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

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.

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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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Genetic diversity and effective population sizes of thirteen Indian cattle breeds

Genetics Selection Evolution ◽

10.1186/s12711-021-00640-3 ◽

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.

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

Archives Animal Breeding ◽

10.5194/aab-62-325-2019 ◽

2019 ◽

Vol 62 (1) ◽

pp. 325-333 ◽

Cited By ~ 1

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.

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Genetic diversity of Sragen Black Cattle based on D-Loop gene sequencing analysis

Livestock and Animal Research ◽

10.20961/lar.v18i2.42934 ◽

2020 ◽

Vol 18 (2) ◽

pp. 124

Author(s):

Rahayu Kusumaningrum ◽

Sutopo Sutopo ◽

Edy Kurnianto

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Genetic Distance ◽

Genetic Relationship ◽

Bos Taurus ◽

Bos Indicus ◽

Evolutionary Genetics ◽

Sequencing Analysis ◽

Dna Sequence Polymorphism ◽

D Loop

Objective: The objective of this study was to investigate the genetic diversity of Sragen Black Cattle based on D-loop sequences analysis.Methods: A total of 25 blood samples belonged to Sragen Black Cattle that had no genetic relationship within sample. The DNA genome was extracted based on the manufacturer’s standard protocol using gSYNC DNA Mini Kit (Geneaid Biotech Ltd.). D-loop gene was amplified using specific primer forward: 5’- TAGTGCTAATACCAACGGCC-3’ and reverse: 5’- AGGCATTTTGAGTGCCTTGC-3’ and then was sequenced. The sequencing result was aligned and analyzed by Molecular Evolutionary Genetics Analysis (MEGA) version 6.0 to reveal genetic distance and phylogenetic tree. Genetic diversity and haplotype were analysed by DNA Sequence Polymorphism (DnaSp) v6.12.03.Results: The results revealed that there were 11 haplotypes with Pi = 0.00675±0.00201 and Hd = 0.767±0.086. Sragen Black Cattle was divided by two cluster in phylogenetic tree with average of genetic distance was 0.0032.Conclusions: In conclusion, all of Sragen Black Cattle are on the same cluster and have closer genetic relationship to Bos indicus rather than Bos taurus with similarity level 85.76 % based on BLAST program.

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Current situation and diversity of indigenous cattle breeds of Saudi Arabia

Animal Genetic Resources/Ressources génétiques animales/Recursos genéticos animales ◽

10.1017/s2078633615000247 ◽

2015 ◽

Vol 57 ◽

pp. 39-49 ◽

Cited By ~ 1

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.

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GENEBANK ANALYSIS: SINGLE NUCLEOTIDE POLYMORPHISMS OF ANIMALS MITOCHONDRIAL GENOME UKRAINIAN GRAY AND UKRAINIAN WHITEHEAD CATTLE BREEDS

Animal Breeding and Genetics ◽

10.31073/abg.53.33 ◽

2017 ◽

Vol 53 ◽

pp. 241-248

Author(s):

Yu. V. Podoba ◽

V. O. Pinchuk ◽

V. P. Boroday

Keyword(s):

Mitochondrial Dna ◽

Mitochondrial Genome ◽

Dna Sequences ◽

Bos Taurus ◽

Bos Indicus ◽

Ex Situ ◽

Single Nucleotide ◽

Cattle Breeds ◽

D Loop ◽

Mtdna Haplogroup

Examination of variation in mitochondrial DNA (mtDNA) control region sequences has been pivotal in the elucidation of bovine phylogeography. Initial studies have demonstrated a deep bifurcation in bovine mtDNA phylogeny, which indicates a predomestic divergence between the two major taxa of cattle, humped zebu (Bos indicus) and humpless taurine (Bos taurus). Subsequent genetic investigations have yielded further inference regarding origins within the B. taurus lineage. B. taurus mtDNA sequences fall into one of five ancestral star-like haplotypic clusters, which are geographically distributed. Just one of these clusters, T3, predominates in Western Europe. Symmetrically, diversity within Africa is composed almost exclusively of members of a separate haplotypic cluster, T1, which is rarely detected elsewhere. The almost mutually exclusive geographic distribution of these two haplotypic clusters allows geographical exceptions to be securely identified as secondary introductions. We investigated a comparative analysis of mitochondrial genome sequences for different breeds of cattle (Bos taurus, Bos indicus) with global genetic bank. Mitochondrial DNA sequences from bovine animals (Bos taurus) breeds Ukrainian Whitehead and Ukrainian Gray freely available on the global genetic bank (http://www.ncbi.nlm.nih.gov/Genebank/). Local alignment of sequences for mitochondrial genome of different cattle breeds was performed using the program MEGA 4.0. For the detection of nucleotide replacements used mitochondrial DNA sequence of Bos taurus Hereford breed (Anderson S. at al., 1982) as a reference (accession number V00645). Here we report the analysis results of testing for 9 genotypes Ukrainian Gray mitochondrial DNA sequences showed that one animal (GQ129208) has haplotype Bos indicus, other belongs to haplogroup T1 with European origin mtDNA. Analysis of single nucleotide replacement in one of the hypervariable regions mtDNA (position number 16019-16339) shows, that among 10 submitted genotypes of Ukrainian Whitehead the 3 of them (FJ014303, FJ014298, FJ014294) relating to T1a mtDNA haplogroup of African origin, which characterized by replacement of T to C at position 16255. Also have been two animals (FJ014301, FJ014295) with single nucleotide replacements with relatives to Bos indicus mtDNA haplogroup. We performed alignment with reference sequences (Bos_taurus_v00654.1) and comparative nucleotide sequences analysis of another hypervariable D-loop (position number 1-240) mtDNA with 5 Ukrainian Whitehead genotypes and 5 Ukrainian Gray genotypes represented in genetics bank. Among the Ukrainian Whitehead genotypes (FJ014298, FJ014297, FJ014296, FJ014295, FJ014294) all were polymorphic that characterizes large differentiation these animals for maternal and describe deep heterogeneous parent population of studied group. We determined one animal with genotype FJ014295 was significantly different by the number of segregation sites. The analyzed sequences (FJ014290, FJ014289, FJ014288, FJ014287, FJ014286) of 5 Ukrainian Gray genotypes showed no polymorphism in hypervariable D-loop (position number 1-240) mtDNA. The mtDNA analysis of different species of animals allowed to distribute their mtDNA belonging to European, African and Asian haplogroups. The technique, which allows to differentiate the animals represented by their belonging to the respective haplogroups. The process that gave rise to different genotypes in one lineage is clearly of fundamental importance in understanding intraspecific mitochondrial polymorphism and evolution in mammals. Сomprehensive study genetic material provide more opportunities to optimize costs in-situ conservation of different cattle breeds, to optimize methods and techniques which used in ex-situ conservation programmes of National gene bank of animal genetic resources.

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