Background: Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. Results: Whereas a relatively small number of molecular phenotypes were significantly heritable (h ² > 0, P  < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly ( P < 0.05) larger than expected by chance. The identified eQTL were significantly ( P  < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles. Conclusions: We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.

Background: The presence and concentration of lipids in serum of dairy cows have significant implications for both animal health and productivity and are potential biomarkers for several common diseases. However, information on serum lipid composition is rather fragmented, and lipid remodelling during the transition period is only partially understood. Methods: Using a combination of reversed-phase liquid chromatography-mass spectrometry (RP-LC-MS), hydrophilic interaction-mass spectrometry (HILIC-MS), and lipid annotation software, we performed a comprehensive identification and quantification of serum of dairy cows in pasture-based Holstein-Friesian cows. The lipid remodelling induced by negative energy balance was investigated by comparing the levels of all identified lipids between the fresh lactation (5–14 days in milk, DIM) and full lactation (65–80 DIM) stages. Results: We identified 535 lipid molecular species belonging to 19 classes. The most abundant lipid class was cholesteryl ester (CE), followed by phosphatidylcholine (PC), sphingomyelin (SM), and free fatty acid (FFA), whereas the least abundant lipids included phosphatidylserine (PS), phosphatidic acid (PA), phosphatidylglycerol (PG), acylcarnitine (AcylCar), ceramide (Cer), glucosylceramide (GluCer), and lactosylceramide (LacCer). Conclusions: A remarkable increase in most lipids and a dramatic decrease in FFAs, AcylCar, and DHA-containing species were observed at the full lactation compared to fresh lactation stage. Several serum lipid biomarkers for detecting negative energy balance in cows were also identified.

Background: Negative energy balance (NEB) during the transition period is associated with profound changes in the body condition and metabolic dynamics of dairy cows. However, the detailed lipidomic changes in milk induced by NEB are unclear, and lipid biomarkers that indicate the energy status of cows remain to be established. Methods: Using a combination of GC-FID, HILIC-MS and RP-LC-MS, we performed a systematic comparison of lipid composition between early lactating (DIM: 5–14) and mid-lactating (DIM: 65–80) milk. Results: We found that NEB in cows caused a profound modification in the profile of all the lipid classes surveyed, including phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylinositol (PI), sphingomyelin (SM), lysophosphatidylcholine (LPC), PC-plasmalogen (PCP), PE-plasmalogen (PEP), lactosylceramide (LacCer), acylcarnitine (AcylCar) and triglycerides (TAGs). Except for LPC and AcylCar, which were reduced and increased, respectively, by NEB, the responses of other lipid classes varied across different species. For phospholipids and TAGs, species containing de novo FAs (C4:0–C16:0) and odd-chain FAs (C15:0 and C17:0) were markedly downregulated, whereas those comprising long-chain preformed FAs were upregulated by NEB. Conclusions: Comprehensive lipidomic profiling of early and mid-lactating milk from two large cohorts of cows allowed us to identify nine lipids (PE 33:1, LacCer 32:1, LacCer 39:1, LacCer 41:1, SM 36:1, SM 36:2, SM 37:1, PEP 38:4 and PEP 38:5) as potential biomarkers of NEB in dairy cows.

The current clinical test for ketosis in dairy cows, which is based on measuring blood β-hydroxybutyrate (BHB) concentrations, is an invasive procedure that impacts herd welfare. Alternative biomarkers, especially non-invasive ones, are urgently needed for subclinical ketosis (SCK) diagnosis. To address this, we examined the milk lipidomic profiles of healthy and SCK cows from a research dairy farm over two consecutive years. A total of 125 polar lipid species were quantified in milk samples using a targeted liquid chromatography–mass spectrometry (LC-MS) approach. Chemometric analysis identified four potential biomarkers (PC 28:0, PC 29:0, PC 30:1 and PC 31:0), which met the thresholds for p value ( 2). Global fatty acid (FA) profiling by gas chromatography–flame ionization detection (GC-FID) after transesterification of all lipids revealed that the levels of C8:0, C10:0, C12:0, C14:0, C15:0 and C18:1t11 were significantly suppressed in the SCK group (15–52% lower compared to the control group, p < 0.01), and C15:0 and C18:1t11 were the most promising markers for SCK in dairy cows at the FA level (43–50% reduction compared to the control group, p < 0.0001). Tandem LC-MS and FA data generated by GC demonstrated that SCK also caused significant changes in regio-isomer and double bond isomer composition of a model phospholipid molecule (PC 34:1) and a model triglyceride molecule TAG 52:2; these fine-structural alterations could also be explored for discovering novel SCK biomarkers in dairy cows. The PLS-DA predictive model built from lipidomic data showed excellent accuracy (>95%) in predicting cows with SCK. All of the promising biomarkers identified and the predictive model built in this study need further validation using larger SCK cohorts from different herds.