scholarly journals Genome-wide local ancestry and direct evidence for mitonuclear co-adaptation in African hybrid cattle populations (Bos taurus/indicus)

2021 ◽  
Author(s):  
James A. Ward ◽  
Gillian P. McHugo ◽  
Michael J. Dover ◽  
Thomas J. Hall ◽  
Said Ismael Ng’ang’a ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Phenotypic Diversity ◽  
Bos Indicus ◽  
Snp Array ◽  
Human Migration ◽  
Nuclear Genes ◽  
Local Ancestry ◽  
African Cattle ◽  
Mitochondrial Haplotypes ◽  
Wide Range

AbstractDomestic cattle have a key economic role in African societies, providing an important source of mobile wealth through supply of meat, milk, cowhide, fuel, transport, and traction. The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which share a common ancestor 150-500 thousand years ago. Human migration and trade from Asia have left a peak of zebu nuclear ancestry in East Africa and most cattle populations across the continent have a hybrid genetic composition. Notwithstanding this, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu nuclear ancestry. In this regard, the efficient functioning of the mitochondrion relies on a network of biochemical interactions between the products of 37 mitochondrial genes and more than one thousand nuclear genes; therefore, admixed African cattle represent ideal populations for evaluating mitonuclear interactions and mismatch between the nuclear and mitochondrial genomes. Using high-density SNP array data from 18 different cattle populations, including ten African admixed breeds, we find strong evidence for mitonuclear coevolution in hybrid African cattle with significant retention of Bos taurus alleles at mitochondrially-targeted nuclear genes, particularly those genes with products that directly interact with mtDNA-encoded protein subunits in OXPHOS and ribosomal complexes, or that have functions in mtDNA replication. We also show that subspecific local ancestry varies substantially across the genomes of admixed populations, with a marked signal of taurine ancestry at the major histocompatibility (MHC) gene cluster, which likely reflects adaptation to infectious disease challenges facing African livestock. Our results demonstrate that African admixed cattle represent an excellent comparative model for studying the phenotypic consequences of mitonuclear mismatch and genomic introgression in humans and other large mammals.

scholarly journals Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1312
Author(s):  
Warren M. Snelling ◽  
Jesse L. Hoff ◽  
Jeremiah H. Li ◽  
Larry A. Kuehn ◽  
Brittney N. Keel ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Genomic Sequence ◽  
Bos Taurus ◽  
Low Cost ◽  
Bos Indicus ◽  
Snp Array ◽  
Attractive Alternative ◽  
Functional Variant ◽  
Low Pass ◽  
Low Coverage

Decreasing costs are making low coverage sequencing with imputation to a comprehensive reference panel an attractive alternative to obtain functional variant genotypes that can increase the accuracy of genomic prediction. To assess the potential of low-pass sequencing, genomic sequence of 77 steers sequenced to >10X coverage was downsampled to 1X and imputed to a reference of 946 cattle representing multiple Bos taurus and Bos indicus-influenced breeds. Genotypes for nearly 60 million variants detected in the reference were imputed from the downsampled sequence. The imputed genotypes strongly agreed with the SNP array genotypes (r¯=0.99) and the genotypes called from the transcript sequence (r¯=0.97). Effects of BovineSNP50 and GGP-F250 variants on birth weight, postweaning gain, and marbling were solved without the steers’ phenotypes and genotypes, then applied to their genotypes, to predict the molecular breeding values (MBV). The steers’ MBV were similar when using imputed and array genotypes. Replacing array variants with functional sequence variants might allow more robust MBV. Imputation from low coverage sequence offers a viable, low-cost approach to obtain functional variant genotypes that could improve genomic prediction.

