scholarly journals Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 940 ◽  
Author(s):  
Alexandra S. Abdelmanova ◽  
Veronika R. Kharzinova ◽  
Valeria V. Volkova ◽  
Arina I. Mishina ◽  
Arsen V. Dotsev ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Average Frequency ◽  
Genetic Distances ◽  
Drop Out ◽  
Cattle Breeds ◽  
Polymorphic Microsatellite ◽  
Consensus Genotypes ◽  
The 19Th Century ◽  
Allelic Drop Out ◽  
Historical Samples

Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r2 = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of FST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.

COMPARATIVE STUDY OF THE GENOMIC ARCHITECTURE OF MODERN AND HISTORICAL SAMPLES OF TWO RUSSIAN CATTLE BREEDS

2021 ◽  
Vol 1 (19) ◽  
pp. 338-340
Author(s):  
A.S. Abdelmanova ◽  
A.V. Dotsev ◽  
V.R. Kharzinova ◽  
O.I. Boronetskaya ◽  
A.A. Sermyagin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Comparative Study ◽  
Cattle Breeds ◽  
Genomic Architecture ◽  
Genome Wide ◽  
Historical Samples

Based on the analysis of genome-wide SNP genotypes, a study of the genetic diversity and genetic structure of modern and historical samples of cattle of the Kholmogor and Yaroslavl breeds was performed. The preservation of historical genomic components in modern representatives of breeds is shown.

scholarly journals Genetic variability of dairy cattle breeds in Lithuania

Biologija ◽  
2021 ◽  
Vol 67 (3) ◽  
Author(s):  
Romualdas Lapickis ◽  
Loreta Griciuvienė ◽  
Asta Aleksandravičienė ◽  
Indrė Lipatova ◽  
Algimantas Paulauskas
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Dairy Cattle ◽  
Genetic Material ◽  
Genetic Distances ◽  
Principal Coordinates Analysis ◽  
Black And White ◽  
Cattle Breeds ◽  
Principal Coordinates ◽  
High Degree

Large numbers of different scientific studies are conducted to preserve the breeds and improve the existing ones by introducing the variability of the plate genes, which best shows the phenotypic characteristics that can improve the health of dairy cattle and the quality of their production. The main purpose of this study was to perform an analysis of genetic variability of Lithuanian cattle breeds. Three subpopulation groups were studied: Lithuanian Black and White (95 individuals), Lithuanian Red (49), and Lithuanian White and Red (48). Bovine genetic material was genotyped using a total of 11 fluorescent microsatellite primers to estimate genetic variability. All loci presented a high degree of polymorphism and a total of 292 different alleles (Na) were detected. Thirty-two private alleles were detected in all evaluated subpopulations. After completing pairwise population assignment, which is based on the distribution of allelic frequencies, three populations showed the tendency to group into three separate clusters. However, the performed Principal Coordinates Analysis (PCoA), which is based on genetic distances, showed no anticipated clear grouping. Bayesian structure analysis revealed three genetic clusters. Analysis of FST (0.001–0.027) and Nei genetic distance (0.029–0.084) revealed that the genetic diversity of inter subpopulation in cattle groups was estimated to be lower than the genetic diversity of intra subpopulation.

Genetic diversity between Italian and Greek buffalo populations

2001 ◽  
Vol 29 ◽  
pp. 31-40 ◽  
Author(s):  
B. Moioli ◽  
A. Georgoudis ◽  
F. Napolitano ◽  
G. Catillo ◽  
S. Lucioli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Distances ◽  
Allele Frequency Distribution ◽  
Average Gene Diversity ◽  
Polymorphic Microsatellite ◽  
Average Gene ◽  
Degree Of Differentiation ◽  
Two Populations ◽  
Global Project

