scholarly journals Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole-Genome Sequences

2016 ◽  
Author(s):  
Mathieu Gautier ◽  
Katayoun Moazami-Goudarzi ◽  
Leveziel Hubert ◽  
Hugues Parinello ◽  
Cécile Grohs ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Bos Indicus ◽  
Food Resource ◽  
Extended Period ◽  
Whole Genome ◽  
Genome Sequences ◽  
Population Sizes ◽  
Limited Gene Flow ◽  
Bovine Species ◽  
The Last Glacial

AbstractAs the largest European herbivore, the wisent (Bison bonasus) is emblematic of the continent wildlife but has unclear origins. Here, we infer its demographic and adaptive histories from two individual whole genome sequences via a detailed comparative analysis with bovine genomes. We estimate that the wisent and bovine species diverged from 1.7×106 to 850,000 YBP through a speciation process involving an extended period of limited gene flow. Our data further support the occurrence of more recent secondary contacts, posterior to the Bos taurus and Bos indicus divergence (ca. 150,000 YBP), between the wisent and (European) taurine cattle lineages. Although the wisent and bovine population sizes experienced a similar sharp decline since the Last Glacial Maximum, we find that the wisent demography remained more fluctuating during the Pleistocene. This is in agreement with a scenario in which wisents responded to successive glaciations by habitat fragmentation rather than southward and eastward migration as for the bovine ancestors.We finally detect 423 genes under positive selection between the wisent and bovine lineages, which shed a new light on the genome response to different living conditions (temperature, available food resource and pathogen exposure) and on the key gene functions altered by the domestication process.

scholarly journals Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

2020 ◽  
Author(s):  
Archile Eric paguem ◽  
Babette Abanda ◽  
Mbunkah Daniel Achukwi ◽  
Praveen Baskaran ◽  
Stefan Czemmel ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Phenotypic Traits ◽  
Zebu Cattle ◽  
Whole Genome ◽  
Genetic Traits ◽  
Cattle Breeds ◽  
Taurine Breed ◽  
Taurine Cattle

Abstract BackgroundWest African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with a number of factors, amongst others small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their populations size rendering them vulnerable to extinction. The Namchi (Doayo) taurine cattle breed has documented resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced for the first time the genomes of five cattle breeds from Cameroon: the Namchi (Doayo), an endangered trypanotolerant taurine breed, the Kapsiki, an indigenous trypanosusceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.ResultsApproximately 167 Giga bases of raw sequencing data were generated and mapped to the cattle reference genome UMD3.1. The coverage was 22 to 30-fold. The single nucleotide polymorphisms (SNPs) were compared with reference genomes of European Bos taurus Holstein and of Asian Bos indicus Brahman and the African trypanotolerant N’Dama breeds.Of a total of 50 million SNPs identified, 3.43 million were breed-specific ranging from 0.37 to 0.47 million SNPs in the domestic Cameroonian breeds and approximately 0.58 million constituted of small insertions and deletions. We identified breed specific-non-synonymous variants as genetic traits that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi (Doayo) breed, heat tolerance in the Kapsiki breed, and growth, metabolism and meat quality in the Gudali breeds. Phylogenetic comparison grouped Namchi (Doayo) to the African Zebu clade indicating a hybrid status of the selected animal with a Zebu breed, albeit it showed the Namchi breed’s phenotype.ConclusionsThe findings provide the first comprehensive set of full genome variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.

scholarly journals Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

2020 ◽  
Author(s):  
Archile Eric Paguem ◽  
Babette Abanda ◽  
Mbunkah Daniel Achukwi ◽  
Praveen Baskaran ◽  
Stefan Czemmel ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genetic Traits ◽  
Cattle Breeds ◽  
Taurine Breed ◽  
Taurine Cattle ◽  
Reference Genomes

