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

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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 ◽

10.3390/d13080351 ◽

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.

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

Journal of Animal Science ◽

10.1093/jas/skaa278.438 ◽

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.

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Genetic structure of the Southern meat cattle breed based on microsatellite markers

Scientific Messenger of LNU of Veterinary Medicine and Biotechnologies ◽

10.32718/nvlvet-a9104 ◽

2019 ◽

Vol 21 (91) ◽

pp. 21-28

Author(s):

A. S. Kramarenko

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Microsatellite Markers ◽

Bos Taurus ◽

Bos Indicus ◽

Cattle Breed ◽

Animal Husbandry ◽

State Enterprise ◽

Tissue Samples ◽

Cattle Breeds

The Southern Meat cattle is a composite breed developed by crossing Cuban zebu (Bos indicus) with different cattle breeds (Bos taurus) – local the Red Steppe, Hereford, Charolais, Santa Gertrudis, Dairy Shorthorn. Genetic structure of the Southern meat cattle breed from the State Enterprise Experimental Farm “Askaniyske” NAAS Ukraine (Kherson region) were investigated based on the microsatellite DNA loci. Analysis included 192 animals. A panel of 12 bovine-speciﬁc microsatellite markers (TGLA227, BM2113, TGLA53, ETH10, SPS115, TGLA122, INRA23, TGLA126, BM1818, ETH3, ETH225 and BM1824), recommended of the ISAG for cattle genetic diversity studies, was selected for genetic characterization and revealing the extent of genetic diversity in the Southern Meat cattle breed. Genomic DNA was extracted from tissue samples using Nexttec column (Nexttec Biotechnology GmbH, Germany) following the manufacturer's instructions. All laboratory tests were conducted in the laboratory of Molecular Genetics, Animal Center of Biotechnology and Molecular Diagnostics, All-Russian Research Institute for Animal Husbandry named after academy member L.K. Ernst. We report the distribution and the frequency of a taurine and an indicine specific alleles in the Southern Meat cattle breed using literature data about the Zebu and different cattle breeds genetic structure based on microsatellite loci from our list. It can be assumed that the TGLA22777, BM2113141-143, ETH10209-211, TGLA122149, INRA23194-198, TGLA126123, ETH225156-158-160 alleles among the Southern Meat cattle breed examined individuals were inherited from a B. indicus ancestor. On the other hand, the TGLA53156, ETH10217-219, TGLA122143, INRA23202, TGLA126115, ETH225148-150, BM1824188-190 alleles in the Southern Meat cattle gene pool may be inherited from a B. taurus ancestor (i.e., taurine breeds diagnostic alleles).

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Genetic characterization among some Austrian and Hungarian cattle breeds

Archives Animal Breeding ◽

10.5194/aab-51-426-2008 ◽

2008 ◽

Vol 51 (5) ◽

pp. 426-437 ◽

Cited By ~ 1

Author(s):

S. Manatrinon ◽

F. Fischerleitner ◽

R. Baumung

Keyword(s):

Genetic Characterization ◽

Microsatellite Analysis ◽

Fixation Index ◽

The Past ◽

Cattle Breeds ◽

Expected Heterozygosity ◽

Correct Assignment ◽

Conservation Breeding ◽

Relationship Of ◽

Private Alleles

Abstract. Microsatellite analysis was used to estimate genetic diversity and relationship of 180 individuals belonging to two native endangered Austrian cattle breeds, Carinthian Blond (CB) and Waldviertler Blond (WV), and Hungarian Grey (HU) from Hungary. Twenty-five markers were used, and a total of 213 alleles were detected, of which 54 alleles (~25 %) were private alleles. Three breeds are clearly separated from each other with a correct assignment higher than 90 %. No bottlenecks were detected in any of the populations. A small amount of gene flow among the three populations occurred in the past. The closest genetic relationship is between Carinthian Blond and Waldviertler Blond (NEI et al.’s distance DA, [1983]; DA=0.11). However, Carinthian Blond showed higher mean number of alleles per locus (6.76), number of private alleles (17) and expected heterozygosity (0.663) than Waldviertler Blond (6.04, 9 and 0.631, respectively). The negative values of fixation index FIS (−0.018 and −0.037 for CB and WV, respectively) indicated that inbreeding is avoided, a sign for a successful conservation breeding program.

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

BIOTECHNOLOGY: STATE OF THE ART AND PERSPECTIVES ◽

10.37747/2312-640x-2021-19-338-340 ◽

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.

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

Genes ◽

10.3390/genes11080940 ◽

2020 ◽

Vol 11 (8) ◽

pp. 940 ◽

Cited By ~ 1

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.

