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 diversity and effective population sizes of thirteen Indian cattle breeds

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Eva M. Strucken ◽  
Netsanet Z. Gebrehiwot ◽  
Marimuthu Swaminathan ◽  
Sachin Joshi ◽  
Mohammad Al Kalaldeh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Allele Frequencies ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Population Sizes ◽  
Indian Cattle

Abstract Background The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds. Results Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds. Conclusions The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.

scholarly journals Genetic Diversity of Nepalese Indigenous Cattle Breeds Based on D-Loop Mitochondrial DNA

2021 ◽  
Vol 19 (2) ◽  
pp. 103-108
Author(s):  
Neena Amatya Gorkhali ◽  
Chhiring Sherpa ◽  
Aashish Dhakal ◽  
Sanjay Dhungana ◽  
Saroj Sapkota ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Sample Population ◽  
Cattle Population ◽  
Indigenous Cattle ◽  
Ancestral Origin ◽  
Cattle Breeds ◽  
North East ◽  
D Loop

Nepalese cattle are known for their genetic potentiality concerning inhabitant in extreme climatic conditions, surviving in the scarce food supply, and resistant to several diseases. We aimed to assess Nepal’s ancestral origin and genetic diversity of indigenous cattle breeds based on hyper-variable D loop mtDNA sequences. Three cattle breeds (Siri, Achammi, & Lulu) comprising the total sample population (n= 75) were employed in the study where the mt DNA information of two breeds (Achammi & Lulu) were retrieved from the published source. Hyper-variable D loop (910bp) of Siri cattle was PCR amplified and sequenced. This study claims that the possible ancestral origin of Bos taurus and Bos indicus mtDNA lineage in the Nepalese cattle population is majorly influenced by China and India, respectively. This study suggests that Nepalese cattle can be divided into two major groups: Bos taurus and Bos indicus, where most of the cattle population was of Bos indicus origin. The sampled population can be classified into three significant haplogroups: T3 (25%), I1 (48%), and I2 (27%) revealing a higher genetic diversity among the Nepalese cattle population. Only T3 taurine haplogroup was found in the sampled population. It was consistent with the fact that the absence of T1 haplogroup in North-East Asian cattle. In terms of Bos indicus, the I1 haplogroup was dominant over I2. Higher genetic diversity can be appropriate reasoning for Nepalese cattle’s survival in a harsh environment and low food conditions.

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 Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA

2019 ◽  
Vol 62 (1) ◽  
pp. 325-333 ◽  
Author(s):  
Linjun Yan ◽  
Yifan She ◽  
Mauricio A. Elzo ◽  
Chunlei Zhang ◽  
Xingtang Fang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Haplotype Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Cattle Breeds ◽  
Chinese Cattle

Abstract. The objective of this research was to characterize the genetic diversity and phylogenetic diversity among 12 cattle breeds (10 Chinese breeds and two foreign taurine breeds as controls) utilizing gene mtDNA 16S rRNA. The complete sequences of the mtDNA 16S rRNA genes of the 251 animals were 1570 bp long. The mean percentages of the four nitrogen bases were 37.8 % for adenine (A), 23.7 % for thymine (T), 20.9 % for cytosine (C), and 17.6 % for guanine (G). The mtDNA 16S rRNA gene base percentages had a strong bias towards A + T. All detected nucleotide variations in gene mtDNA 16S rRNA were either transitions (62.3 %) or transversions (37.7 %); no indels (insertions and deletions) were found. A total of 40 haplotypes were constructed based on these mutations. A total of 36 haplotypes of these 40 haplotypes were present in 10 Chinese cattle breeds. The haplotype diversity of all Chinese cattle populations was 0.903±0.077, while the nucleotide diversity was 0.0071±0.0039. Kimura's two-parameter genetic distances between pairs of the studied 12 breeds ranged from 0.001 to 0.010. The phylogenetic analysis assigned the 10 Chinese breeds to two distinct lineages that likely differed in their percentage of Bos taurus and Bos indicus ancestry.

scholarly journals Unraveling the Genetic Diversity and Population Structure of Bangladeshi Indigenous Cattle Populations Using 50K SNP Markers

