Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattleReport as inadecuate

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BMC Genetics

, 14:94

First Online: 25 September 2013Received: 08 October 2012Accepted: 12 September 2013DOI: 10.1186-1471-2156-14-94

Cite this article as: Serão, N.V., González-Peña, D., Beever, J.E. et al. BMC Genet 2013 14: 94. doi:10.1186-1471-2156-14-94


BackgroundGeneral, breed- and diet-dependent associations between feed efficiency in beef cattle and single nucleotide polymorphisms SNPs or haplotypes were identified on a population of 1321 steers using a 50 K SNP panel. Genomic associations with traditional two-step indicators of feed efficiency – residual feed intake RFI, residual average daily gain RADG, and residual intake gain RIG – were compared to associations with two complementary one-step indicators of feed efficiency: efficiency of intake EI and efficiency of gain EG. Associations uncovered in a training data set were evaluated on independent validation data set. A multi-SNP model was developed to predict feed efficiency. Functional analysis of genes harboring SNPs significantly associated with feed efficiency and network visualization aided in the interpretation of the results.

ResultsFor the five feed efficiency indicators, the numbers of general, breed-dependent, and diet-dependent associations with SNPs P-value < 0.0001 were 31, 40, and 25, and with haplotypes were six, ten, and nine, respectively. Of these, 20 SNP and six haplotype associations overlapped between RFI and EI, and five SNP and one haplotype associations overlapped between RADG and EG. This result confirms the complementary value of the one and two-step indicators. The multi-SNP models included 89 SNPs and offered a precise prediction of the five feed efficiency indicators. The associations of 17 SNPs and 7 haplotypes with feed efficiency were confirmed on the validation data set. Nine clusters of Gene Ontology and KEGG pathway categories mean P-value < 0.001 including, 9nucleotide binding; ion transport, phosphorous metabolic process, and the MAPK signaling pathway were overrepresented among the genes harboring the SNPs associated with feed efficiency.

ConclusionsThe general SNP associations suggest that a single panel of genomic variants can be used regardless of breed and diet. The breed- and diet-dependent associations between SNPs and feed efficiency suggest that further refinement of variant panels require the consideration of the breed and management practices. The unique genomic variants associated with the one- and two-step indicators suggest that both types of indicators offer complementary description of feed efficiency that can be exploited for genome-enabled selection purposes.

KeywordsFeed efficiency Beef cattle Single nucleotide polymorphism Haplotype Functional analysis MAPK pathway Serine-Threonine kinase activity Electronic supplementary materialThe online version of this article doi:10.1186-1471-2156-14-94 contains supplementary material, which is available to authorized users.

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Author: Nick VL Serão - Dianelys González-Peña - Jonathan E Beever - Dan B Faulkner - Bruce R Southey - Sandra L Rodriguez-Z


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