Combining information from genome-wide association and multi-tissue gene expression studies to elucidate factors underlying genetic variation for residual feed intake in Australian Angus cattle

Abstract

BackgroundGenome-wide association studies (GWAS) are extensively used to identify single nucleotide polymorphisms (SNP) underlying the genetic variation of complex traits. However, much uncertainly often still exists about the causal variants and genes at quantitative trait loci (QTL). The aim of this study was to identify QTL associated with residual feed intake (RFI) and genes in these regions whose expression is also associated with this trait. Angus cattle (2190 steers) with RFI records were genotyped and imputed to high density arrays (770 K) and used for a GWAS approach to identify QTL associated with RFI. RNA sequences from 126 Angus divergently selected for RFI were analyzed to identify the genes whose expression was significantly associated this trait with special attention to those genes residing in the QTL regions.ResultsThe heritability for RFI estimated for this Angus population was 0.3. In a GWAS, we identified 78 SNPs associated with RFI on six QTL (on BTA1, BTA6, BTA14, BTA17, BTA20 and BTA26). The most significant SNP was found on chromosome BTA20 (rs42662073) and explained 4% of the genetic variance. The minor allele frequencies of significant SNPs ranged from 0.05 to 0.49. All regions, except on BTA17, showed a significant dominance effect. In 1 Mb windows surrounding the six significant QTL, we found 149 genes from which OAS2, STC2, SHOX, XKR4, and SGMS1 were the closest to the most significant QTL on BTA17, BTA20, BTA1, BTA14, and BTA26, respectively. In a 2 Mb windows around the six significant QTL, we identified 15 genes whose expression was significantly associated with RFI: BTA20) NEURL1B and CPEB4; BTA17) RITA1, CCDC42B, OAS2, RPL6, and ERP29; BTA26) A1CF, SGMS1, PAPSS2, and PTEN; BTA1) MFSD1 and RARRES1; BTA14) ATP6V1H and MRPL15.ConclusionsOur results showed six QTL regions associated with RFI in a beef Angus population where five of these QTL contained genes that have expression associated with this trait. Therefore, here we show that integrating information from gene expression and GWAS studies can help to better understand the genetic mechanisms that determine variation in complex traits.

Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

“…Of these, we identified several genes to be related to body conformation, meat quality, susceptibility, and reproductive efficiency. For instance, BCKDHB was found to be related to the attachment width in Chinese Holstein cattle [52], and this gene was also reported to display a significant expression associated with RFI in Australian Angus cattle [53]. MAB21L1 were detected with a higher expression in longissimus lumborum and psoas major [54], which may result in distinct metabolic patterns and physiological processes for meat quality.…”

Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle

“…The BovineHD1400007035-rs136017102 SNP on Chr14, located close to the XKR4 gene, in previous studies, was reported to be associated with feed intake and growth phenotypes in cattle [ 75 ], residual feed intake in Australian Angus cattle [ 76 ], carcass weight (CWT) and eye muscle area (EMA) in Korean Hanwoo cattle [ 77 ], carcass trait [ 78 ], fat deposition in genome-wide association study for carcass trait in Brazilian Nellore cattle [ 79 ] and subcutaneous rump fat thickness in indicine and composite cattle [ 80 ].…”

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

“…VEPH1 influenced other cattle conformation traits such as udder cleft in Holstein and rump fat thickness in Nellore cattle, reflecting its role in lipid metabolism [78,79]. Furthermore, recent studies observed an association of VEPH1 with residual feed intake and antibody response to parasites in cattle [80,81].…”