Abstract Background:West African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with amongst others, small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their population size rendering them vulnerable to extinction. The Namchi taurine cattle breed is referred to as [Namchi (Doayo)] and shows resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced with high depth for the first time the genomes of five cattle breeds from Cameroon in order to provide a valuable genetic resource for future African cattle breeding: the Namchi , an endangered trypano-tolerant taurine breed, the Kapsiki, an indigenous trypano-susceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.Results: Approximately 167 Gigabases of raw sequencing data were generated for each breed and mapped to the cattle reference genomes ARS-UCD1.2 and UMD3.1.The coverage was 103 to 140-fold when aligning the reads to ARS-UCD1.2 with an average mapping rate of ~99%, and 22 to 30-fold when aligning the reads to UMD3.1 with an average mapping rate of ~64%. The single nucleotide polymorphisms (SNPs) obtained from analysis using the genome ARS-UCD1.2 were compared with reference genomes of European Bos taurus Holstein, the Asian Bos indicus Brahman, and the African trypanotolerant N’Dama breeds.A total of ~100 million (M) SNPs were identified and 7.7 M of those were breed-specific. Approximately 11.1 M constituted of small insertions and deletions. By using only breed-specific non-synonymous variants we identified genes as genetic traits and associated Gene Ontology (GO) terms that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi breed and heat tolerance in the Kapsiki breed. Phylogenetic analysis grouped, except for Namchi, the Bos taurus breeds Kapsiki, N’Dama and Holstein together while the B. indicus breeds White and Red Fulani, Gudali and Brahman clustered separately. The deviating result for Namchi indicates a hybrid status of the selected animal with a recent introgression of Zebu genes into its genome.Conclusions:The findings provide the first comprehensive set of genome-wide variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.

scholarly journals Toxoplasma gondii in experimentally infected Bos taurus and Bos indicus semen and tissues

2009 ◽  
Vol 29 (1) ◽  
pp. 59-64 ◽  
Author(s):  
Leslie Scarpelli ◽  
Welber Daniel Zanetti Lopes ◽  
Matheus Migani ◽  
Katia Denise Saraiva Bresciani ◽  
Alvimar José da Costa
Keyword(s):  
Toxoplasma Gondii ◽  
Lymph Nodes ◽  
Bos Taurus ◽  
Sexual Transmission ◽  
Bos Indicus ◽  
Antibody Test ◽  
Indirect Fluorescence Antibody Test ◽  
Skeletal Musculature ◽  
Bovine Species ◽  
Indirect Fluorescence Antibody

Eighteen young steers were inoculated with Toxoplasma gondii and randomly distributed into three groups of six animals each: GI, 2.5x10(5) "P" strain oocysts, GII, 5.0x10(6) "RH" strain tachyzoites, and GIII (Control). Clinical, serological and parasitemia exams were realized. Parasite investigation by bioassay and PCR was realized on semen and fragments of skeletal musculature, lymph nodes, brain, retina, spleen, liver, lung, testicle, epididymis and seminal vesicle. Blood and semen samples were collected on days -2, -1, 1, 3, 5, 7, 14 and weekly thereafter, up to postinfection day (PID) 84. The inoculated steers (GI and GII) presented hyperthermia from PID 3 to 16. Antibodies against T. gondii were detected through the indirect fluorescence antibody test (IFAT) on PID 5 (1:16) in both inoculated groups (oocysts and tachyzoites), reaching peaks of 1:4096 on PID 7. Parasitemia outbursts occurred in all infected bovines, principally from PID 7 to 28, independent of the strain and inoculate used. Bioassays revealed the presence of parasites in semen samples of animals infected with oocysts (GI) and tachyzoites (GII) on several experimental days between PID 7 and 84. Tissue parasitism by T. gondii was diagnosed by bioassay and the PCR technique in several organ and tissue fragments. These findings suggest the possibility of sexual transmission of T. gondii in the bovine species.

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.

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 Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

2020 ◽  
Author(s):  
Archile Eric Paguem ◽  
Babette Abanda ◽  
Mbunkah Daniel Achukwi ◽  
Praveen Baskaran ◽  
Stefan Czemmel ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genetic Traits ◽  
Cattle Breeds ◽  
Taurine Breed ◽  
Taurine Cattle ◽  
Reference Genomes

