scholarly journals Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers

2022 ◽  
Vol 25 (8) ◽  
pp. 831-838
Author(s):  
R. B. Aitnazarov ◽  
T. M. Mishakova ◽  
N. S. Yudin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Population Distribution ◽  
Cattle Breed ◽  
Principal Component ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Novosibirsk Region ◽  
Breed Improvement ◽  
Two Populations

There are currently over a thousand indigenous cattle breeds well adapted to local habitat conditions thanks to their long history of evolution and breeding. Identification of the genetic variations controlling the adaptation of local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great relevance. Studying individual populations of the same breed with the use of microsatellite markers makes it possible to assess their genetic diversity, relationships, and breed improvement potential. Although the Black Pied breed is the most common dairy cattle breed in Russia, there are only a few studies on genetic diversity in local Black Pied populations in some Russian regions. The goal of the present study was to analyze the genetic diversity in Black Pied cattle populations in the Novosibirsk Region and compare them with other Russian populations; to identify significantly divergent populations with a view to preserving them under the programs aimed at maintaining the genetic diversity of the domestic Black Pied breed. DNA samples from 4788 animals of the Black Pied breed from six breeding enterprises in the Novosibirsk Region have been studied using 11 microsatellite markers. No significant differences in genetic variability parameters were found between individual populations. Private alleles have been identified in five out of six populations. Five populations have shown inbreeding coefficient values (FIS) below zero, which indicates heterozygosity excess. The population distribution test, principal component analysis, FST and DEST values, cluster analysis, and phylogenetic analysis have revealed two populations genetically distinct from the others. Essentially, the genetic diversity parameters of the six studied Black Pied cattle populations from the Novosibirsk Region show no significant differences from other Russian populations of the breed. Excess heterozygosity is observed in most breeding enterprises, which is a sign of a low inbreeding rate. To maintain the genetic diversity of the Russian Black Pied cattle, we recommend focusing on the two populations with significant genetic distinctions from the others.

scholarly journals The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
N. Z. Gebrehiwot ◽  
E. M. Strucken ◽  
H. Aliloo ◽  
K. Marshall ◽  
J. P. Gibson
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Large Population ◽  
Bos Indicus ◽  
Principal Component ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
African Cattle ◽  
Snp Data

Abstract Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

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

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).

scholarly journals Genome-wide genetic diversity, population structure and admixture analysis in Eritrean Indigenous Cattle

2020 ◽  
Vol 49 (6) ◽  
pp. 1083-1092
Author(s):  
S Goitom ◽  
M.G. Gicheha ◽  
F.K. Njonge ◽  
N Kiplangat
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Population Differentiation ◽  
Principal Component ◽  
Vital Role ◽  
Group Method ◽  
Indigenous Cattle ◽  
Ecological Zones ◽  
Genome Wide

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes. Keywords: genetic variability, molecular characterization, population differentiation

POLISH RED CATTLE: A SCHEME FOR THEIR CONSERVATION

1990 ◽  
Vol 7 ◽  
pp. 71-76
Author(s):  
Kazimierz Zukowski
Keyword(s):  
Total Population ◽  
Cattle Breed ◽  
Gene Bank ◽  
Indigenous Cattle ◽  
Dual Purpose ◽  
Frozen Semen ◽  
Improvement Programme ◽  
Breed Improvement ◽  
The 1960S ◽  
The 19Th Century

SUMMARYPolish Red is the only indigenous cattle breed in Poland. Breeding was first started at the end of the 19th century. At the end of the 1960s the breed constituted more than 20 percent of the total cattle population in Poland. During the 1970s Polish Red cattle were superseded by Friesian,-and now there are about 200 000 cows left (i.e., 3 percent of the total population).These dual-purpose (dairy-beef) animals are hardy and well adapted to rather poor feeding conditions. An improvement programme, through crossbreeding, would likely diminish their original characteristics. Therefore, together with breed improvement, a gene reserve in the form of a conservation herd of 300 cows and a gene bank of frozen semen and embryos have been implemented. A systematic breeding programme has been implemented also to maintain the old genotype and ensure wider genetic variation within the herd.

Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers

2007 ◽  
Vol 38 (6) ◽  
pp. 550-559 ◽  
Author(s):  
G. X. Zhang ◽  
Z. G. Wang ◽  
W. S. Chen ◽  
C. X. Wu ◽  
X. Han ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Cattle Breeds ◽  
Yellow Cattle

scholarly journals Multivariate characterization of morphological traits in West African cattle sires

2016 ◽  
Vol 59 (3) ◽  
pp. 337-344 ◽  
Author(s):  
Amadou Traoré ◽  
Delphin O. Koudandé ◽  
Iván Fernández ◽  
Albert Soudré ◽  
Isabel Álvarez ◽  
...  
Keyword(s):  
Cattle Breed ◽  
Principal Component ◽  
West African ◽  
The Body ◽  
Body Measurements ◽  
Qualitative Traits ◽  
Cattle Breeds ◽  
African Cattle ◽  
Type Traits

Abstract. A total of 183 adult sires belonging to nine West African cattle breeds sampled in 67 villages of Mali, Burkina Faso and Benin were assessed for 16 body measurements and 18 qualitative traits. Within type of cattle (zebu, sanga or taurine), the different breeds analysed showed large differences in body measurements. In general, taurine breeds had lower average values than the zebu breeds while sanga cattle tended to have intermediate values. Principal component analysis identified three factors characterising body measurements. Factor 1 summarised the information provided by those traits characterising the size of the individuals and explained 59.0 % of the variability. Factor 2 tended to gather information characterising the body width and explained 8.0 % of the variation. Less representative, Factor 3 (6.6 % of the variability) had no clear interpretation. Qualitative traits did not allow to distinguish among either cattle groups or breeds. Two Correspondence Analysis Dimensions computed on qualitative traits (explaining 26.2 and 15.5 % of the variability, respectively) did not allow to differentiate between zebu, sanga or taurine cattle breeds. Our results confirm that, in the framework of a general appearance, body measurements are the main criteria for differentiating West African cattle breeds. Furthermore, the current research has not allowed to identify breeding preferences on qualitative type traits in West African cattle sires. Therefore, homogenisation of the appearance of individuals within cattle breed is not expected.

scholarly journals Short Communication: A Within- and Across-country Assessment of the Genomic Diversity and Autozygosity of South African and Eswatini Nguni Cattle

2021 ◽  
Author(s):  
Simon Frederick Lashmar ◽  
Carina Visser ◽  
Moses Okpeku ◽  
Farai Catherine Muchadeyi ◽  
Ntanganedzeni Olivia Mapholi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Standard Deviation ◽  
Cattle Breed ◽  
Principal Component ◽  
Genomic Diversity ◽  
Potential Threat ◽  
Inbreeding Coefficients ◽  
Agroecological Zones ◽  
Nguni Cattle

Abstract In southern Africa, the Nguni cattle breed is classified as an indigenous and transboundary animal genetic resource that manifests unique adaptation abilities across distinct agroecological zones. The genetic integrity of various ecotypes is under potential threat due to both indiscriminate crossbreeding and uncontrolled inbreeding. The aim of this study was to assess the genetic diversity and autozygosity that exists both across countries (ES: eSwatini; SA: South Africa) and within-country (SA), between purebred stud animals (SA-S) and research herds (SA-R). Subsets of 96 ES, 96 SA-S and 96 SA-R genotyped for 40 930 common SNPs were used to study inbreeding, runs of homozygosity (ROH) and heterozygosity (ROHet) profiles as well as population structure. The highest proportion (0.513) of the 3 595 ROH was <4Mb in length, while the majority (0.560) of the 4 409 ROHet segments fell within the 0.5-1Mb length category. Inbreeding coefficients indicated low inbreeding (FROH range: 0.025 for SA-S to 0.029 for SA-R). Principal component (PCA) and population structure (K=5) analyses illustrated genomic distinctiveness between SA and ES populations, greater admixture for SA-R (mean±standard deviation proportion shared=0.631±0.353) compared to SA-S (mean±standard deviation proportion shared=0.741±0.123), and three subpopulations for ES. Overall, results illustrated that genetic distinctiveness in the Nguni resulted from both geographic isolation and exposure to different production strategies. Although no impending threat to genetic diversity was observed, further loss should be monitored to prevent endangerment of unique and beneficial indigenous resources.

scholarly journals Genetic diversity and population structure of four cattle breeds raised in Turkey using microsatellite markers

2019 ◽  
Vol 64 (No. 10) ◽  
pp. 411-419 ◽  
Author(s):  
Eymen Demir ◽  
Murat Soner Balcioğlu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Factorial Correspondence Analysis ◽  
Cattle Breeds ◽  
Expected Heterozygosity ◽  
Bottleneck Analysis ◽  
Holstein Friesian ◽  
Native Cattle ◽  
Marker Level

