Genomics in the United States beef industry

Rolf, Megan M; Decker, Jared E.; McKay, Stephanie; Tizioto, P. C.; Branham, Kimberly A.; Whitacre, Lynsey K.; Hoff, Jesse L.; Regitano, Luciana Correia de Almeida; Taylor, Jeremy F.

doi:10.1016/j.livsci.2014.06.005

Cited by 19 publications

(15 citation statements)

References 68 publications

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“…As new deleterious alleles are discovered, including those causing early embryonic loss, this approach will become untenable. The seven new putative autosomal recessive lethal haplotypes may now be predicted in hundreds of thousands of genotyped animals [ 29 ] and many more deleterious loci may be discovered as the number of genotyped animals increases and new lineages rise to prominence that contain yet to be detected recessive alleles. Management of the U.S. registered Angus population must shift from registration exclusion to a means of incorporating marker diagnostics into genomic selection and mate selection protocols to enable the long-term sustainability of the population.…”

Section: Discussionmentioning

confidence: 99%

Candidate lethal haplotypes and causal mutations in Angus cattle

et al. 2017

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BackgroundIf unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, candidates for developmentally lethal recessive loci can be localized. This analysis comes without the need for observation of the loss-associated phenotype (e.g., failure to implant, first trimester abortion, deformity at birth). In this study, haplotypes were estimated for 3961 registered Angus individuals using 52,545 SNP loci using findhap v2, which exploited the complex pedigree among the individuals in this population.ResultsSeven loci were detected to possess haplotypes that were not observed in homozygous form despite a sufficiently high frequency and pedigree-based expectation of homozygote occurrence. These haplotypes were identified as candidates for harboring autosomal recessive lethal alleles. Of the genotyped individuals, 109 were resequenced to an average 27X depth of coverage to identify putative loss-of-function alleles genome-wide and had variants called using a custom in-house developed pipeline. For the candidate lethal-harboring haplotypes present in these bulls, sequence-called genotypes were used to identify concordant variants. In addition, whole-genome sequence imputation of variants was performed into the set of 3961 genotyped animals using the 109 resequenced animals to identify candidate lethal recessive variants at the seven loci. Following the imputation, no variants were identified that were fully concordant with the marker-based diplotypes.ConclusionsSelective breeding programs could utilize the predicted lethal haplotypes associated with SNP genotypes. Sequencing and other methods for identifying the causal variants underlying these haplotypes can allow for more efficient methods of management such as gene editing. These two methods in total will reduce the negative impacts of inbreeding on fertility and maximize overall genetic gains.

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Section: Discussionmentioning

confidence: 99%

Candidate lethal haplotypes and causal mutations in Angus cattle

et al. 2017

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“…Epigenome-wide association studies are a vital analysis necessary for determining the epigenetic contribution toward phenotypic variation in economically important traits and diseases. Utilizing high resolution DNA methylation arrays, as has been done in humans ( Bibikova et al, 2011 ), will enhance the ability of the livestock industry to perform EWAS and permit the resolution of mechanisms underlying epigenetic inheritance and possibly enable the livestock industry to utilize epigenetic modifications for livestock production and breeding ( Rolf et al, 2014 ).…”

Section: Epigenetic Effect On Livestock Productionmentioning

confidence: 99%

Nutritional Influence on Epigenetic Marks and Effect on Livestock Production

Murdoch

Greenwood

et al. 2016

Front. Genet.

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Nutrition represents one of the greatest environmental determinants of an individual’s health. While nutrient quantity and quality impart direct effects, the interaction of nutrition with genetic and epigenetic modifications is often overlooked despite being shown to influence biological variation in mammals. Dissecting complex traits, such as those that are diet or nutrition related, to determine the genetic and epigenetic contributions toward a phenotype can be a formidable process. Epigenetic modifications add another layer of complexity as they do not change the DNA sequence itself but can affect transcription and are important mediators of gene expression and ensuing phenotypic variation. Altered carbohydrate metabolism and rates of fat and protein deposition resulting from diet-induced hypo- or hyper-methylation highlight the capability of nutritional epigenetics to influence livestock commodity quality and quantity. This interaction can yield either products tailored to consumer preference, such as marbling in meat cuts, or potentially increasing productivity and yield both in terms of carcass yield and/or offspring performance. Understanding how these and other desirable phenotypes result from epigenetic mechanisms will facilitate their inducible potential in livestock systems. Here, we discuss the establishment of the epigenome, examples of nutritional mediated alterations of epigenetics and epigenetic effects on livestock production.

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“…Indeed, RFI has been incorporated into the Australian dairy industry’s genomic breeding programme 9 . Unlike the situation that predominates for dairy production systems worldwide, effective identification of selection markers of RFI for beef cattle must take into account a multiplicity of breeds and the mainly crossbred nature of cattle typically utilised within the global beef industry through employing multi-breed populations in order to identify variants of interest 10 , 11 . Differences in linkage disequilibrium (LD) between breeds may impact the association of markers and quantitative trait loci across breeds.…”

Section: Introductionmentioning

confidence: 99%

GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle

Higgins

Fitzsimons

McClure

et al. 2018

Sci Rep

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Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10−5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.

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Genomics in the United States beef industry

Cited by 19 publications

References 68 publications

Candidate lethal haplotypes and causal mutations in Angus cattle

Candidate lethal haplotypes and causal mutations in Angus cattle

Nutritional Influence on Epigenetic Marks and Effect on Livestock Production

GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle

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