Systems genetics and genome-wide association approaches for analysis of feed intake, feed efficiency, and performance in beef cattle

Abstract

ABSTRACT. Feed intake, feed efficiency, and weight gain are important economic traits of beef cattle in feedlots. In the present study, we investigated the physiological processes underlying such traits from the point of view of systems genetics. Firstly, using data from 1334 Nellore (Bos indicus) cattle and 943,577 single nucleotide polymorphisms (SNPs), a genome-wide association analysis was performed for dry matter intake, average daily weight gain, feed conversion ratio, and residual feed intake with a Bayesian Lasso procedure. Genes within 50-kb SNPs, most relevant for explaining the genomic variance, were annotated and the biological processes underlying the traits were inferred from Database for Annotation, Visualization and Integrated Discovery (DAVID) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Our results indicated several putative genomic regions associated with the target phenotypes and showed that almost all genomic variances were in the SNPs located in the intergenic and intronic regions. We further identified five main metabolic pathways related to ion transport, body composition, and feed intake control, which influenced the four phenotypes simultaneously. The systems genetics approach used in this study revealed novel pathways related to feed efficiency traits in beef cattle.

Functional Partitioning of Genomic Variance and Genome-Wide Association Study for Carcass Traits in Korean Hanwoo Cattle Using Imputed Sequence Level SNP Data

“…Our results are close to the findings of Koufariotis et al (2014) who reported the proportion of SNPs based on 777-K data in the aforementioned four classes to be 67.0, 31.0, 8.0, and 1.0%, respectively, in beef cattle. Santana et al (2016) reported the distribution of SNPs in intergenic, intron, and exon regions was 63.64, 28.17, and 1.46%, respectively, in Nellore cattle, which also supports our results. Taken together, the results indicate that several attributes like SNP density, LD among SNPs, poor functional annotation, and types of traits may affect the annotation results.…”

“…These studies showed that genic regions usually contributed more additive genetic variation than non-genic regions. However, Santana et al (2016) reported maximum genomic variance to be attributed to intergenic and intronic regions in beef cattle, whereas Do et al (2015) found almost similar genomic contributions from annotated genic and non-genic regions in pigs. The differences among these studies might be associated with several factors, such as SNP density in the marker panel, statistical models used, species, and types of traits investigated.…”

Genome-Wide Association Study of Growth and Feeding Traits in Pekin Ducks

“…A large number of QTL for feeding efficiency and growth rate in livestock have been located using genome scanning. In studies in beef cattle, several genes affecting the residual intake of beef cattle were discovered (Santana et al, 2014; Santana et al, 2016). Studies on pigs have also reported that multiple genes and biological pathways are associated with feeding efficiency and growth traits in growing pigs (Do et al, 2014a; Do et al, 2014b).…”

An examination of skeletal muscle and hepatic tissue transcriptomes from beef cattle divergent for residual feed intake 

“…Aldosterone is secreted by the adrenal glands and has a major role in electrolyte and uid homeostasis. The aldosterone signalling pathway has been implicated in feed e ciency previously in the spleen of ine cient animals 31 and, interestingly, a GWAS analysis with cattle identi ed this pathway to be associated with variation in feed conversion ratio 51 . The protein encoded by HSPA5 is a member of the HSP70 family and as this protein interacts with many endoplasmic reticulum (ER) proteins it is likely to be important in monitoring protein transport through the cell 52 .…”