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 Microsatellite DNA Variation and the Evolution, Domestication and Phylogeography of Taurine and Zebu Cattle (Bos taurus and Bos indicus)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 1071-1086 ◽  
Author(s):  
David E MacHugh ◽  
Mark D Shriver ◽  
Ronan T Loftus ◽  
Patrick Cunningham ◽  
Daniel G Bradley
Keyword(s):  
Bos Taurus ◽  
Bos Indicus ◽  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Strong Support ◽  
Zebu Cattle ◽  
Genetic Introgression ◽  
African Cattle ◽  
African Populations ◽  
Taurine Cattle

Genetic variation at 20 microsatellite loci was surveyed to determine the evolutionary relationships and molecular biogeography of 20 different cattle populations from Africa, Europe and Asia. Phylogenetic reconstruction and multivariate analysis highlighted a marked distinction between humpless (taurine) and humped (zebu) cattle, providing strong support for a separate origin for domesticated zebu cattle. A molecular clock calculation using bison (Bison sp.) as an outgroup gave an estimated divergence time between the two subspecies of 610,000-850,000 years. Substantial differences in the distribution of alleles at 10 of these loci were observed between zebu and taurine cattle. These markers subsequently proved very useful for investigations of gene flow and admixture in African populations. When these data were considered in conjunction with previous mitochondrial and Y chromosomal studies, a distinctive male-mediated pattern of zebu genetic introgression was revealed. The introgression of zebu-specific alleles in African cattle afforded a high resolution perspective on the hybrid nature of African cattle populations and also suggested that certain West African populations of valuable disease-tolerant taurine cattle are under threat of genetic absorption by migrating zebu herds.

Oestrous cycle synchronization and oestrus induction in indigenous and European cattle in Tanzania

1973 ◽  
Vol 81 (3) ◽  
pp. 381-389 ◽  
Author(s):  
H. Schmidt ◽  
W. Jöchle ◽  
D. Smidt
Keyword(s):  
Bos Taurus ◽  
Oral Treatment ◽  
Treatment Success ◽  
Bos Indicus ◽  
Oestrous Cycle ◽  
Estradiol Valerate ◽  
Wide Range ◽  
Reproductive Life ◽  
The Tropics ◽  
European Cattle

SUMMARYFrom 1969 to 1971, 743 animals (indigenous Zebu and European dairy cattle, lactating or dry cows and heifers) received oestrous cycle synchronization treatments at government-owned and private ranches and farms in the Tanzanian highlands (West Kilimanjaro); 445 matching animals served as controls. Treatment schedules consisted of chlormadinone acetate (CAP) given daily for 14 days (10 mg/day) orally; or a single CAP injection (50 mg) followed by 4 or 5 days of oral treatment (10 mg/day) 9–12 or 11–15 days later. In addition, some groups received either estradiol valerate (5 mg) together with the CAP injection, or 10 mg/day mestranol from day 11 to 15, together with CAP; one treatment group received 1000 i.u. of HCG after the last CAP medication and were inseminated 12 and 24 h thereafter. Animals were either inseminated or bred naturally. With all treatment schedules, good synchronization, unimpaired fertility and consistently a significant reduction of anoestrus was achieved. Oestrogen treatments had no effects; treatment with 1000 i.u. of HCG was unsuccessful. Management factors, food supply and phase of reproductive life had significant impacts on treatment success and fertility. Synchronization can be used successfully under a wide range of management conditions to unfold existing potentials of artificial insemination in Bos indicus and Bos taurus in the tropics.

scholarly journals Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cuili Pan ◽  
Zhaoxiong Lei ◽  
Shuzhe Wang ◽  
Xingping Wang ◽  
Dawei Wei ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Adipocyte Differentiation ◽  
Bos Taurus ◽  
Adipogenic Differentiation ◽  
Critical Role ◽  
Bos Indicus ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

Expression of candidate genes for residual feed intake in tropically adapted Bos taurus and Bos indicus bulls under thermoneutral and heat stress environmental conditions

2021 ◽  
pp. 102998
Author(s):  
Bianca Vilela Pires ◽  
Nedenia Bonvino Stafuzza ◽  
Luara Afonso de Freitas ◽  
Maria Eugênia Zerlotti Mercadante ◽  
Ester Silveira Ramos ◽  
...  
Keyword(s):  
Heat Stress ◽  
Candidate Genes ◽  
Feed Intake ◽  
Environmental Conditions ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Residual Feed Intake

scholarly journals Morphometric and Molecular Analyses of Ostertagia leptospicularis Assadov, 1953 from Ruminants: Species Diversity or Host Influence?

