Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle

BMC Genetics

Sandra L Rodriguez-Zas²  Bruce R Southey³  Dan B Faulkner¹  Jonathan E Beever³  Dianelys González-Peña³  Nick VL Serão³ 

[1]Animal Sciences Department, University of Arizona, Tucson, AZ, USA

[2]Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA

[3]Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA

关键词: Serine/Threonine kinase activity;    MAPK pathway;    Functional analysis;    Haplotype;    Single nucleotide polymorphism;    Beef cattle;    Feed efficiency;   

Others  :  1086590
DOI  :  10.1186/1471-2156-14-94

 received in 2012-10-08, accepted in 2013-09-12,  发布年份 2013

【 摘 要 】

Background

General, 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.

Results

For 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.

Conclusions

The 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.

【 授权许可】

   
2013 Serão et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

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