scholarly journals Populations of Transcarpathia and Bukovina on the genetic landscape of surrounding regions

2015 ◽  
Vol 6 (2) ◽  
pp. 133-140
Author(s):  
O. M. Utevska ◽  
M. I. Chukhraeva ◽  
A. T. Agdzhoyan ◽  
L. A. Atramentova ◽  
E. V. Balanovska ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Ethnically Diverse ◽  
Principal Component ◽  
Snp Markers ◽  
East European ◽  
Parental Gene ◽  
Genetic Landscape ◽  
Western Border ◽  
Genetic Specificity ◽  
Major Haplogroups

The territory of present-day Ukraine is subdivided into some regions with specific demographic and politic history. Nevertheless, the corresponding subdivision in genetic structure is not revealed in previous investigations: populations of Ukrainians under study were genetically homogeneous on SNP markers of Y chromosome. In the current investigation we studied the Y-chromosomal genetic structure of Transcarpathia and Bukovina populations. Several factors exist to expect the genetic specificity of these populations. Both ones are placed in the Carpathian foothills, at the south-western border of the Ukrainian area. During the last millennium these territories were the parts of different states and were open for ethnically diverse migrations. It was revealed that the major Y chromosomal haplogroups in Transcarpathia population were R1a1a1*(М198), I2a (Р37.2), R1a1a1g (М458), E1b1b1a1 (M78). The major haplogroups in Bukovina population were I2a (Р37.2), R1a1a1*(М198), R1a1a1g (М458), R1b1b2 (М269), E1b1b1a1 (M78), I1 (М253). The Bukovina population differs from the typical Ukrainian population by higher frequency of I2a (Р37.2) and lower frequency of R1a1a1*(М198). Moreover, this is the only population among ones studied in Ukraine where the most frequent haplogroup is I2a (Р37.2) but not R1a1a1*(М198). Such a deviation can be caused by possible mixing with neighbouring southern groups, and Carpathian mountains were not a border for exchange in this case. Interestingly, the haplogroup N1c (M178) is not revealed in Transcarpathia at all, obviously due to the mountain barrier. It was revealed by principal component analysis that Ukrainians from Transcarpathia and Bukovina despite some specific peculiarities are more similar to other Ukrainian populations than to the surrounding ethnic groups such as Poles, Slovaks, Hungarians, Romanians, Moldavians and Gagauzes. Ukrainians of Transcarpathia and Bukovina form the entire genetic continuum with the whole Ukraine on maps of gene distances, confirming the homogeneity of Ukrainian parental gene pool and it’s differentiation from other groups. After performing the analysis of Y-haplogroup spatial distribution, it is supposed that the northern ridges ofCarpathian mountainsare the East-European barrier decreasing the gene flow. It decreases the spreading of haplogroups N1c (М178) and R1a (М198) southward and movement of E1b (М78), R1b (М269), J (М304) and G (М201) northward. 

scholarly journals High-throughput genotype-based population structure analysis of selected buffalo breeds

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Prakash B Thakor ◽  
Ankit T Hinsu ◽  
Dhruv R Bhatia ◽  
Tejas M Shah ◽  
Nilesh Nayee ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Structure Analysis ◽  
Principal Component ◽  
Snp Markers ◽  
Sequence Information ◽  
Population Structure Analysis ◽  
Geographical Regions ◽  
Indian River ◽  
Single Cluster

Abstract India is considered as the home tract of some of the best buffalo breeds. However, the genetic structure of the Indian river buffalo is poorly understood. Hence, there is a need to characterize the populations and understand the genetic structure of various buffalo breeds for selection and to design breeding strategies. In this study, we have analyzed genetic variability and population structure of seven buffalo breeds from their respective geographical regions using Axiom Buffalo Genotyping Array. Diversity, as measured by expected heterozygosity, ranged from 0.364 in Surti to 0.384 in Murrah breed, and pair-wise FST values revealed the lowest genetic distance between Murrah and Nili-Ravi (0.0022), while the highest between Surti and Pandharpuri (0.030). Principal component analysis and structure analysis unveiled the differentiation of Surti, Pandharpuri, and Jaffarabadi in first two principal components and at K = 4, respectively, while remaining breeds were grouped together as a separate single cluster and admixed. Murrah and Mehsana showed early linkage disequilibrium (LD) decay, while Surti breed showed late decay. In LD blocks to quantitative trait locis (QTLs) concordance analysis, 4.65% of concordance was observed with 873 LD blocks overlapped with 2,330 QTLs. Overall, total 4,090 markers were identified from all LD blocks for six types of traits. Results of this study indicated that these single-nucleotide polymorphism (SNP) markers could differentiate phenotypically distinct breeds like Surti, Pandharpuri, and Jaffarabadi but not others. So, there is a need to develop SNP chip based on SNP markers identified by sequence information of local breeds.

