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 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 SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Netsanet Z. Gebrehiwot ◽  
Eva M. Strucken ◽  
Karen Marshall ◽  
Hassan Aliloo ◽  
John P. Gibson
Keyword(s):  
Allele Frequency ◽  
Bos Taurus ◽  
Low Cost ◽  
Bos Indicus ◽  
High Density ◽  
Indigenous Populations ◽  
Genetic Admixture ◽  
Genotype Data ◽  
Parentage Assignment ◽  
Snp Panels

Abstract Background Understanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows. Methods Medium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny. Results For the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2. Conclusions The identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.

scholarly journals Genomic prediction using low-coverage portable Nanopore sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261274
Author(s):  
Harrison J. Lamb ◽  
Ben J. Hayes ◽  
Imtiaz A. S. Randhawa ◽  
Loan T. Nguyen ◽  
Elizabeth M. Ross
Keyword(s):  
Genomic Prediction ◽  
Disease Risk ◽  
Sequence Data ◽  
Snp Array ◽  
Genotyping By Sequencing ◽  
Risk Scores ◽  
Genomic Breeding ◽  
Breeding Values ◽  
Low Coverage ◽  
On Farm

Most traits in livestock, crops and humans are polygenic, that is, a large number of loci contribute to genetic variation. Effects at these loci lie along a continuum ranging from common low-effect to rare high-effect variants that cumulatively contribute to the overall phenotype. Statistical methods to calculate the effect of these loci have been developed and can be used to predict phenotypes in new individuals. In agriculture, these methods are used to select superior individuals using genomic breeding values; in humans these methods are used to quantitatively measure an individual’s disease risk, termed polygenic risk scores. Both fields typically use SNP array genotypes for the analysis. Recently, genotyping-by-sequencing has become popular, due to lower cost and greater genome coverage (including structural variants). Oxford Nanopore Technologies’ (ONT) portable sequencers have the potential to combine the benefits genotyping-by-sequencing with portability and decreased turn-around time. This introduces the potential for in-house clinical genetic disease risk screening in humans or calculating genomic breeding values on-farm in agriculture. Here we demonstrate the potential of the later by calculating genomic breeding values for four traits in cattle using low-coverage ONT sequence data and comparing these breeding values to breeding values calculated from SNP arrays. At sequencing coverages between 2X and 4X the correlation between ONT breeding values and SNP array-based breeding values was > 0.92 when imputation was used and > 0.88 when no imputation was used. With an average sequencing coverage of 0.5x the correlation between the two methods was between 0.85 and 0.92 using imputation, depending on the trait. This suggests that ONT sequencing has potential for in clinic or on-farm genomic prediction, however, further work to validate these findings in a larger population still remains.

scholarly journals In-situ genomic prediction using low-coverage Nanopore sequencing

2021 ◽  
Author(s):  
Harry Lamb ◽  
Ben Hayes ◽  
Imtiaz Randhawa ◽  
Loan Nguyen ◽  
Elizabeth Ross
Keyword(s):  
Genomic Prediction ◽  
Disease Risk ◽  
Sequence Data ◽  
Snp Array ◽  
Genotyping By Sequencing ◽  
Risk Scores ◽  
Genomic Breeding ◽  
Breeding Values ◽  
Low Coverage ◽  
On Farm

Most traits in livestock, crops and humans are polygenic, that is, a large number of loci contribute to genetic variation. Effects at these loci lie along a continuum ranging from common low-effect to rare high-effect variants that cumulatively contribute to the overall phenotype. Statistical methods to calculate the effect of these loci have been developed and can be used to predict phenotypes in new individuals. In agriculture, these methods are used to select superior individuals using genomic breeding values; in humans these methods are used to quantitatively measure an individual’s disease risk, termed polygenic risk scores. Both fields typically use SNP array genotypes for the analysis.  Recently, genotyping-by-sequencing has become popular, due to lower cost and greater genome coverage (including structural variants).   Oxford Nanopore Technologies’ (ONT) portable sequencers have the potential to combine the benefits genotyping-by-sequencing with portability and decreased turn-around time. This introduces the potential for in-house clinical genetic disease risk screening in humans or calculating genomic breeding values on-farm in agriculture. Here we demonstrate the potential of the later by calculating genomic breeding values for four traits in cattle using low-coverage ONT sequence data and comparing these breeding values to breeding values calculated from SNP arrays. At sequencing coverages between 2X and 4X the correlation between ONT breeding values and SNP array-based breeding values was > 0.92 when imputation was used and > 0.88 when no imputation was used. With an average sequencing coverage of 0.5x the correlation between the two methods was between 0.85 and 0.92 using imputation, depending on the trait.  This demonstrates that ONT sequencing has great potential for in clinic or on-farm genomic prediction.

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 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.

scholarly journals Light Cross-Linkable Marine Collagen for Coaxial Printing of a 3D Model of Neuromuscular Junction Formation

Biomedicines ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 16
Author(s):  
Borja Sanz ◽  
Ane Albillos Sanchez ◽  
Bonnie Tangey ◽  
Kerry Gilmore ◽  
Zhilian Yue ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Neuromuscular Junction ◽  
Disease Transmission ◽  
Low Cost ◽  
Attractive Alternative ◽  
Waste Products ◽  
Environmentally Sustainable ◽  
Zoonotic Disease Transmission ◽  
And Migration

Collagen is a major component of the extracellular matrix (ECM) that modulates cell adhesion, growth, and migration, and has been utilised in tissue engineering applications. However, the common terrestrial sources of collagen carry the risk of zoonotic disease transmission and there are religious barriers to the use of bovine and porcine products in many cultures. Marine based collagens offer an attractive alternative and have so far been under-utilized for use as biomaterials for tissue engineering. Marine collagen can be extracted from fish waste products, therefore industry by-products offer an economical and environmentally sustainable source of collagen. In a handful of studies, marine collagen has successfully been methacrylated to form collagen methacrylate (ColMA). Our work included the extraction, characterization and methacrylation of Red Snapper collagen, optimisation of conditions for neural cell seeding and encapsulation using the unmodified collagen, thermally cross-linked, and the methacrylated collagen with UV-induced cross-linking. Finally, the 3D co-axial printing of neural and skeletal muscle cell cultures as a model for neuromuscular junction (NMJ) formation was investigated. Overall, the results of this study show great potential for a novel NMJ in vitro 3D bioprinted model that, with further development, could provide a low-cost, customizable, scalable and quick-to-print platform for drug screening and to study neuromuscular junction physiology and pathogenesis.

Chemical composition of whole body and carcass of Bos indicus and tropically adapted Bos taurus breeds

2011 ◽  
Vol 89 (9) ◽  
pp. 2859-2866 ◽  
Author(s):  
S. F. M. Bonilha ◽  
L. O. Tedeschi ◽  
I. U. Packer ◽  
A. G. Razook ◽  
R. F. Nardon ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Whole Body

scholarly journals Y chromosome variants in cattle Bos taurus and Bos indicus

1982 ◽  
Vol 14 (1) ◽  
pp. 1 ◽  
Author(s):  
CRE Halnan ◽  
Janine I Watson
Keyword(s):  
Y Chromosome ◽  
Bos Taurus ◽  
Bos Indicus
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