A Functional SNP Variant of the 3′ UTR Within the ELF5 Gene Affects Lactation Traits Through bta-miR-487a-Mediated Regulation in Holstein Dairy Cattle

Genome-Wide Association Screening and Candidate SNP Analysis Identify an Intergenic Variant Near CTNND2 Associated with Litter Size Traits in Saanen Dairy Goats

Litter size is an economically important reproductive trait in dairy goats, but its genetic improvement remains challenging because of its complex genetic architecture and the influence of multiple environmental factors. This study aimed to identify genomic loci associated with litter size-related traits and to evaluate the potential of an intergenic variant near the candidate gene CTNND2 as a molecular marker in Saanen dairy goats. A total of 341 does with reproductive records were analyzed using a genome-wide association study (GWAS), followed by candidate SNP genotyping and association analysis. A shared association signal for litter size and live-born kid number was identified on chromosome 20, leading to the selection of the intergenic SNP CM048886.1:g.61357858G>A located near CTNND2 for further evaluation. Three genotypes (GG, AG, and AA) were detected, and the locus exhibited moderate genetic diversity (PIC = 0.27) while conforming to Hardy–Weinberg equilibrium. Association analysis revealed nominal associations between the SNP and both litter size (p = 0.0445) and live-born kid number (p = 0.0448), whereas no significant association was observed with average kid birth weight (p = 0.125). Goats carrying the A allele showed numerically higher litter size and live-born kid number than those carrying the G allele. These findings identify CM048886.1:g.61357858G>A, an intergenic variant near CTNND2, as a promising candidate marker for litter size-related traits in Saanen dairy goats and provide a foundation for future validation studies and the development of molecular breeding strategies to improve reproductive performance.

Exploratory identification of coding and splicing-related SNV variants in A1A1 and A2A2 β-casein Holstein dairy cows

Abstract The A2 β-casein variant has gained considerable interest in the dairy industry due to proposed health-related benefits, leading to an increasing frequency of the A2A2 genotype in dairy herds. Although the A1/A2 substitution in the β-casein gene (CSN2) does not directly affect gene regulation, previous transcriptomic studies have reported differences in mRNA isoform expression between A1A1 and A2A2 cows. Therefore, the objective of this study was to identify single nucleotide variants (SNVs) in A1A1 and A2A2 β-casein groups of cows using milk fat globule (MFG) RNA-seq data and to evaluate their predicted functional consequences. RNA sequencing was performed on MFG samples obtained from 14 lactating Holstein cows (A1A1, n = 7; A2A2, n = 7). Variants were classified according to their predicted effects as amino acid changing (AAC) variants, splice site effect (SSE) variants, or variants presenting both consequences. Additionally, variant data were integrated with previously reported mRNA isoform expression results, and only variants located in genes showing expression levels ≥ 0.2 FPKM were retained for further analysis. Candidate RNA-seq-derived variants differing between A1A1 and A2A2 β-casein genotype groups were identified in genes involved in mammary gland function and lactation, including mitochondrial function, lipid metabolism, vesicle trafficking and secretion, and RNA processing. Among the prioritized genes, A1A1 cows showed a greater representation of SNVs located in genes involved in mitochondrial oxidative phosphorylation (NDUFV2, NDUFAB1, COX7A2, and ATP5PF), while additional SNVs were identified in lipid metabolism-related genes (ACSL1, ATP10A, and MFGE8). In contrast, A2A2 group of cows showed a greater representation of SNVs located in genes involved in lipid metabolism (LPIN1, FASN, SPTLC2, and ATP11B) and vesicle trafficking and secretion (SEC31A, LRRK2, DBNL, EIPR1, and ABCG2). Overall, these findings provide additional insight into the molecular differences detected between A1A1 and A2A2 groups of cows. Although the predicted functional consequences of the identified variants are currently based on in silico analyses, the novel SNVs reported here constitute a valuable resource for future studies investigating the biological consequences associated with selection for the A2A2 β-casein genotype in Holstein dairy cattle.

Integrative GWAS, eQTL, and functional validation identify ZNF280B as a key regulator of growth and carcass traits in Hu sheep

Hu sheep are a well-known Chinese dual-purpose breed valued for meat production, early sexual maturity, high prolificacy, and adaptability to hot, humid environments. In this study, we combined whole-genome sequencing, GWAS, and eQTL analyses to investigate the genetic basis of growth and slaughter traits in 420 eight-month-old Hu sheep. Using a discovery cohort ( N  = 112) and a validation cohort ( N  = 308), we integrated high-throughput SNP genotyping and RNA sequencing, identifying 559,996 high-quality SNPs and multiple significant loci associated with traits such as live weight and carcass weight. Among the 2,368 cis-eQTLs detected, the most significant was linked to ZNF280B expression in the longissimus lumborum muscle. Functional validation showed that ZNF280B downregulation significantly inhibited skeletal muscle satellite cell proliferation and induced apoptosis, highlighting its critical role in muscle development and fat metabolism. The novelty of this study lies in its large sample size, comprehensive multi-trait analysis, and the integration of functional validation, providing reliable genetic markers for marker-assisted selection in Hu sheep. These findings deepen our understanding of the genetic mechanisms underlying growth and slaughter performance and offer valuable insights for improving production efficiency and promoting sustainable livestock development.

Identification of candidate genes for reproductive traits in Chinese Holstein cattle using single-step genome-wide association study

Abstract In dairy farming, reproductive efficiency is vital to both profitability and sustainability. However, years of selective breeding for increased milk yield have adversely affected reproductive potential. This study aimed to pinpoint genomic regions and identify potential candidate genes associated with reproductive traits in Chinese Holstein cattle. In this study, a single-step genome-wide association study (ssGWAS) was conducted using 33,202 phenotypic records from 16,379 animals, 55,244 pedigree records, and genomic data from 1,698 cows. These data were integrated into the ssGWAS analysis, resulting in a total pedigree structure of 21,635 animals. A total of 12 significant markers were identified for calving interval (IC), days open (DO), number of services per conception (NS), and conception rate (CR). Among these significant SNPs, three SNPs were for IC, two SNPs were for DO, three SNPs were for NS, and four SNPs were for CR. Several promising candidate genes located near these SNPs have been identified, including SFXN4, B3GAT2, GRK5, PRDX3, and MTHFD1L, highlighting their potential involvement in fertility-related biological processes. Furthermore, functional enrichment analysis identified significant enrichment of pathways associated with cell adhesion and embryonic development, suggesting a potential mechanistic role for DSG family members (DSG1, DSG2, DSG3, and DSG4) in fertility regulation. Collectively, our findings enhance understanding of the complex genetic basis of reproductive traits in dairy cattle and may offer a valuable set of genomic targets for precision breeding of Chinese Holsteins. Integrating these markers into genomic selection programs may contribute to genetic improvements in reproductive efficiency and support the long-term sustainability of dairy production.

Uncovering genetic markers for growth and fat-tail traits in Kurdi sheep: associations with DGAT1 and PPARGC1B variants

Integrated Analysis of CRY1 Gene Expression and InDel Polymorphism Reveals Associations with Ovarian Morphological Traits in Chinese Holstein Dairy Cattle

The preliminary findings suggest that CRY1 is associated with specific ovarian morphological traits and may serve as a basis for further investigation of its potential role in bovine reproductive function.