Identification of cis-eQTLs Associated with Feed Efficiency in Nellore Cattle

The search for genomic regions associated with feed efficiency (FE) in beef cattle has been the focus of many researches in the past years by trying to associate SNPs in the DNA with the phenotypic trait. Recently, a new approach called “functional genomic selection” seeks to identify variants most likely to be the cause of phenotypic change, to improve the portability of genomic predictions between breeds and across populations. With this aim, we combined data from liver gene expression (RNAseq) and 80k genotype (GeneSeek GGP Bos Indicus HD^®, Illumina) of 14 Nellore bulls identified as extremes of FE, on a cis-eQTL analysis. Only SNPs with MAF>0.4 and at least 3 samples in at least 2 genotypes were tested, considering a 2Mb window surrounding 100 candidate genes for FE that were identified in our previous work. Gene expression was estimated by HTseq counts, using Bos taurus UMD3.1 as reference genome, and then normalized by library size. Data were analyzed considering a standard additive linear model and an ANOVA model that account for both additive and dominance effects, using Matrix eQTL package in R. After chromosome wise Bonferroni correction, 4 eQTLs were detected on chromosomes 4, 21, 23 and 28. Cis-acting SNPs can play a regulatory role in expression of genes related to FE and need to be validated in a bigger population.