SummaryThe present study is a first step of a global project aiming at the estimation of the genetic distances and relationships among buffalo breeds and sub-populations and the investigation of the production potential and adaptability of different buffalo genotypes in various environments.Genetic diversity of Italian and Greek buffalo populations was estimated on the basis of allele frequencies at nine polymorphic microsatellite loci: CSSM43, CSSM38, DRB3, D21S4, CYP21, CSSM47, CSSM60, CSSM36 and CSSM33. The number of detected alleles per locus varied from two (D21S4) to thirteen (CSSM47). Allele frequency distribution was similar in the two populations, which have the same alleles at the highest frequency at all loci, except loci CSSM47 and CSSM60. Average gene diversity over all loci was 0.60. Across-loci average gene diversity increased with the number of alleles. Observed average heterozygosity was 0.167 and 0.177 in the Italian and Greek populations, respectively. The degree of differentiation between Italian and Greek buffalo was moderate and estimated at 0.021 ± 0.009.

scholarly journals Comparative Study of the Genetic Diversity of Local Steppe Cattle Breeds from Russia, Kazakhstan and Kyrgyzstan by Microsatellite Analysis of Museum and Modern Samples

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 351
Author(s):  
Alexandra S. Abdelmanova ◽  
Veronika R. Kharzinova ◽  
Valeria V. Volkova ◽  
Arsen V. Dotsev ◽  
Alexander A. Sermyagin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Genetic ◽  
Microsatellite Analysis ◽  
Molecular Genetic Study ◽  
Cattle Breeds ◽  
Genetic Components ◽  
Museum Samples ◽  
Consensus Genotypes ◽  
Selection Of ◽  
Allele Pool

The comparative molecular genetic study of museum and modern representatives of cattle breeds can help to elucidate the origin and maintenance of historical genetic components in modern populations. We generated the consensus genotypes for 11 microsatellite loci for 24 museum samples of Kalmyk, Kyrgyz, and Kazakh cattle, dated from the first quarter of the 20th century, and compared them with those of modern Kalmyk, Kyrgyz, and Kazakh white-headed breeds. The level of genetic diversity of the modern Kalmyk and Kyrgyz cattle (uHe = 0.771–0.778) was similar to those observed in the museum samples (uHe = 0.772–0.776), while a visible decrease in genetic variability in the modern Kazakh white-headed breed compared to museum Kazakh cattle was detected (uHe = 0.726 and 0.767, respectively). The PCA plot, FST- and Jost’s D-based networks, and STRUCTURE clustering provided strong evidence of the maintenance of the historical genetic background in modern populations of Kalmyk and Kyrgyz cattle. In spite of the allele pool of Kazakh white-headed cattle having undergone great changes compared to the museum Kazakh cattle, several animals still carry the visible aspect of the historical genetic components. Our results can be used for the selection of individuals for the creation of gene banks and may significantly improve the efficiency of conservation programs aimed at preserving genetic diversity in the national genetic resources of cattle.

PSXII-1 Tracing the historical genetic components in turano-mongolian cattle breeds based on the microsatellite analysis of modern and museum samples

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 253-254
Author(s):  
Alexandra S Abdelmanova ◽  
Veronika R Kharzinova ◽  
Valeria Volkova ◽  
Arsen V Dotsev ◽  
Alexander A Sermyagin ◽  
...  
Keyword(s):  
Genetic Structure ◽  
20Th Century ◽  
Animal Husbandry ◽  
Microsatellite Analysis ◽  
Cattle Breeds ◽  
Genetic Components ◽  
Expected Heterozygosity ◽  
Museum Samples ◽  
Consensus Genotypes ◽  
Historical Samples

