Meat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 CNVs and 10,102 CNV regions (CNVRs) based on the Bovine HD SNP array. Next, we performed a CNV-based genome-wide association analysis (GWAS) of six meat quality traits and identified 12 significant CNV segments corresponding to eight candidate genes, including PCDH15, CSMD3, etc. Using region-based association analysis, we further identified six CNV segments relevant to meat quality in beef cattle. Among these, TRIM77 and TRIM64 within CNVR4 on BTA29 were detected as candidate genes for backfat thickness (BFT). Notably, we identified a 34 kb duplication for meat color (MC) which was supported by read-depth signals, and this duplication was embedded within the keratin gene family including KRT4, KRT78, and KRT79. Our findings will help to dissect the genetic architecture of meat quality traits from the aspects of CNVs, and subsequently improve the selection process in breeding programs.

Genomic selection (GS) plays a crucial role in livestock breeding. However, its implementation in Chinese beef cattle breeding is constrained by a limited reference population and incomplete data records. To address these challenges, this study aimed to identify more effective models for multi-population genomic selection. We simulated five different beef cattle populations and selected three populations with varying levels of kinship to investigate the impact of population relationships on genomic prediction. Utilizing results from a genome-wide association study (GWAS), we preselected different proportions of single nucleotide polymorphism (SNP). Subsequently, we employed three models—genomic best linear unbiased prediction (GBLUP), multi-genomic best linear unbiased prediction (MGBLUP), and weighted multi-genomic best linear unbiased prediction (WMGBLUP)—for within-population and multi-population genomic prediction. Our results showed that increasing the size of the training set improved within-population prediction accuracy. Furthermore, both MGBLUP and WMGBLUP outperformed GBLUP in terms of prediction accuracy for both within-population and multi-population analyses. Among the models evaluated, the WMGBLUP model, which utilized the top 5% of preselected SNPs based on GWAS findings, demonstrated superior performance, yielding an improvement of up to 11.1% in within-population prediction and 16.5% in multi-population prediction. In summary, both WMGBLUP and MGBLUP models exhibit enhanced efficacy in improving genomic prediction accuracy, and the incorporation of GWAS results can further optimize their performance.

Context: Diarrhoea linked to helminth resistance is a major problem in sheep health. Aims: To test whether the distribution of mast cells and eosinophils along the gastrointestinal tract is related to helminth resistance and to susceptibility to diarrhoea. Methods: At weaning, lambs were selected according to extreme (high or low) estimated breeding values for diarrhoea score (50 lambs per genotype, balanced for sex), and for faecal worm egg counts (FWEC). They grazed in single-sex groups in separate but similar enclosures under normal farm conditions (dry summer, wet winter) from autumn until spring, during which time diarrhoea score and FWEC were recorded monthly. Lambs that presented extreme phenotypic values for diarrhoea score and FWEC in August and September were slaughtered (n = 38) at the age of 14 months. For the abomasum, duodenum, ileum, jejunum, caecum and colon, we recorded the densities of eosinophils and mast cells, the number of helminths, their species and developmental stages. The data were pooled across enclosures/sexes and regression analysis was used to assess the relationships among pre-slaughter phenotype, helminth counts, and densities of mast cells and eosinophils. Results: Eosinophil density was five- to seven-fold greater in the ileum and jejunum than in the abomasum, duodenum, or colon. Mast cell density was greatest in the abomasum and duodenum, and gradually declined along the jejunum, ileum, caecum and colon. In the most immunologically active site, the jejunum, increasing eosinophil density was related to a decrease in the number of helminths (P < 0.05). Similarly, in the next most active site, the abomasum, increasing eosinophil density was related to decreases in the numbers of fourth-stage larvae and the total number of helminths (P < 0.05). In the abomasum, increasing mast cell density was related to declines in the numbers of Teladorsagia circumcincta, total helminth counts (P < 0.05) and FWEC, but was not related to diarrhoea score. Conclusions: Cell-mediated immune mechanisms in the gastrointestinal mucosa enhance resistance to internal parasites but also increase susceptibility to the diarrhoea in sheep. Implications: Eosinophil and mast cell responses to helminth infection help explain ‘hypersensitivity diarrhoea’.

Aflatoxin B₁ (AFB₁) is a prevalent mycotoxin contaminating food and environmental matrices that can induce hepatic injury, thereby posing a substantial threat to livestock production. Portulaca oleracea L. polysaccharide (POP) possesses diverse biological activities, including antioxidant and anti-inflammatory properties. However, the protective effects of POP against AFB₁-induced hepatic injury have not been fully elucidated. In the present study, a rabbit model of AFB₁-induced hepatic injury was established to investigate the hepatoprotective mechanisms of POP. Histopathological examination and liver function assessments demonstrated that POP markedly ameliorated hepatic histopathological alterations and decreased serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and alkaline phosphatase (ALP). Molecular analyses further demonstrated that POP attenuated AFB₁-induced oxidative stress and hepatocyte apoptosis, effects that were associated with activation of the PI3K/AKT signaling pathway and suppression of the mitochondria-mediated apoptotic pathway. Furthermore, microbiome profiling and targeted short-chain fatty acid (SCFA) metabolomics analyses indicated that POP supplementation contributed to the preservation of intestinal barrier integrity and intestinal microbiota stability, concurrent with the attenuation of AFB₁-induced intestinal and hepatic injury and elevated SCFA production by intestinal microbes. Overall, POP exerts prominent preventive protective effects against AFB₁-induced liver injury, which may be closely associated with alterations in intestinal microbiota composition and microbial short-chain fatty acid metabolism, as well as the activation of the PI3K/AKT signaling pathway. These findings provide novel insights into the mechanisms underlying AFB₁-induced hepatic injury.