scholarly journals Analysis of the Genetic Structure and Diversity of Upland Cotton Groups in Different Planting Areas Based on SNP Markers

2021 ◽  
Author(s):  
Zeliang Zhang ◽  
Junduo Wang ◽  
Zhaolong Gong ◽  
Yajun Liang ◽  
Xiantao Ai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Gossypium Hirsutum ◽  
Diversity Index ◽  
Principal Component ◽  
Snp Markers ◽  
High Genetic Diversity ◽  
Origin And Evolution ◽  
Population Structure Analysis ◽  
Genetic Structure And Diversity

Genetic diversity, kinship and population genetic structure analyses of Gossypium hirsutum germplasm can provide a better understanding of the origin and evolution of G. hirsutum biodiversity. In this study, 1313331 SNP molecular markers were used to construct a phylogenetic tree of each sample using MEGAX, to perform population structure analysis by ADMIXTURE software and principal component analysis (PCA) by EIGENSOFT software, and to estimate relatedness using SPAGeDi. ADMIXTURE software divided the experimental cotton population into 16 subgroups, and the Gossypium hirsutum samples could be roughly clustered according to source place, but there were some overlapping characteristics among samples. The experimental cotton population was divided into six groups according to source to calculate the genetic diversity index (H), and the obtained value (0.306) was close to that for germplasm collected by others in China. Cluster 4 had a relatively high genetic diversity level (0.390). The degrees of genetic differentiation within the experimental cotton population groups were low (the population differentiation indexes ranged from 0.02368 to 0.10664). The genetic distance among cotton accessions varied from 0.000332651 to 0.562664014, with an average of 0.25240429. The results of this study may provide a basis for mining elite alleles and using them for subsequent association analysis.

Segmental Volatility in Ethnically Divided Societies: (Re)assessing Party System Stability in Southeast Europe

2021 ◽  
pp. 1-19
Author(s):  
Damir Kapidžić ◽  
Olivera Komar
Keyword(s):  
Ethnic Identity ◽  
Party System ◽  
Ethnically Diverse ◽  
Party Systems ◽  
System Stability ◽  
Southeast Europe ◽  
East European ◽  
Ethnic Parties ◽  
Stabilizing Factors

Abstract This article examines the role of ethnicity and ethnic parties as stabilizing factors in Southeast European party systems. It compares two ethnically divided countries in Southeast Europe: Bosnia and Herzegovina, where ethnic identities that form the political cleavage are firm, and Montenegro, where they are malleable. Theoretically, it addresses the debate between scholars who either find stability or instability in East European post-communist party systems. The article traces the role of ethnicity in the formation and development of electoral contests and compares the two cases by utilizing measures of block volatility, based on analysis of official electoral data. We argue that party systems in ethnically diverse countries are stable at the subsystems level, but unstable within them. In BiH, firm ethnic identity stabilizes the party system by limiting competition between blocks, leading to closure. Malleable ethnic identity in Montenegro opens competition to non-ethnic parties seeking to bridge ethnic divisions, leading to more instability. We find that party system dynamics in ethnically divided new democracies depend on identity rigidity and cleavage salience, in addition to levels of heterogeneity.

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 Genetic diversity and population structure among goat genotypes in Kenya

2020 ◽  
Author(s):  
Ruth W. Waineina ◽  
Kiplangat Ngeno ◽  
Tobias O. Otieno ◽  
Evans D. Ilatsia
Keyword(s):  
Population Structure ◽  
Principal Component ◽  
Genetic Distances ◽  
Snp Markers ◽  
Founder Population ◽  
Good Opportunity ◽  
Model Based Clustering ◽  
Population Structuring ◽  
Improvement Programs ◽  
Genotype Clustering

AbstractPopulation structure and relationship information among goats is critical for genetic improvement, utilization and conservation. This study explored population structure and level of gene intermixing among four goat genotypes in Kenya: Alpine (n = 30), Toggenburg (n = 28), Saanen (n = 24) and Galla (n = 12). The population structuring and relatedness were estimated using principal component analysis utilizing allele frequencies of the SNP markers. Genotype relationships were evaluated based on the calculated Reynolds genetic distances. A phylogenetic tree was constructed to represent genotype clustering using iTOL software. Population structure was investigated using model-based clustering (ADMIXTURE) Genotypes relationships revealed four distinctive clusters: Alpine, Galla, Saanen and Toggenburg. The ADMIXTURE results revealed some level of gene intermixing among Alpine, Toggenburg and Saanen with Galla. Saanen goats were the most admixed genotype with 84%, 7% and 4% of its genome derived from Galla, Alpine and Toggenburg respectively. Alpine and Toggenburg goats shared some associations with the Galla goat; 10% and 1% respectively. The association of Galla with other genotypes was anticipated since Galla goat was used as the founder population for crossbreeding with Saanen, Alpine and Toggenburg breed. The genetic variations among the goat genotypes observed, will provide a good opportunity for sustainable utilization, conservation and future genetic resource improvement programs in goat genotypes in Kenya.