In the present study, genetic diversity and population structure of Holstein Friesian and three native cattle breeds of Turkey including Turkish Grey Steppe, Eastern Anatolian Red and Anatolian Black were assessed. Totally 120 individuals of 4 breeds were genotyped using 20 microsatellite markers and 204 different alleles, of which 31 were private alleles, were detected. The average observed and expected heterozygosity values were 0.63 and 0.74, respectively. Observed heterozygosity at the marker level ranged from 0.30 (DRBP1) to 0.88 (ILSTS011), while expected heterozygosity ranged from 0.51 (INRABERN172) to 0.88 (SPS113). Inbreeding coefficient values for Turkish Grey Steppe, Eastern Anatolian Red, Anatolian Black and Holstein Friesian were 0.216, 0.202, 0.128 and 0.069, respectively. The lowest pairwise F<sub>ST</sub> value (0.030) was detected between Turkish Grey Steppe and Anatolian Black breeds, while the highest value (0.070) was detected between Turkish Grey Steppe and Holstein Friesian. Results of structure and factorial correspondence analysis revealed that Turkish native cattle breeds and Holstein Friesian were genetically different enough to separate the two breeds. Results of bottleneck analysis indicated heterozygosity deficiency in Turkish Grey Steppe (P &lt; 0.05).

scholarly journals Livestock Keepers’ Attitudes: Keystone of Effective Community-Based Breeding Programs

2021 ◽  
Vol 13 (5) ◽  
pp. 2499
Author(s):  
Bienvenue Zoma-Traoré ◽  
Lorenz Probst ◽  
Salifou Ouédraogo-Koné ◽  
Albert Soudré ◽  
Dominique Ouédraogo ◽  
...  
Keyword(s):  
Positive Attitude ◽  
Cattle Breed ◽  
Principal Component ◽  
Zebu Cattle ◽  
Community Based ◽  
Cattle Breeding ◽  
Breeding Programs ◽  
Taurine Breed ◽  
Effective Community ◽  
Breed Improvement

Livestock keepers in southwestern Burkina Faso hold the local Lobi taurine breed, local Zebu cattle, and their crosses. Some communities in the region have begun to implement community-based cattle breeding programs (CBBPs), which involve animal tagging and recording and, potentially, also bull sharing. Based on the hypothesis that the participation of livestock keepers in CBBPs depends on their attitudes towards these programs, we used questionnaires to survey the attitudes of 125 farmers towards cattle breeding strategies and tools. Results were analyzed using principal component analysis. Farmers showed a highly positive attitude towards maintaining the features of their preferred cattle breed, but their attitudes varied substantially towards crossbreeding for breed improvement. Farmers generally agreed that performance was more important than animal appearance, and most of them were willing to cooperate with breeders’ associations but were skeptical about sharing their bulls with other farmers. The majority was reluctant to record performance data, which may be due to a capacity deficit and their confidence in being able to select the best animals based purely on phenotype. Our analysis suggests that breeders’ associations, as a key component of CBBPs, should lay down clear rules and obligations for their members from the outset. Timely consideration of farmers’ attitudes towards different breeding tools may improve their uptake and guarantee the sustainability of CBBPs.

Genetic Diversity and Population Structure in Two Captive Rhesus Monkey (Macaca Mulatta) Populations as Revealed by Microsatellite Markers

2021 ◽  
Author(s):  
Chao Du ◽  
Bai Mo ◽  
Wujiao Li ◽  
Wencong Liu ◽  
Zongxiu Hu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Macaca Mulatta ◽  
Psychological Research ◽  
Effect Analysis ◽  
Bottleneck Effect ◽  
Genetic Lineages ◽  
Captive Populations ◽  
Two Populations

Abstract Rhesus monkeyss (Macaca mulatta) are extensively used in the field of medical and psychological research as valuable experimental animals. 15 polymorphic chromosome-specific microsatellite markers were used to analyze the genetic diversity and population structure in two captive individuals. A total of 155 alleles were identified, with the number of alleles per locus ranging from 7 to 15, giving an average number of 10.3 alleles per locus. The mean number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were 5.602, 0.7297, 0.8016, and 0.7716, respectively. The populations HS and XJ shared partial common alleles, however, the remaining in XJ were not detected. Structure analysis indicated that two populations belong to three genetic lineages. AMOVA showed that the genetic variance was 91% among individuals, while it was 9% among populations, respectively. The bottleneck effect analysis revealed that the two captive populations were in accordance with mutation-drift equilibrium. In the comparison of the genetic parameters and structure between the HS and XJ, we speculated that the genetic diversity was higher, which may be attributed to the exchange of germplasm resources and the input of new individuals from wild populations.

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