Identification of genomic regions associated with feed efficiency in Nelore cattle

Authors: SN DE OLIVEIRA, PRISCILA SN - Universidade Federal De Sao Carlos; CESAR, ALINE SM - Universidad De Sao Paulo; DO NASCIMENTO, MICHELE - Universidad De Sao Paulo; CHAVES, AMALIA - Universidad De Sao Paulo; TULLIO, RYMER - Embrapa; LANNA, DANTE PD - Universidad De Sao Paulo; ROSA, ANTONIO - Embrapa; Sonstegard, Tad; MOURAO, GERSON - Universidad De Sao Paulo; REECY, JAMES - Iowa State University; GARRICK, DORIAN - Iowa State University; MUDADU, MAURICIO - Embrapa; COUTINHO, LUIZ - Universidad De Sao Paulo; REGITANO, LUCIANA - Embrapa

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2014
Publication Date: 9/26/2014
Citation: Sn De Oliveira, P., Cesar, A., Do Nascimento, M.L., Chaves, A.S., Tullio, R.R., Lanna, D., Rosa, A.N., Sonstegard, T.S., Mourao, G.B., Reecy, J.M., Garrick, D.J., Mudadu, M.A., Coutinho, L.L., Regitano, L.C. 2014. Identification of genomic regions associated with feed efficiency in Nelore cattle. BioMed Central (BMC) Genetics 15:100. DOI:10.1186/s12863-014-0100-0.

Interpretive Summary: It is possible to analyze high-density DNA marker (single nucleotide polymorphism or SNP-based data) to find regions of the genome that affect feed efficiency traits. This study is the first high-density (700,000 SNP marker) scan of a Bos indicus cattle from Brazil for 9 feed efficiency traits. Besides some previously reported genomic regions associated with feed efficiency in Bos taurus, the present genome-wide association study identified several novel genomic regions, indicating that feed efficiency in Nelore is controlled by some Bos indicus-specific mechanisms. Genes within these regions could be candidate genes for feed efficiency traits in Nelore cattle. Once the genes and/or genomic segments that control feed efficiency-related traits have been identified, it should be possible to determine the biological mechanisms and the genetic basis underlying these traits. Because feed is the main component of cattle production costs, and Nelore is the breed of greatest economic importance in Brazil, the ability to identify and select for feed-efficient animals should have a considerable economic impact. Development of molecular criteria for improving feed efficiency in Nelore should also contribute to reductions in the environmental impact of beef production in the tropics.

Technical Abstract: Feed efficiency is jointly determined by productivity and feed requirements, both of which are economically relevant traits in beef cattle production systems. The objective of this study was to identify genes/QTLs associated with components of feed efficiency in Nelore cattle using Illumina BovineHD BeadChip (770k SNP) genotypes from 593 Nelore steers. The traits analyzed included: average daily gain (ADG), dry matter intake (DMI), feed-conversion ratio (FCR), feed efficiency (FE), residual feed intake (RFI), maintenance efficiency (ME), efficiency of gain (EG), partial efficiency of growth (PEG) and relative growth rate (RGR). The Bayes B analysis was completed with Gensel software parameterized to fit fewer markers than animals. Genomic windows containing all the SNP loci in each 1 Mb that accounted for more than 0.5% of genetic variance were considered as QTL. Candidate genes within windows that explained more than 1% of genetic variance were annotated by putative function based on DAVID and Gene Ontology. Thirty-six QTL (1-Mb SNP window) were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25 and 26 (UMD 3.1). The amount of genetic variance explained by individual QTL windows for feed efficiency traits ranged from 0.5% to 9.07%. The largest QTLs were located on BTA 2, 9 and 12. These QTL minimally overlapped with previously reported feed efficiency QTL for other breeds. The QTL regions described in this study harbor genes with biological functions related to metabolic processes, lipid and protein metabolism, generation of energy and growth. Among the positional candidate genes for feed efficiency are: HRH4, ALDH7A1, APOA2, LIN7C, MGC157263, PTGS1, ENPP2, DNAJC9, CXADR, ADAM12 and MAP7. Some positional candidate genes reported in this study were never reported before for feed efficiency traits in Bos indicus. Comparison with published results indicates that different genetic mechanisms may be involved in the control of feed efficiency traits for Nelore cattle, as compared to Bos taurus cattle.