Genome-wide SNP discovery and evaluation of genetic diversity among six Chinese indigenous cattle breeds in Sichuan

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

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Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle

BMC Genetics ◽

10.1186/s12863-018-0705-9 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 12

Author(s):

Wengang Zhang ◽

Xue Gao ◽

Yang Zhang ◽

Yumin Zhao ◽

Jiabao Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Indigenous Cattle ◽

Genome Wide

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

South African Journal of Animal Science ◽

10.4314/sajas.v49i6.12 ◽

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

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

BMC Genomics ◽

10.1186/s12864-020-07270-x ◽

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.

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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 Three Indigenous Cattle Breeds Reared in Benin

American Journal of Animal and Veterinary Sciences ◽

10.3844/ajavsp.2019.40.49 ◽

2019 ◽

Vol 14 (1) ◽

pp. 40-49

Author(s):

Mahugnon Santoze Adido ◽

Mathew Gitau Gicheha ◽

Mahougnon Camus Adoligbe ◽

Kodzo Atchou

Keyword(s):

Genetic Diversity ◽

Indigenous Cattle ◽

Cattle Breeds

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Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer (Cervus nippon) in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing

G3 Genes|Genome|Genetics ◽

10.1534/g3.117.300082 ◽

2017 ◽

Vol 7 (9) ◽

pp. 3169-3176 ◽

Cited By ~ 14

Author(s):

Hengxing Ba ◽

Boyin Jia ◽

Guiwu Wang ◽

Yifeng Yang ◽

Gilead Kedem ◽

...

Keyword(s):

Genetic Diversity ◽

Dna Sequencing ◽

Northeast China ◽

Sika Deer ◽

Restriction Site ◽

Cervus Nippon ◽

Snp Discovery ◽

Genome Wide

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Genomic relatedness and diversity of Swedish native cattle breeds

Genetics Selection Evolution ◽

10.1186/s12711-019-0496-0 ◽

2019 ◽

Vol 51 (1) ◽

Cited By ~ 7

Author(s):

Maulik Upadhyay ◽

Susanne Eriksson ◽

Sofia Mikko ◽

Erling Strandberg ◽

Hans Stålhammar ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Trees ◽

Genetic Relatedness ◽

Demographic History ◽

Genomic Diversity ◽

Founder Population ◽

Southern Sweden ◽

Cattle Breeds ◽

Genome Wide ◽

Native Cattle

Abstract Background Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds. Results We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed. Conclusions This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.

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