Identification of genomic regions associated with feed efficiency in Nelore cattle

Abstract\ud \ud Background\ud 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 (770 k 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 1.0% of genetic variance were considered as QTL region. Candidate genes within windows that explained more than 1% of genetic variance were selected by putative function based on DAVID and Gene Ontology.\ud \ud \ud Results\ud 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%. Some of these QTL minimally overlapped with previously reported feed efficiency QTL for Bos taurus. 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 selected for feed efficiency are: HRH4, ALDH7A1, APOA2, LIN7C, CXADR, ADAM12 and MAP7.\ud \ud \ud \ud Conclusions\ud Some genomic regions and some positional candidate genes reported in this study have not been previously reported for feed efficiency traits in Bos indicus. Comparison with published results indicates that different QTLs and genes may be involved in the control of feed efficiency traits in this Nelore cattle population, as compared to Bos taurus cattle.CNPqCAPE

Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle

Abstract\ud \ud Background\ud Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample.\ud \ud \ud Results\ud Our results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. The application of the AWM/PCIT methodology revealed a trio of transcription factors (comprising VDR, LHX9 and ZEB1) which in combination connected 66 genes through 359 edges and whose biological functions were inspected, some revealing to participate in biological growth processes in literature searches.\ud \ud \ud Conclusions\ud The diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle.This study was conducted with funding from EMBRAPA (Macroprograma1,\ud 01/2005) and FAPESP (process number 2012/23638-8). GBM, LLC, LCAR and\ud MMA were granted CNPq fellowships. We thank Sean McWilliam, Marina R. S.\ud Fortes, Edilson Guimaraes, Robson Rodrigues Santiago, Roselito F. da Silva,\ud Fernando F. Cardoso, Flavia Aline Bressani, Wilson Malago Jr., Avelardo U. C.\ud Ferreira, Michel E. B. Yamaguishi and Fabio D. Vieira for the help and\ud technical assistance. The authors would like to acknowledge the\ud collaborative efforts among EMBRAPA, University of Sao Paulo and CSIRO

Significantly associated SNPs for birth weight (BW), weaning weight (WW), and long-yearling weight (LYW) obtained by the Generalized Quasi-Likelihood Score method (GQLS).

<p>Single locus regression was carried out to estimate allele substitution effects for significant SNPs.</p><p>*Coefficient of regression (P<0.001); FDR  =  False discovery rate; MAF  =  Minor allele frequency; bp  =  base pairs; BTA  =  <i>Bos taurus</i> autosome.</p

Manhattan plots of p-values for birth weight (BW), weaning weight (WW), and long-yearling weight (LYW).

<p>Significance levels were determined by false discovery rate (FDR) correction at levels of 1% (red line), 5% (blue line), and 10% (black line). Positions were presented in megabase pair (Mbp). Associations were observed in autosome (BTA) 4, 6, 7, 9, 11, 22, 25, and 27.</p