Sheep have evolved remarkable phenotypic diversity through artificial and natural selection, with reproductive traits being pivotal for breeding economics. As a unique genetic resource, Pishan red sheep exhibit exceptional advantages, including perennial estrus, high fecundity, and stable hereditary characteristics, establishing them as an optimal model for investigating reproductive genetics. In this study, we performed whole-genome resequencing of Pishan red sheep, generating 9084.81 Gb of raw data and identifying 53,968,686 high-quality single-nucleotide polymorphisms (SNPs). Through selective sweep analysis, 92 genomic regions under selection were detected, containing 90 positional candidate genes significantly associated with growth, reproduction, and immune functions. Notably, we revealed BMPRIB, UNC5C, PDLIM5, GRID2, and HPGDS as core positional candidate genes influencing litter size, operating through the TGF-beta and Thyroid hormone signaling pathways. A genome-wide association study (GWAS) further identified 59 trait-related SNPs, including 39 loci linked to growth traits (affecting positional candidate genes such as PROM1, TAPT1, LDB2, and KIF16B) and 20 loci of positional candidate genes associated with reproductive traits (involving ASPA, RAP1GAP2, PHIP, and WDR82).These findings not only elucidate the molecular basis of superior reproductive performance in Pishan red sheep, but also provide functional markers for precision breeding.

Background/Objectives: The resistance to occult mastitis in dairy cows is a multifaceted trait influenced by a variety of genetic and environmental factors, posing significant challenges to its prevention and treatment. Methods: In this study, a cohort of 389 Holstein dairy cows was selected for investigation. The genes NOD2, CXCR1, SPP1 and LF, which are implicated in resistance to occult mastitis, were genotyped utilizing the efficient and cost-effective Kompetitive Allele-Specific PCR (KASP) technology. Additionally, the study analyzed the association between various single nucleotide polymorphisms (SNPs) and the somatic cell score in Holstein dairy cows. Multi-locus penetrance variance analysis (MPVA) analysis was also conducted to assess the resistance of different genotypic combinations to recessive mastitis in dairy cows. A genotyping kit for occult mastitis resistance was developed. Subsequently, 300 Holstein cows were randomly selected to evaluate the accuracy of the kit’s classification and resistance detection. Results: The findings revealed that the most effective genotype combination was SPP1(AA)-CXCR1(CC)-NOD2(CA)-LF(GA). Upon verification, the genotyping kit for recessive mastitis resistance in dairy cows exhibited an accuracy rate of 100% for individual genotyping and 95.90% for resistance detection. Conclusions: From the perspective of disease resistance genetics, this study lays a foundation for the precise management of dairy cow herds. It enables the early identification and removal of individuals susceptible to subclinical mastitis, thereby improving the overall quality of the cattle population.

The cashmere fibers produced by the secondary hair follicles of cashmere goats are precious textile raw materials. The secondary hair follicles exhibit a distinct annual cyclical pattern, comprising anagen, catagen, and telogen phases. Although a large amount of skin transcriptome data is currently available for cashmere goats, this study aims to systematically investigate the regulatory factors controlling the cyclical dynamics of secondary hair follicles through re-analysis of these data. Skin transcriptome data of Inner Mongolian cashmere goats were downloaded from the Sequence Read Archive (SRA) database. Bioinformatics analyses, including quality control, read mapping, quantification, differential expression analysis, Gene Ontology (GO) enrichment analysis, and KEGG pathway analysis, were performed to identify key regulatory genes governing the secondary hair follicle cycle. The results revealed a total of 1232 differentially expressed genes (DEGs) from comparisons across different phases. KEGG pathway analysis identified three signaling pathways associated with cashmere development: the cAMP signaling pathway (chx04024), the relaxin signaling pathway (chx04926), and the estrogen signaling pathway (chx04915). GO analysis yielded 335 terms, of which 236 were statistically significant (P-adj < 0.05). The DEGs were predominantly involved in biological processes such as regulation of transcription by RNA polymerase II, proteolysis, and positive regulation of transcription by RNA polymerase II. Significantly enriched cellular components included the plasma membrane, membrane, and extracellular space, and molecular functions were mainly related to protein binding, identical protein binding, and DNA-binding transcription factor activity, RNA polymerase II-specific. Based on their expression patterns, five key genes were selected: KRT25, KRT39, MAPK12, SPP1, and TCHHL1. These genes displayed significantly distinct expression profiles across the hair follicle cycle. TCHHL1 exhibited the highest expression in anagen, intermediate expression in catagen, and the lowest expression in telogen, with significant differences among all three phases. MAPK12 was specifically upregulated in telogen and was significantly more highly expressed than in both anagen and catagen. SPP1 showed high expression in anagen and catagen but extremely low expression in telogen. KRT39 displayed significantly higher expression in both anagen and catagen compared to telogen. KRT25 reached its highest expression in catagen, which was significantly different from that in telogen, while its expression in anagen showed no significant difference from either telogen or catagen. This study characterized the regulatory genes of the secondary hair follicle cycle in cashmere goats at the transcriptional level and analyzed the association between their expression patterns and cycle regulation.