scholarly journals Genetic Diversity and Phylogenetic Relationship between Indigenous Cattle Breeds

2017 ◽  
Vol 6 (3) ◽  
pp. 1650-1654
Author(s):  
S. Vani K. Sakunthala Devi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationship ◽  
Indigenous Cattle ◽  
Cattle Breeds

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.

Genome-wide scanning reveals genetic diversity and signatures of selection in Chinese indigenous cattle breeds

2018 ◽  
Vol 216 ◽  
pp. 100-108 ◽  
Author(s):  
L. Xu ◽  
W.G. Zhang ◽  
H.X. Shen ◽  
Y. Zhang ◽  
Y.M. Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Signatures Of Selection

scholarly journals Genetic Diversity of Three Indigenous Cattle Breeds Reared in Benin

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

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 Short tandem repeat (STR) based genetic diversity and relationship of indigenous Niger cattle

2017 ◽  
Vol 60 (4) ◽  
pp. 399-408 ◽  
Author(s):  
Moustapha Grema ◽  
Amadou Traoré ◽  
Moumouni Issa ◽  
Marichatou Hamani ◽  
Maaouia Abdou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Gene Diversity ◽  
Allele Sharing ◽  
High Genetic Diversity ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Relationship Of ◽  
Short Tandem

Abstract. The diversity of cattle in Niger is predominantly represented by three indigenous breeds: Zebu Arabe, Zebu Bororo and Kuri. This study aimed at characterizing the genetic diversity and relationship of Niger cattle breeds using short tandem repeat (STR) marker variations. A total of 105 cattle from all three breeds were genotyped at 27 STR loci. High levels of allelic and gene diversity were observed with an overall mean of 8.7 and 0.724 respectively. The mean inbreeding estimate within breeds was found to be moderate with 0.024, 0.043 and 0.044 in Zebu Arabe, Zebu Bororo and Kuri cattle respectively. The global F statistics showed low genetic differentiation among Niger cattle with about 2.6 % of total variation being attributed to between-breed differences. Neighbor-joining tree derived from pairwise allele sharing distance revealed Zebu Arabe and Kuri clustering together while Zebu Bororo appeared to be relatively distinct from the other two breeds. High levels of admixture were evident from the distribution of pairwise inter-individual allele sharing distances that showed individuals across populations being more related than individuals within populations. Individuals were assigned to their respective source populations based on STR genotypes, and the percent correct assignment of Zebu Bororo (87.5 to 93.8 %) was consistently higher than Zebu Arabe (59.3 to 70.4 %) and Kuri (80.0 to 83.3 %) cattle. The qualitative and quantitative tests for mutation drift equilibrium revealed absence of genetic bottleneck events in Niger cattle in the recent past. High genetic diversity and poor genetic structure among indigenous cattle breeds of Niger might be due to historic zebu–taurine admixture and ongoing breeding practices in the region. The results of the present study are expected to help in formulating effective strategies for conservation and genetic improvement of indigenous Niger cattle breeds.

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

PLoS ONE ◽  
2018 ◽  
Vol 13 (8) ◽  
pp. e0201534 ◽  
Author(s):  
Wei Wang ◽  
Jia Gan ◽  
Donghui Fang ◽  
Hui Tang ◽  
Huai Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Snp Discovery ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Genome Wide

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.

Genetic diversity and origin of mitochondria DNA D-loop region of some Chinese indigenous cattle breeds

2009 ◽  
Vol 31 (2) ◽  
pp. 160-168 ◽  
Author(s):  
Gui-Xiang ZHANG ◽  
You-Min ZHENG ◽  
Zhi-Gang WANG ◽  
Xu HAN ◽  
Shan-Gang JIA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Loop Region ◽  
D Loop ◽  
Mitochondria Dna

scholarly journals Genetic characterisation of non-descript cattle populations in communal areas of South Africa

2021 ◽  
Vol 61 (1) ◽  
pp. 84
Author(s):  
M. D. Mamogobo ◽  
N. O. Mapholi ◽  
K. A. Nephawe ◽  
T. L. Nedambale ◽  
T. J. Mpofu ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Genetic Material ◽  
Climatic Conditions ◽  
Eastern Cape ◽  
Indigenous Cattle ◽  
North West ◽  
Cattle Breeds ◽  
Kwazulu Natal ◽  
Communal Areas

Context Indigenous cattle breeds represent an important genetic resource for livelihood of communal-area inhabitants. Indigenous breeds have the ability to withstand harsh climatic conditions, can adapt genetically to poor-quality forages and are resistant to parasites and diseases. These unique traits possessed by indigenous breeds are under threat because of unrestrained crossing with exotic commercial breeds, and this can lead to total loss of a breed. Aims The study was conducted to assess the genetic diversity and population structure of South African non-descript communal beef cattle populations by using 25 microsatellite markers. Methods Unrelated and non-descript animals (n = 150) were sampled from communal areas from five (5) provinces of South Africa, namely, Eastern Cape, KwaZulu–Natal, Limpopo, Mpumalanga and the North West, with 30 samples per breed taken. Six (6) known cattle breeds (n = 180) were used as a reference population. This included Angus, Afrikaner, Bonsmara, Brahman, Drakensberger and the Nguni, with 30 samples per breed. Key results High level of genetic diversity was found across the five non-descript populations, with an average heterozygosity of 75%. The Limpopo population was found to be the most diverse population, with the highest average number of alleles (8.5) and heterozygosity (ranging between observed heterozygosity of 70% and expected heterozygosity of 79%). STRUCTURE software assigned populations (2 ≤ K ≤ 20), with the most probable cluster being at K = 7. The Eastern Cape, KwaZulu–Natal and Limpopo populations had genetic material similar to those possessed by the Nguni and Bonsmara reference populations. Conclusions Results from the study showed that most genetic differentiation occurred within populations rather than among populations, and this might be due to the fact that there is no selection for or against any specific production trait expressed in the populations. Implications The obtained information will serve as a baseline for the development and implementation of sound breeding programs that will assist in controlling the gene flow, so as to lower the possible genetic dilution of the currently available genetic material.

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