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Saronville, NE, United States

Lindholm-Perry A.K.,U.S. Department of Agriculture | Kuehn L.A.,U.S. Department of Agriculture | Smith T.P.L.,U.S. Department of Agriculture | Ferrell C.L.,F and J Livestock Consulting LLC | And 3 more authors.
Animal Genetics | Year: 2012

Feed cost for beef cattle is the largest expense incurred by cattle producers. The development of genetic markers to enhance selection of more efficient animals that require less feed while still achieving acceptable levels of production has the potential to substantially reduce production costs. A genome-wide marker association approach based on the Illumina BovineSNP50 BeadChip™ was used to identify genomic regions affecting average daily feed intake (ADFI), average daily gain (ADG) and residual feed intake traits in a population of 1159 crossbred steers. This approach identified a region on BTA14 from 22.02 to 23.92 Mb containing several single-nucleotide polymorphisms (SNPs) that have significant association with at least one of the traits. Two genes in this region, lysophospholipase 1 (LYPLA1) and transmembrane protein 68 (TMEM68), appeared to be logical positional and functional candidate genes. LYPLA1 deacylates ghrelin, a hormone involved in the regulation of appetite in the rat stomach, while TMEM68 is expressed in bovine rumen, abomasum, intestine and adipose tissue in cattle, and likely affects lipid biosynthetic processes. SNPs lying in or near these two genes were identified by sequencing a subset of animals with extreme phenotypes. A total of 55 SNPs were genotyped and tested for association with the same population of steers. After correction for multiple testing, five markers within 22.79-22.84 Mb, located downstream of TMEM68, and between TMEM68 and the neighbouring gene XKR4, were significant for both ADFI and ADG. Genetic markers predictive of feed intake and weight gain phenotypes in this population of cattle may be useful for the identification and selection of animals that consume less feed, although further evaluation of these markers for effects on other production traits and validation in additional populations will be required. © 2011 Stichting International Foundation for Animal Genetics. No claim to original US government works.

Lindholm-Perry A.K.,U.S. Department of Agriculture | Kuehn L.A.,U.S. Department of Agriculture | Snelling W.M.,U.S. Department of Agriculture | Smith T.P.L.,U.S. Department of Agriculture | And 8 more authors.
Animal Genetics | Year: 2012

With the high cost of feed for animal production, genetic selection for animals that metabolize feed more efficiently could result in substantial cost savings for cattle producers. The purpose of this study was to identify DNA markers predictive for differences among cattle for traits associated with feed efficiency. Crossbred steers were fed a high-corn diet for 140 days and average daily feed intake (ADFI), average daily gain (ADG), and residual feed intake (RFI) phenotypes were obtained. A region on chromosome 14 was previously associated with RFI in this population of animals. To develop markers with the highest utility for predicting an animal's genetic potential for RFI, we genotyped additional markers within this chromosomal region. These polymorphisms were genotyped on the same animals (n = 1066) and tested for association with ADFI, ADG and RFI. Six markers within this region were associated with RFI (P ≤ 0.05). After conservative correction for multiple testing, one marker at 25.09 Mb remained significant (P = 0.02) and is responsible for 3.6% of the RFI phenotypic variation in this population of animals. Several of these markers were also significant for ADG, although none were significant after correction. Marker alleles with positive effects on ADG corresponded to lower RFI, suggesting an effect increasing growth without increasing feed intake. All markers were also assessed for their effects on meat quality and carcass traits. All of the markers associated with RFI were associated with adjusted fat thickness (AFT, P ≤ 0.009) and three were also associated with hot carcass weight (HCW, P ≤ 0.003). Marker alleles associated with lower RFI were also associated with reduced AFT, and if they were associated for HCW, the effect was an increase in weight. These markers may be useful as prediction tools for animals that utilize feed more efficiently; however, validation with additional populations of cattle is required. © Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Lindholm-Perry A.K.,U.S. Department of Agriculture | Sexten A.K.,U.S. Department of Agriculture | Sexten A.K.,Kansas State University | Kuehn L.A.,U.S. Department of Agriculture | And 10 more authors.
BMC Genetics | Year: 2011