Abstract In their centuries-long history, the nomads of the south of Russia developed the local cattle breeds, which are well adapted to the harsh steppe conditions. In 20th century, the population size of such cattle breeds was dramatically decreased. At the same time, intensive cross breeding with high-producing transboundary breeds had been practiced on the small remaining part of population. The aim of our study was to trace the historical genetic components in modern populations of local cattle breeds of the turano-mongolian origin. The historical specimens of Kalmyk (n = 10), Kyrgyz (n = 11) and Kazakh (n = 3) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry and subjected to the study. The modern representatives of Kalmyk (n = 28), Kyrgyz (n = 20), Kazakh White-headed (n = 30), Hereford (n = 26), and Mongolian (n = 41) cattle were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst research Center for Animal Husbandry. The samples were genotyped for 11 microsatellite loci (BM1818, BM2113, BM1824, ETH10, ETH225, INRA023, SPS115, TGLA53, TGLA122, TGLA126, and TGLA227). For historical samples, the PCR reactions were carried out in five replicates to determine the consensus genotypes. In total, 132 alleles were identified, including 97 alleles in historical samples and 124 alleles in modern samples. The values of unbiased expected heterozygosity were 0.767–0.776 and 0.653–0.778 for the historical and modern samples, respectively. The STRUCTURE clustering showed the visible differences in genetic structure between the historical and modern populations of Kalmyk, Kyrgyz and Kazakh cattle breeds; however, the historical genetic components were still maintained in modern representatives of all of studied breeds. The research results will be useful for the sustainable breeding and conservation of valuable local genetic resources. The study was funded by the RSF No. 19-76-20012.

scholarly journals Genetic diversity between seven Central European cattle breeds as revealed by microsatellite analysis

2011 ◽  
Vol 51 (No. 1) ◽  
pp. 1-7 ◽  
Author(s):  
V. Czerneková ◽  
T. Kott ◽  
G. Dudková ◽  
Z. Sztankóová ◽  
J. Soldát
Keyword(s):  
Genetic Distances ◽  
Arithmetic Mean ◽  
Microsatellite Analysis ◽  
Group Method ◽  
Effective Population ◽  
Central European ◽  
Cattle Breeds ◽  
Pair Group ◽  
Polymorphic Microsatellite ◽  
European Cattle

This study compares the genetic variation in seven cattle breeds from theterritory ofCentralEurope. Eleven polymorphic microsatellite loci were used to detect differences in the polymorphism of genetic markers in Czech Pied (Simmental), Slovakian Pied (Simmental), Slovakian Pinzgau,Holstein, Polish Red, German Red, and Czech Red breeds. For these loci, allele frequencies, heterozygosity, polymorphism information content, effective population size, and genetic distances were evaluated. The phylogenetic tree was constructed using the unweighted pair group method with arithmetic mean and it showed that the Central European Red breeds tended to cluster together, whereas theHolstein was the most divergent from the remaining breeds. These data are discussed in the context of the known origin of respective breeds.  

scholarly journals PSXII-27 Microsatellite analysis of the historical and modern populations of the Russian local cattle breeds

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 240-241
Author(s):  
Alexandra Abdelmanova ◽  
Arina I Mishina ◽  
Valeria Volkova ◽  
Arsen V Dotsev ◽  
Alexander A Sermyagin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Climatic Conditions ◽  
Microsatellite Analysis ◽  
Science Center ◽  
Holstein Breed ◽  
Cattle Breeds ◽  
Expected Heterozygosity ◽  
Native Cattle ◽  
Private Alleles ◽  
Historical Samples

Abstract During the last centuries, a variety of cattle breeds adapted to the local climatic conditions have been developed in different countries. However, in the 20th century many of them were replaced by high-producing industrial breeds, which can lead to the losses of biodiversity. Our aim was to estimate the genetic diversity of Russian native cattle breeds based on the analysis of historical (museum) and modern samples. Historical samples were derived from the craniological collection of the Museum of Livestock named after E.F. Liskun (Moscow). Forty-six samples including Kholmogor (n = 18), Yaroslavl (n = 19), Saratov (n = 5), Novgorod (n = 2) and Great Russian cattle (n = 2) were subjected to the study. Holland cattle (n = 3) was additionally included in the study due to their possible contribution in forming Russian cattle breeds. The modern samples were presented by Yaroslavl (n = 62) and Kholmogor (n = 177) breeds, and Holstein breed (n = 158) was used as an outgroup. All of the works with historical samples were carried out in the facility of the L.K. Ernst Federal Science Center dedicated for the work with ancient DNA. Nine microsatellite loci (TGLA227, BM2113, ETH10, SPS115, TGLA122, INRA23, TGLA126, ETH225, and BM1824) were successfully amplificated in all samples. We observed the higher variability in historical samples comparing to modern samples: the values of unbiased expected heterozygosity were 0.65–0.85 and 0.70–0.74; the values of rarified allele richness were 2.72–3.11 and 2.63–2.76, respectively. The total number of private alleles was higher in historical populations (16) comparing to modern ones (12). The genetic relationship between historical and modern populations were evaluated. Our results indicate a decrease in genetic diversity in modern populations and a possible loss of valuable allelic combinations. The research results will be useful for development of comprehensive strategies for the conservation of the Russian native genetic resources of cattle. The study was funded by RSF №19-76-20012.