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2381
Author(s):  
Mohammad Shamsul Alam Bhuiyan ◽  
Soo-Hyun Lee ◽  
Sheikh Mohammad Jahangir Hossain ◽  
Gautam Kumar Deb ◽  
Most Farhana Afroz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Snp Markers ◽  
Gene Pools ◽  
Effective Population ◽  
Phylogenetic Tree Analysis ◽  
Indigenous Cattle ◽  
Geographic Separation ◽  
First Time ◽  
North Bengal

Understanding the genetic basis of locally adapted indigenous cattle populations is essential to design appropriate strategies and programs for their genetic improvement and conservation. Here, we report genetic diversity measures, population differentiation, and structure of 218 animals sampled from six indicine cattle populations of Bangladesh. Animals were genotyped with Illumina Bovine SNP50K BeadChip along with genotyped data of 505 individuals included from 19 zebu and taurine breeds worldwide. The principal component analysis (PCA) showed clear geographic separation between taurine and indicine lineages where Bangladeshi indigenous cattle clustered with South Asian zebu populations. However, overlapped clusters in PCA, heterozygosity estimates, and Neighbor-Joining phylogenetic tree analysis revealed weak genetic differentiation among the indigenous cattle populations of Bangladesh. The admixture analysis at K = 5 and 9 suggests distinct genetic structure of the studied populations along with 1 to 4% of taurine ancestry. The effective population size suggested a limited pool of ancestors particularly for Sahiwal and North Bengal Grey cattle. In conclusion, these findings shed insights into the genetic architecture of six indigenous cattle populations of Bangladesh for the first time and suggested as distinct gene pools without potential admixture with zebu or taurine populations.

Current situation and diversity of indigenous cattle breeds of Saudi Arabia

2015 ◽  
Vol 57 ◽  
pp. 39-49 ◽  
Author(s):  
R.M. Al-Atiyat ◽  
R.S. Aljumaah ◽  
A.M. Abudabos ◽  
A.A. Alghamdi ◽  
A.S. Alharthi ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Current Situation ◽  
Zebu Cattle ◽  
Eastern Region ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Population Sizes ◽  
Conservation Plan

SummaryThis study aims to evaluate the current situation and diversity of indigenous cattle breeds in the Kingdom of Saudi Arabia (KSA). A survey was executed in five regions of the KSA. We recorded population sizes, phenotypes and rearing conditions. TaurineBos taurusand zebuBos indicuspopulations were found. The zebu cattle include two breeds; the Hassawi and the Janobi. The Hassawi breed was found in the eastern region and it is in decreasing number. It may become extinct soon in the absence of conservation plan. Janobi remains common with thousand animals in the south-western part of the country. Only one indigenous taurine cow, showing no phenotypic evidence of zebu introgression, was found in the Central region of KSA (Najd Plateau). This cow might be the last pure indigenous Saudi Arabia taurine animal and therefore, the breed is now close to extinction. We advocate the urgency to design conservation plan for the indigenous livestock of the KSA and to complement these with phenotypic as well as genotypic information.

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 On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Gabriele Senczuk ◽  
Salvatore Mastrangelo ◽  
Paolo Ajmone-Marsan ◽  
Zsolt Becskei ◽  
Paolo Colangelo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Indices ◽  
Melting Pot ◽  
Cattle Breeds ◽  
Snp Data ◽  
Early Migration ◽  
Genome Wide ◽  
European Colonization ◽  
Approximate Bayesian ◽  
European Cattle

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.

scholarly journals Characterization of a haplotype- reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

2021 ◽  
Author(s):  
Adéla Nosková ◽  
Meenu Bhati ◽  
Naveen Kumar Kadri ◽  
Danang Crysnanto ◽  
Stefan Neuenschwander ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Cost Effective ◽  
Reference Panel ◽  
Effective Population ◽  
Large White ◽  
Breeding Populations ◽  
Low Pass ◽  
Signatures Of Selection ◽  
Genomic Inbreeding

Abstract Background The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads. Results Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and FST analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches (CLR and iHS), we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using GLIMPSE. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping. Conclusions We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

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