Background: In a previously reported genome-wide association study based on a high-density bovine SNP genotyping array, 8 SNP were nominally associated (P ≤ 0.003) with average daily gain (ADG) and 3 of these were also associated (P ≤ 0.002) with average daily feed intake (ADFI) in a population of crossbred beef cattle. The SNP were clustered in a 570 kb region around 38 Mb on the draft sequence of bovine chromosome 6 (BTA6), an interval containing several positional and functional candidate genes including the bovine LAP3, NCAPG, and LCORL genes. The goal of the present study was to develop and examine additional markers in this region to optimize the ability to distinguish favorable alleles, with potential to identify functional variation.Results: Animals from the original study were genotyped for 47 SNP within or near the gene boundaries of the three candidate genes. Sixteen markers in the NCAPG-LCORL locus displayed significant association with both ADFI and ADG even after stringent correction for multiple testing (P ≤ 005). These markers were evaluated for their effects on meat and carcass traits. The alleles associated with higher ADFI and ADG were also associated with higher hot carcass weight (HCW) and ribeye area (REA), and lower adjusted fat thickness (AFT). A reduced set of markers was genotyped on a separate, crossbred population including genetic contributions from 14 beef cattle breeds. Two of the markers located within the LCORL gene locus remained significant for ADG (P ≤ 0.04).Conclusions: Several markers within the NCAPG-LCORL locus were significantly associated with feed intake and body weight gain phenotypes. These markers were also associated with HCW, REA and AFT suggesting that they are involved with lean growth and reduced fat deposition. Additionally, the two markers significant for ADG in the validation population of animals may be more robust for the prediction of ADG and possibly the correlated trait ADFI, across multiple breeds and populations of cattle. © 2011 Lindholm-Perry et al; licensee BioMed Central Ltd.

Snelling W.M.,U.S. Department of Agriculture | Allan M.F.,U.S. Department of Agriculture | Allan M.F.,Pfizer | Keele J.W.,U.S. Department of Agriculture | And 10 more authors.
Journal of Animal Science | Year: 2011

The effects of individual SNP and the variation explained by sets of SNP associated with DMI, metabolic midtest BW, BW gain, and feed efficiency, expressed as phenotypic and genetic residual feed intake, were estimated from BW and the individual feed intake of 1,159 steers on dry lot offered a 3.0 Mcal/kg ration for at least 119 d before slaughter. Parents of these F 1 × F 1 (F 1 2) steers were AI-sired F 1 progeny of Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental bulls mated to US Meat Animal Research Center Angus, Hereford, and MARC III composite females. Steers were genotyped with the BovineSNP50 BeadChip assay (Illumina Inc., San Diego, CA). Effects of 44,163 SNP having minor allele frequencies >0.05 in the F 1 2 generation were estimated with a mixed model that included genotype, breed composition, heterosis, age of dam, and slaughter date contemporary groups as fixed effects, and a random additive genetic effect with recorded pedigree relationships among animals. Variance in this population attributable to sets of SNP was estimated with models that partitioned the additive genetic effect into a polygenic component attributable to pedigree relationships and a genotypic component attributable to genotypic relationships. The sets of SNP evaluated were the full set of 44,163 SNP and subsets containing 6 to 40,000 SNP selected according to association with phenotype. Ninety SNP were strongly associated (P < 0.0001) with at least 1 efficiency or component trait; these 90 accounted for 28 to 46% of the total additive genetic variance of each trait. Trait-specific sets containing 96 SNP having the strongest associations with each trait explained 50 to 87% of additive variance for that trait. Expected accuracy of steer breeding values predicted with pedigree and genotypic relationships exceeded the accuracy of their sires predicted without genotypic information, although gains in accuracy were not sufficient to encourage that performance testing be replaced by genotyping and genomic evaluations. © 2011 American Society of Animal Science. All rights reserved.

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