Identification of Expression QTLs Targeting Candidate Genes for Residual Feed Intake in Dairy Cattle Using Systems Genomics

Abstract

Background: Residual feed intake (RFI) is the difference between actual and predicted feed intake and an important factor determining feed efficiency (FE). Recently, 170 candidate genes were associated with RFI, but no expression quantitative trait loci (eQTL) mapping has hitherto been performed on FE related genes in dairy cows. In this study, an integrative systems genetics approach was applied to map eQTLs in Holstein and Jersey cows fed two different diets to improve identification of candidate genes for FE. Methods: Liver RNA-seq transcriptomics data from nine Holstein and ten Jersey cows that had been fed control (C) or high concentrate (HC) diets were integrated with genomic data (from 777k BovineHD Illumina BeadChip) by using the Matrix eQTL R package. A total of 170 previously identified candidate genes for FE (89 differentially expressed genes (DEGs) between high and low RFI groups and 81 hub genes (HG) in a group of co-expressed genes) were used in the data integration analysis. Results: From the 241,542 SNPs used in the analysis, we identified 20 significant (FDR < 0.05) local-eQTLs targeting seven candidate genes and 16 significant (FDR < 0.05) local-eQTLs targeting five candidate genes related to RFI for the C and HC diet group analysis, respectively, in a breed-specific way. Conclusions: Interestingly, Holstein and Jersey cows appear to rely on different strategies (lipid and cholesterol metabolism versus immune and inflammatory function) to achieve low RFI. The eQTLs overlapped with QTLs previously associated with FE trait (e.g. dry matter intake, longevity, body weight gain and net merit). The eQTLs and biological pathways identified in this study improve our understanding of the complex biological and genetic mechanisms that determine FE traits in dairy cattle. The identified eQTLs/genetic variants can potentially be used in new genomic selection methods that include biological/functional information on SNPs.

Genetic factors influencing milk and fat yields in tropically adapted dairy cattle: insights from quantitative trait loci analysis and gene associations

“…The KIT gene is known to be involved in hematopoiesis, gametogenesis, and melanogenesis and has been reported to be a candidate gene for spotting loci in various cattle breeds including Italian Holstein-Friesian, Italian Brown, Italian Simmental, Jersey, Rendena, Reggiana, Modenese, Angus, and Hereford [ 30 , 31 ]. Furthermore, PTPRE has been identified as a candidate gene for residual feed intake in dairy cattle [ 32 ].…”

Cross-population selection signatures in Canchim composite beef cattle

“…The ARHGEF37, ARRB1, FGD3, and FGD3 genes were found as associated with residual feed intake [71], post-weaning weight gain [72], carcass weight [73], and dry matter intake [74], respectively. Genes related to fat thickness, fat deposition, and adipogenesis were found by Xu et al [75] (EHBP1, CYFIP1, and EEF1A2), Mokry et al [76] (DARS), Zhang et al [77] (CDH20), Seong et al [32] (EPB41L4A and TCEA2), Yamashita-Sugahara et al [78] (FAM57B), Li et al [79] (LAMA5), and Crespo-Piazuelo et al [80] (ABHD12).…”

Genome-Wide Association Study for Body Weight and Carcass Weight in Sumba Ongole Bulls (Bos indicus)

“…Lee & Shin (2018) reported that the substitution rate of the CEP63 gene in Hanwoo was higher than in Friesian Holstein cattle (7.49E-11 vs 5.70E-11). The CEP63 gene has been identified as a potential gene for milk phosphorus content (Chen et al, 2018) and feed intake (Salleh et al, 2018) in dairy cattle. Rowan et al (2021) also identified CEP63 as the et al, 2015) and familial short stature (Lin et al, 2017) disorders.…”