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PSXV-10 Study of allelic pattern of PLAG1 gene in the historical and modern populations of two oldest Russian dairy cattle breeds

Journal of Animal Science ◽

10.1093/jas/skab235.474 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 259-260

Author(s):

Alexandra S Abdelmanova ◽

Veronika R Kharzinova ◽

Arsen V Dotsev ◽

Alexander A Sermyagin ◽

Oxana Boronetskaya ◽

...

Keyword(s):

Dairy Cattle ◽

Body Height ◽

Animal Husbandry ◽

Dna Arrays ◽

Breeding Programs ◽

Cattle Breeds ◽

History Of ◽

Strong Candidate ◽

Modern Breeding ◽

Historical Samples

Abstract Increasing animal stature is one of the goals of modern breeding programs for many dairy cattle breeds, because stature related to higher milk yield. The PLAG1 gene was shown to be a strong candidate responsible for stature in different cattle breeds. The polymorphic SNP BovineHD1400007259, located within PLAG1 gene, is considered as a causal mutation responsible for stature. The aim of our work was to evaluate the effect of long selection for the increased body height on the alterations of the allele’s frequencies of the PLAG1 gene in the historical and modern populations of the Russian Yaroslavl and Kholmogor dairy cattle breeds. The historical specimens of Yaroslavl (n = 22) and Kholmogor (n = 12) 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. The modern representatives of Yaroslavl (n = 31) and Kholmogor (n = 25) breeds 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 using high-density DNA arrays (Illumina Inc., USA). The historical DNA was treated by USER enzyme before genotyping to avoid the misincoporated nucleotides occurred due to postmortem DNA damage. We observed significant differences in allele frequencies of PLAG1 genes between historical and modern populations of both breeds. The frequencies of G allele, which is associated with higher stature, were increased from 0.114 in historical Yaroslavl cattle and from 0.167 in historical Kholmogor cattle to 0.633 and 0.860 in the modern breeds’ representatives, respectively. Our data suggest that PLAG1 gene was affected by artificial selection in studied cattle breeds. The research results will be useful for elucidation of the history of these two oldest Russian dairy cattle breeds. The study was funded by the RSF No. 21-66-00007.

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Autosomal Microsatellite Investigation Reveals Multiple Genetic Components of the Highlanders from Thailand

Genes ◽

10.3390/genes12030383 ◽

2021 ◽

Vol 12 (3) ◽

pp. 383

Author(s):

Aornpriya Mawan ◽

Nonglak Prakhun ◽

Kanha Muisuk ◽

Suparat Srithawong ◽

Metawee Srikummool ◽

...

Keyword(s):

Genetic Structure ◽

Genetic Relationships ◽

Forensic Investigation ◽

Northern Thailand ◽

Hill Tribe ◽

Genetic Components ◽

Large Populations ◽

Population Interactions ◽

Hill Tribes ◽

The Hill

The hill tribes of northern Thailand comprise nine officially recognized groups: the Austroasiatic-speaking (AA) Khmu, Htin and Lawa; the Hmong-Mien-speaking (HM) IuMien and Hmong; and the Sino-Tibetan-speaking (ST) Akha, Karen, Lahu and Lisu. Except the Lawa, the rest of the hill tribes migrated into their present habitats only very recently. The Thai hill tribes were of much interest to research groups focusing on study of cultural and genetic variation because of their unique languages and cultures. So far, there have been several genetic studies of the Thai hill tribes. However, complete forensic microsatellite database of the Thai hill tribes is still lacking. To construct such database, we newly generated 654 genotypes of 15 microsatellites commonly used in forensic investigation that belong to all the nine hill tribes and also non-hill tribe highlanders from northern Thailand. We also combined 329 genotypes from previous studies of northern Thai populations bringing to a total of 983 genotypes, which were then subjected to genetic structure and population relationships analyses. Our overall results indicated homogenous genetic structure within the HM- and Tai-Kadai (TK)-speaking groups, large genetic divergence of the HM-speaking Hmong but not IuMien from the other Thai groups, and genetic heterogeneity within the ST- and AA-speaking groups, reflecting different population interactions and admixtures. In addition to establishing genetic relationships within and among these populations, our finding, which provides a more complete picture of the forensic microsatellite database of the multiple Thai highland dwellers, would not only serve to expand and strengthen forensic investigation in Thailand, but would also benefit its neighboring countries of Laos and Myanmar, from which many of the Thai hill tribes originated and where large populations of these ethnic groups still reside.

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