Cryptic Lineages and a Population Dammed to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish

2019 ◽  
Vol 110 (5) ◽  
pp. 535-547 ◽  
Author(s):  
Amanda S Ackiss ◽  
Binh T Dang ◽  
Christopher E Bird ◽  
Ellen E Biesack ◽  
Phen Chheng ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Natural Populations ◽  
Principal Component ◽  
Flood Pulse ◽  
Mekong River ◽  
Effective Population ◽  
Long Distance ◽  
Genetic Lineages ◽  
Low Genetic Diversity ◽  
Population Size Estimates

Abstract An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller subpopulations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development—the Mekong River basin. Our results revealed the presence of 2 highly divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal component analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically important resources.

Identification of molecular markers for starch content in barley (Hordeum vulgare L.) by genome-wide association studies based on bulked samples

2020 ◽  
Vol 18 (3) ◽  
pp. 111-119
Author(s):  
Yinghu Zhang ◽  
Haiye Luan ◽  
Hui Zang ◽  
Hongyan Yang ◽  
Xiao Xu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Association Studies ◽  
Starch Content ◽  
Principal Component ◽  
Mixed Linear Model ◽  
High Linkage Disequilibrium ◽  
Snp Markers ◽  
Genome Wide Association Studies ◽  
Hordeum Vulgare L ◽  
Growing Seasons

AbstractStarch content is an important trait in barley. To evaluate the genetic diversity and identify molecular markers of starch content in barley, 40 cultivated barley genotypes collected from different regions, including genotypes whose starch content is at either the high or low end of the spectrum (15), were used in this study. All the genotypes were re-sequenced by the double-digest-restriction associated DNA sequencing method, and a total of 299,103 single-nucleotide polymorphism (SNP) markers were obtained. The genotypes were divided into four sub-populations based on FASTSTRUCTURE, principal component analysis and neighbour-joining tree analysis. All four sub-populations had a high linkage disequilibrium, especially group 3, whose members were recently bred for malting in the Jiangsu coastal area. The starch content of the barley lines was evaluated during three growing seasons (2014–2017), and the average values of starch content across the three growing seasons at the low and high ends were 51.5 and 55.0%, respectively. The starch content was affected by population structure, the barley in group 2 had a low starch content, while the barley in group 4 had a high starch content. Twenty-six SNP markers were identified as being significantly associated with starch content (P ⩽ 0.001) based on the average values across the three growing seasons using the mixed linear model method. These SNP markers were located on chromosomes 1H and 4H, and were considered loci of qSC1-1 and qSC4-1, respectively. The major identified QTLs for starch content are helpful for further research on carbohydrates and for barley breeding.

scholarly journals Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1190 ◽  
Author(s):  
Eunju Seo ◽  
Kipoong Kim ◽  
Tae-Hwan Jun ◽  
Jinsil Choi ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Principal Component ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Useful Knowledge ◽  
Population Structure Analysis ◽  
Group 3 ◽  
Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

scholarly journals Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris rarus) in a Successive Generation Closed Colony

Diversity ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 483
Author(s):  
Lei Cai ◽  
Miaomiao Hou ◽  
Chunsen Xu ◽  
Zhijun Xia ◽  
Jianwei Wang
Keyword(s):  
Genetic Structure ◽  
Snp Markers ◽  
Dynamic Changes ◽  
Single Nucleotide ◽  
Gobiocypris Rarus ◽  
Rare Minnow ◽  
Genetic Diversity And Structure ◽  
Closed Colony ◽  
Successive Generations ◽  
F Statistics

The complex genetic architecture of closed colonies during successive passages poses a significant challenge in the understanding of the genetic background. Research on the dynamic changes in genetic structure for the establishment of a new closed colony is limited. In this study, we developed 51 single nucleotide polymorphism (SNP) markers for the rare minnow (Gobiocypris rarus) and conducted genetic diversity and structure analyses in five successive generations of a closed colony using 20 SNPs. The range of mean Ho and He in five generations was 0.4547–0.4983 and 0.4445–0.4644, respectively. No significant differences were observed in the Ne, Ho, and He (p > 0.05) between the five closed colony generations, indicating well-maintained heterozygosity. The F-statistics analysis revealed a relatively stable genetic structure of the closed colony. Furthermore, the genetic distance between the newer and older generations increased with the breeding generations in closed colonies. Our results confirmed previous findings in the same samples using microsatellite markers. The results will be beneficial for establishing genetic variability monitoring criteria and restoration of the wild population of the rare minnow and other laboratory fish.

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