclear power plant) origin. Full article

(This article belongs to the Special Issue Population Genetics of Animals and Plants)

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14 pages, 4228 KiB

Open AccessArticle

Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (Juglans regia L.) in Middle Asia

by Xuerong Li, Xiyong Wang, Zhijun Cui, Wei Shi, Junhua Huang and Jiancheng Wang

Diversity 2023, 15(10), 1073; https://doi.org/10.3390/d15101073 - 10 Oct 2023

Viewed by 887

Abstract

The common walnut (Juglans regia L.), a species of significant economic and ecological importance, along with its variant, holds developmental value. Simple sequence repeat (SSR) markers are used as an effective method for material identification due to their co-dominant inheritance. In this [...] Read more.

The common walnut (Juglans regia L.), a species of significant economic and ecological importance, along with its variant, holds developmental value. Simple sequence repeat (SSR) markers are used as an effective method for material identification due to their co-dominant inheritance. In this work, a total of 357629 SSR loci were searched based on previously published walnut genome sequences, with a density of 662.28 (SSRs/Mb). The majority of all these loci were found to be single nucleotide A/T (58.49%), followed by the dinucleotide AT (19.48%). Based on the results of genome-wide SSR site design, 22 effective primer pairs were designed and screened to analyze the genetic diversity of 48 wild walnut samples from three countries. Each locus had an average of 5.17 effective alleles (Ne), with an average polymorphism information content (PIC) of 0.71, average heterozygosity (He) of 0.52, and average genetic differentiation index (Fst) of 0.09. The analysis of 48 wild walnut samples from three countries (Kyrgyzstan, Tajikistan, and China) using the unweighted pairwise clustering method and arithmetic mean (UPGMA) along with principal coordinate analysis revealed the division of all samples into three groups. In summary, these novel SSR markers serve as a reference for the identification of wild walnut germplasm in Central Asia and for the development and utilization of wild walnut seed resources. Full article

(This article belongs to the Special Issue Population Genetics of Animals and Plants)

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17 pages, 3209 KiB

Open AccessEditor’s ChoiceArticle

Population Structure and Genetic Diversity of the Spotted Sleeper Odontobutis interrupta (Odontobutidae), a Fish Endemic to Korea

by Kang-Rae Kim, Hee-kyu Choi, Taek Won Lee, Hyuk Je Lee and Jeong-Nam Yu

Diversity 2023, 15(8), 913; https://doi.org/10.3390/d15080913 - 07 Aug 2023

Cited by 2 | Viewed by 1332

Abstract

The spotted sleeper, Odontobutis interrupta, is a fish species endemic to Korea and shows potential as an aquaculture species. Nevertheless, the population size of this species has declined significantly in recent years. To characterize the population structure and genetic diversity of O. [...] Read more.

The spotted sleeper, Odontobutis interrupta, is a fish species endemic to Korea and shows potential as an aquaculture species. Nevertheless, the population size of this species has declined significantly in recent years. To characterize the population structure and genetic diversity of O. interrupta in Korea, we analyzed four microsatellite loci in twelve populations from four major river systems. The provenance of the population was investigated to discern the origin of the translocated populations. The genetic diversity of the microsatellite ranged from 0.440 to 0.756, showing a high level of diversity similar to that of other freshwater fishes. However, mitochondrial DNA analysis exhibited low genetic diversity (H_d: 0.000–0.674, π: 0.00000–0.00159). The F_ST values of microsatellites and mitochondrial DNA ranged from 0.096 to 0.498 and −0.046 to 0.951, suggesting genetic admixture among populations. All populations exhibited an effective population size of <100; therefore, preservation efforts to prevent inbreeding depression would be required. The genetic structure could be divided into unique genotypes from the Seomjingang and Geumgang Rivers. However, genetic admixture was observed in all populations, rendering it impossible to distinguish them. Our findings provide fundamental but significant genetic insights pursuant to devising conservation strategies for O. interrupta. Full article

(This article belongs to the Special Issue Population Genetics of Animals and Plants)

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14 pages, 3620 KiB

Open AccessArticle

Genetic Variation and Evolutionary History of the Threatened Dipterocarpus turbinatus C.F.Gaertn. Detected Using Microsatellites

by Nguyen Minh Duc, Nguyen Huy Hoang, Tran Thi Huong Giang, Nguyen Thi Thuy Huong, Vu Dinh Duy, Nguyen Phan Lan Hong, Truong Ngoc Minh and Nguyen Minh Tam

Diversity 2023, 15(8), 894; https://doi.org/10.3390/d15080894 - 28 Jul 2023

Cited by 1 | Viewed by 779

Abstract

Dipterocarpus turbinatus C.F.Gaertn. is a valuable timber tree indigenous to the lowland tropical forests of southern and central Vietnam. It is in danger of extinction due to fragmented habitats and overexploitation. Therefore, assessing the genetic diversity and demographic history of this species is [...] Read more.

Dipterocarpus turbinatus C.F.Gaertn. is a valuable timber tree indigenous to the lowland tropical forests of southern and central Vietnam. It is in danger of extinction due to fragmented habitats and overexploitation. Therefore, assessing the genetic diversity and demographic history of this species is essential to providing a platform for conservation activities. Herein, we analyzed 281 D. turbinatus trees from 10 populations representing their natural distribution range in Vietnam using nine polymorphic microsatellites to provide valuable information for conservation activities. We detected genetic diversity within these populations (0.285 and 0.328 for observed and expected heterozygosity, respectively), as well as population genetic differentiation (a Wei and Cockerham value of 0.202 and a Hedrick value of 0.32). Clustering analysis based on different approaches revealed three genetic clusters which were significantly correlated to gene flow across the geographic distribution range of D. turbinatus in tropical evergreen forests. Approximate Bayesian computation suggested that the D. turbinatus populations had an evolutionary history consistent with divergence during the last glacial maximum. Based on our results, we recommend the in situ conservation of several populations with high genetic diversity, high allelic richness, or private alleles, and the gathering of the seeds of the remaining populations for ex situ conservation. Full article

(This article belongs to the Special Issue Population Genetics of Animals and Plants)

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