In Friesian horses, withers height is an important trait as a minimum has been set to be eligible to the studbook. Several loci for withers height have been identified in horses. However, withers height has not been studied in the Friesian horse. Therefore, our aim was to identify loci associated with withers height in the Friesian horse population. We performed a genome‐wide association study using 70 K SNP data of 2192 Friesian horses. We found ECA1 and ECA9 to be significantly associated with withers height, explaining 19.6% and 3.5% of the phenotypic variance, respectively. In other horse breeds, the LCORL/NCPAG locus on ECA3 showed the strongest association with withers height, but here we found that the best‐associated SNP for that locus is nearly fixed in Friesian horses for the allele associated with small size. Moreover, we observed a clear decline followed by a marked increase in average withers height of the Friesian horse over time, probably owing to shifts in its primary use over the course of the years. Additionally, the frequency of the best‐associated SNP on ECA1 has increased over time. Together, our study showed that ECA1 and ECA9 are associated with withers height in Friesian horses. Further studies should be performed to confirm candidate causal mutations.

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Abstract We recently described several major‐effect recessive loci impacting anatomical and lactation traits in dairy cattle. Two of these loci in particular presented multiple candidate causative variants, comprising tightly linked coding variants that could not be easily differentiated on a statistical or functional basis. Here, we re‐examine the candidacy of these variants by leveraging a dataset of 1 million genotyped animals. Assessing lactation and bodyweight effects in conjunction with rare, recombined genotypes for the IL4R, KIAA0556, ITGAL, DPF2, and MUS81 candidates, we highlight ITGAL and MUS81 as the most likely causative genes for the two QTL. Recombinant homozygotes for these genes present larger, more significant effects than other candidates at the same loci, with both representing premature stop mutations anticipated to inactivate ITGAL and MUS81. We further examined homozygotes for the ITGAL mutation to better understand the range of phenotypes impacted. While outwardly normal, ITGAL mutants showed significant differences in the number and composition of circulating leukocytes, consistent with the role of ITGAL as a key mediator of leukocyte signalling, adhesion, and migration. These results demonstrate how near‐perfectly linked candidate mutations can be differentiated given population‐scale data, and highlight the ITGAL and MUS81 mutations as diagnostic targets to help manage the frequency of these variants.

Brown bears (Ursus arctos) and black bears (Ursus thibetanus) are important species on the Qinghai-Xizang Plateau. However, limited studies have been conducted on these species due to sampling constraints. This study, using 16S rRNA amplicon sequencing and untargeted metabolomics, analyzed fecal samples from six wild brown bears and six wild black bears. The results revealed distinct gut microbiota profiles, with brown bears showing higher microbial richness, particularly in Proteobacteria, Bacteroidota, and Actinobacteriota, while black bears were mainly enriched in Firmicutes. Lipid metabolism emerged as the primary metabolic pathway for both species, probably aiding adaptation to the plateau environment. Notably, we found positive correlations between differential metabolites and specific microbiota; in addition, traces of pesticides suggested contamination in the region. Our study provides valuable insights into the gut microbial diversity and metabolomic features of wild brown bears and black bears from the Qinghai-Xizang Plateau, contributing to our understanding of wildlife ecology in this unique environment.

Fragile foal syndrome (FFS) is a disease caused by a recessive lethal missense mutation in the PLOD1 gene located on ECA2. Despite its harmful effect, a relatively high frequency of FFS carriers was observed in Warmblood breeds spanning from 7.4% in a random sample of Swedish Warmblood breed to 17% in the Hanoverian and Danish Warmblood, indicating potential heterozygous advantage. Balancing selection can be further studied based on haplotype blocks and via detection of heterozygosity‐rich region (ROHet) around the target of selection. In this study we evaluated the presence of haplotype blocks and ROHet on ECA2 in 380 Swedish Warmblood horses. We compared the results of ROHet with the rest of the genome. On average, 11.7 heterozygosity rich regions were identified per horse on ECA2, with no significant difference in numbers and length compared to what was found in other chromosomes. A unique haplotype block containing 28 markers was found in the FFS haplotype, while there were several haplotype blocks in the non‐carrier haplotype. This unique haplotype block mostly spanned the region upstream of the PLOD1 gene and included the MFN2 gene. The presence of this extended haplotype, shared by multiple individuals and including both the FFS variant and the MFN2 gene, suggests that this region may be under selection. While we did not find a clear heterozygosity‐rich region around the FFS variant, the extended haplotype may reflect either a signature of balancing selection or linkage disequilibrium with a positively selected variant in MFN2, PLOD1, or nearby loci.

The Fuzhou cattle breed, native to northeast China, is widely recognized for its adaptability, disease resistance, and docility. Despite being known for these qualities, its population has declined recently, and there is a significant lack of genomic studies on this species. We sequenced 21 samples from a primary breeding farm to determine the genetic structure, diversity, and selection signature to address this. Additionally, we combined 100 published genomic datasets from diverse geographical regions to characterize the genomic variation of Fuzhou cattle. There were 53 752 978 bi-allelic SNPs retained for downstream analysis. In population structure analysis, Fuzhou cattle show a predominantly East Asian taurine ancestry, with strong genetic affinities to Hanwoo and Yanbian cattle. Despite high nucleotide diversity within the Bos taurine lineage, genetic diversity analysis also revealed significant levels of inbreeding in Fuzhou cattle populations, indicating the need for conservation. Utilizing various methods such as θπ, iHS, FST, π-ratio, and XP-EHH, we identified genes associated with traits like growth, meat quality, energy metabolism, and immunity. Several genes related to cold adaptation were identified, including PLIN5, PLB1, and CPT2. These findings provide a basis for conservation strategies to safeguard the genetic resources of Fuzhou cattle.

A chromosomal rearrangement such as a reciprocal translocation (RT) in a breeding boar can produce unbalanced gametes during meiosis, leading to a decreased litter size with detrimental economic implications for breeders. FISH and standard karyotyping are currently used to detect RTs, but a fresh sample is required, limiting the shipping conditions. Here, we investigated Hi-C as an alternative technique to diagnose chromosome rearrangements. We show that Hi-C can be used to detect such RTs from either a fresh or a frozen blood sample and therefore this technique represents an alternative to FISH for RT detection.

Intramuscular fat (IMF) is an important meat quality trait and a key target for molecular breeding in pigs. Our previous genome-wide association study identified SNP rs80931414 (A>G) as a significant site associated with IMF content. In this study, we further performed genotyping and association analysis of SNP rs80931414 within a Duroc-Landrace-Yorkshire (DLY) pig population. We found that the IMF content in pigs with AA genotype was significantly higher than that in those with GG genotype. SNP rs80931414 is a genetic variation in CTSS, therefore we hypothesized that CTSS is a candidate gene for IMF content trait in DLY pig and conducted research on gene function of CTSS. Our results indicated that both the mRNA and protein expression levels of CTSS were associated with the expressions of adipogenesis-related genes in skeletal muscle. Overexpression of CTSS promoted adipogenesis in intramuscular preadipocytes, while interference with CTSS inhibited this process. Our findings showed that SNP rs80931414 (A>G), which is a genetic variation in CTSS is related to IMF content and CTSS is a candidate gene for IMF content trait in DLY pig. This study provides the first evidence of the role of CTSS in pig intramuscular preadipocytes and offers insights for the development of breeding strategies aimed at genetically improving IMF content in pork.