Abstract Background: West African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with amongst others, small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their population size rendering them vulnerable to extinction. The Namchi taurine cattle breed is referred to as [Namchi (Doayo)] and shows resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced with high depth for the first time the genomes of five cattle breeds from Cameroon in order to provide a valuable genetic resource for future African cattle breeding: the Namchi , an endangered trypano-tolerant taurine breed, the Kapsiki, an indigenous trypano-susceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.Results: Approximately 167 Gigabases of raw sequencing data were generated for each breed and mapped to the cattle reference genomes ARS-UCD1.2 and UMD3.1.The coverage was 103 to 140-fold when aligning the reads to ARS-UCD1.2 with an average mapping rate of ~99%, and 22 to 30-fold when aligning the reads to UMD3.1 with an average mapping rate of ~64%. The single nucleotide polymorphisms (SNPs) obtained from analysis using the genome ARS-UCD1.2 were compared with reference genomes of European Bos taurus Holstein, the Asian Bos indicus Brahman, and the African trypanotolerant N’Dama breeds.A total of ~100 million (M) SNPs were identified and 7.7 M of those were breed-specific. An approximately 11.1 M constituted of small insertions and deletions. By using only breed-specific non-synonymous variants we identified genes as genetic traits and associated Gene Ontology (GO) terms that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi breed and heat tolerance in the Kapsiki breed. Phylogenetic analysis grouped, except for Namchi, the Bos taurus breeds Kapsiki, N’Dama and Holstein together while the B. indicus breeds White and Red Fulani, Gudali and Brahman clustered separately. The deviating result for Namchi indicates a hybrid status of the selected animal with a recent introgression of Zebu genes into its genome. Conclusions: The findings provide the first comprehensive set of genome-wide variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.

scholarly journals Whole-genome sequencing of endangered Zhoushan cattle suggests its origin and the association of MC1R with black coat colour

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lihua Jiang ◽  
Tetsuo Kon ◽  
Chunyan Chen ◽  
Ryota Ichikawa ◽  
Qiyuan Zheng ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bos Taurus ◽  
Eastern China ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Coat Colour ◽  
Whole Genome ◽  
Angus Cattle ◽  
Genomic Regions

AbstractZhoushan cattle are an endangered cattle breed in the Zhoushan islands in China. Since Zhoushan cattle have been bred in isolation, they show unique characteristics, such as dark black coat colour. However, no studies have been conducted on the genome of Zhoushan cattle. Here, we performed whole-genome sequencing of seven individuals of Zhoushan cattle and nine cattle in Wenling, geographically close to the Zhoushan islands. By integrating our data and publicly-available data, we found that Zhoushan cattle are genetically highly similar to Bos indicus cattle in south-eastern China. Furthermore, by identifying the genomic regions shared between Zhoushan cattle and Angus cattle, a Bos taurus breed, we found that the p.F195L mutation in melanocyte-stimulating hormone receptor (MC1R) could be associated with their dark black coat colour. Taken together, our results provide a valuable resource for characterising the uniqueness of Zhoushan cattle.

scholarly journals Kinematic Sub-Populations in Bull Spermatozoa: A Comparison of Classical and Bayesian Approaches

Biology ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 138
Author(s):  
Luis Víquez ◽  
Vinicio Barquero ◽  
Carles Soler ◽  
Eduardo R.S. Roldan ◽  
Anthony Valverde
Keyword(s):  
Bayesian Analysis ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Computer Assisted ◽  
Clustering Methods ◽  
Bayesian Approaches ◽  
Sperm Analysis ◽  
Statistical Relevance ◽  
Multivariate Procedures ◽  
Bovine Species

The ejaculate is heterogenous and sperm sub-populations with different kinematic patterns can be identified in various species. Nevertheless, although these sub-populations are statistically well defined, the statistical differences are not always relevant. The aim of the present study was to characterize kinematic sub-populations in sperm from two bovine species, and diluted with different commercial extenders, and to determine the statistical relevance of sub-populations through Bayesian analysis. Semen from 10 bulls was evaluated after thawing. An ISAS®v1 computer-assisted sperm analysis (CASA)-Mot system was employed with an image acquisition rate of 50 Hz and ISAS®D4C20 counting chambers. Sub-populations of motile spermatozoa were characterized using multivariate procedures such as principal components (PCs) analysis and clustering methods (k-means model). Four different sperm sub-populations were identified from three PCs that involved progressiveness, velocity, and cell undulatory movement. The proportions of the different sperm sub-populations varied with the extender used and in the two species. Despite a statistical difference (p < 0.05) between extenders, the Bayesian analysis confirmed that only one of them (Triladyl®) presented relevant differences in kinematic patterns when compared with Tris-EY and OptiXcell®. Extenders differed in the proportion of sperm cells in each of the kinematic sub-populations. Similar patterns were identified in Bos taurus and Bos indicus. Bayesian results indicate that sub-populations SP1, SP2, and SP3 were different for PC criteria and these differences were relevant. For velocity, linearity, and progressiveness, the SP4 did not show a relevant difference regarding the other sperm sub-populations. The classical approach of clustering or sperm subpopulation thus may not have a direct biological meaning. Therefore, the biological relevance of sperm sub-populations needs to be reevaluated.

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