scholarly journals Stand out from the Crowd: Small-Scale Genetic Structuring in the Endemic Sicilian Pond Turtle

Diversity ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 343
Author(s):  
Luca Vecchioni ◽  
Federico Marrone ◽  
Marco Arculeo ◽  
Uwe Fritz ◽  
Melita Vamberger
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Small Scale ◽  
Moderate Degree ◽  
Geographical Pattern ◽  
Genetic Structuring ◽  
Pond Turtle ◽  
Emys Trinacris ◽  
Polymorphic Microsatellite ◽  
Entire Distribution

The geographical pattern of genetic diversity was investigated in the endemic Sicilian pond turtle Emys trinacris across its entire distribution range, using 16 microsatellite loci. Overall, 245 specimens of E. trinacris were studied, showing high polymorphic microsatellite loci, with allele numbers ranging from 7 to 30. STRUCTURE and GENELAND analyses showed a noteworthy, geographically based structuring of the studied populations in five well-characterized clusters, supported by a moderate degree of genetic diversity (FST values between 0.075 and 0.160). Possible explanations for the genetic fragmentation observed are provided, where both natural and human-mediated habitat fragmentation of the Sicilian wetlands played a major role in this process. Finally, some conservation and management suggestions aimed at preventing the loss of genetic variability of the species are briefly reported, stressing the importance of considering the five detected clusters as independent Management Units.

scholarly journals Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Genetic Resources ◽  
Juglans Regia ◽  
Genetic Distances ◽  
Mean Value ◽  
Central Anatolia ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

scholarly journals Mitochondrial DNA Variation in Peruvian Honey Bee (Apis mellifera L.) Populations Using the tRNAleu-cox2 Intergenic Region

Insects ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 641
Author(s):  
Julio Chávez-Galarza ◽  
Ruth López-Montañez ◽  
Alejandra Jiménez ◽  
Rubén Ferro-Mauricio ◽  
Juan Oré ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Honey Bee ◽  
Intergenic Region ◽  
Current Status ◽  
Dna Variation ◽  
Africanized Honey Bee ◽  
Dna Variations ◽  
The 19Th Century ◽  
Bee Colonies

Mitochondrial DNA variations of Peruvian honey bee populations were surveyed by using the tRNAleu-cox2 intergenic region. Only two studies have characterized these populations, indicating the presence of Africanized honey bee colonies in different regions of Peru and varied levels of Africanization, but the current status of its genetic diversity is unknown. A total of 512 honey bee colonies were sampled from three regions to characterize them. Our results revealed the presence of European and African haplotypes: the African haplotypes identified belong to sub-lineage AI (13) and sub-lineage AIII (03), and the European haplotypes to lineages C (06) and M (02). Of 24 haplotypes identified, 15 new sequences are reported here (11 sub-lineage AI, 2 sub-lineage AIII, and 2 lineage M). Peruvian honey bee populations presented a higher proportion from African than European haplotypes. High proportions of African haplotype were reported for Piura and Junín, unlike Lima, which showed more European haplotypes from lineage C. Few colonies belonging to lineage M would represent accidental purchase or traces of the introduction into Peru in the 19th century.

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