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 182
Author(s):  
Anna Wyrobisz-Papiewska ◽  
Jerzy Kowal ◽  
Elżbieta Łopieńska-Biernat ◽  
Paweł Nosal ◽  
Iwona Polak ◽  
...  
Keyword(s):  
Host Species ◽  
Roe Deer ◽  
Bos Taurus ◽  
Capreolus Capreolus ◽  
Nematode Species ◽  
Molecular Techniques ◽  
Systematic Classification ◽  
Morphological Variations ◽  
Wide Range ◽  
Induced Changes

Ostertagia leptospicularis Assadov, 1953 was formally described in roe deer Capreolus capreolus and has been reported in a wide range of ruminants, including other Cervidae, as well as Bovidae. Nematode specimens derived from various host species exhibit morphological similarity; however, some differences can be observed. It is unclear if this is due to the differential reaction of one nematode species in different host species (i.e., host-induced changes) or because of distinct nematode species in these hosts (i.e., species complex). This paper focuses on specimens resembling O. leptospicularis f. leptospicularis and its closely related species (Ostertagia ostertagi f. ostertagi) collected from various hosts. Morphometric and molecular techniques were applied to assess host-induced changes in nematode morphology and to clarify its systematic classification. There was an overall effect of host species on measurements of nematodes resembling O. leptospicularis (both males and females), but the distinctiveness of the specimens from cattle Bos taurus were highlighted. The results obtained may suggest that the specimens of O. leptospicularis from cattle in Germany and cervids in central Europe belong to different strains. Furthermore, nematodes from the cervid strain appear to circulate within particular host species, which can be seen in the stated morphological variations.

scholarly journals Differences in copper and selenium metabolism between Angus (Bos taurus) and Brahman (Bos indicus) cattle

2021 ◽  
Author(s):  
J Ranches ◽  
R Alves ◽  
M Vedovatto ◽  
E Anne Palmer ◽  
P Moriel ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Bos Indicus ◽  
First Trimester ◽  
Beef Cows ◽  
Experimental Unit ◽  
University Of Florida ◽  
Brahman Cattle ◽  
Research And Education ◽  
The University ◽  
Se Status

Abstract A two-year study was conducted at the University of Florida – IFAS, Range Cattle Research and Education Center (Ona, FL) to evaluate differences in the metabolism of Cu and Se of Angus (Bos taurus) and Brahman (Bos indicus) cattle. Thirty-two pregnant beef cows (n = 8 Brahman and 8 Angus/year) were enrolled in the study in the first trimester of gestation. The study consisted of 3 phases: (1) restriction (d 0 to d 90); (2) supplementation (d 91 to 150), and (3) calving. During all 3 phases, cows were individually fed and housed in partially covered drylot pens. During the restriction and supplementation phases cows were provided a 1.5 kg/d of a grain-based concentrate supplement, which was fortified with flowers of S (50 g of supplemental S/cow daily; restriction phase) or Cu and Se (100 and 3 mg/d of Cu and Se, respectively; supplementation phase). Blood and liver samples were collected from all cows on 30 d intervals and from both cows and calves within 24 h of calving. Colostrum and milk samples were collected at calving and 7 d after birth. All data were analyzed using the MIXED procedure of SAS, where cow and calf were the experimental unit. During the restriction phase, a breed × day effect (P = 0.03) was observed where Brahman had greater liver Cu concentration than Angus cows in all sampling days. For liver Se concentration, a tendency (P = 0.07) for a breed effect was observed where Angus cows tended to have greater liver Se concentration than Brahman. During the supplementation phase, breed (P < 0.001) and day (P < 0.01) effects were observed, where Brahman cows had greater liver Cu concentration than Angus. For liver Se concentration, a day effect (P < 0.001) was observed, where liver Se concentration increased (P < 0.001) from d 90 to 120 and remained unchanged (P = 0.86) until d 150. At calving no effects of breed (P = 0.34) were observed for liver Cu concentration of cows, however, Brahman calves tended (P = 0.09) to have greater liver Cu concentration than Angus calves. For Se liver concentration at calving, Angus cows tended (P = 0.07) to have greater liver Se concentration than Brahman cows, however no breed differences (P = 0.70) were observed for liver Se concentration of calves at birth. In summary substantial differences in multiple indicators of Cu and Se status were observed between Angus and Brahman cattle, implying that Angus and Brahman cattle possibly have different mechanisms to maintain adequate Cu and Se status.

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