DNA methylation (DNAm) is associated with the reproductive system. However, the genetic mechanism through which DNAm regulates gene expression and thus affects litter size in goats is unclear. Therefore, in the present work, genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues were comprehensively analyzed via WGBS, and RNA-Seq data were combined to identify candidate genes associated with litter size traits in the Jining Grey goat. Finally, BSP and RT-qPCR were used to verify the sequencing results of the key genes. Notably, the DNMT genes were downregulated at the expression level in the HP group. Both groups exhibited comparable levels of methylation. A total of 976 differentially methylated regions (DMRs) (973 DMRs for CG and 3 DMRs for CHG) and 310 differentially methylated genes (DMGs) were identified in this study. Through integration of WGBS and RNA-Seq data, we identified 59 differentially methylated and differentially expressed genes (DEGs) and ultimately screened 8 key DMGs (9 DMRS) associated with litter size traits in Jining Grey goats (SERPINB2: chr24_62258801_62259000, NDRG4: chr18_27599201_27599400, CFAP43: chr26_27046601_27046800, LRP1B. chr2_79720201_79720400, EPHA6: chr1_40088601_40088800, TTC29: chr17_59385801_59386000, PDE11A: chr2_117418601_117418800 and PGF: chr10_ 16913801_16914000 and chr10_16916401_16916600). In summary, our research comprehensively analyzed the genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues. The data findings suggest that DNAm in goat ovaries may play an important role in determining litter size.

Wool is produced and controlled by hair follicles (HFs). However, little is known about the mechanisms involved in HF development and regulation. Sheep dermal fibroblasts (SDFs) play a key role in the initial stage of HF development. Analyzing the molecular mechanism that regulates early HF development in superfine wool sheep is of great importance for better understanding the HF morphogenesis process and for the breeding of fine wool sheep. Here, we show that two microRNAs (miRNAs) affect the development of HFs by targeting two genes that are expressed by SDFs. Meanwhile, the overexpression and inhibition of oar-miR-23b and oar-miR-133 in SDFs cells and cell proliferation, apoptosis, and migration were further detected using a CCK-8 assay, an Annexin V-FITC assay, a Transwell assay, and flow cytometry. We found that oar-miR-23b, oar-miR-133, and their cotarget genes TGFβ2 and NOTCH1 were differentially expressed during the six stages of HF development in superfine wool sheep. Oar-miR-23b and oar-miR-133 inhibited the proliferation and migration of SDFs and promoted the apoptosis of SDFs through TGFβ2 and NOTCH1. oar-miR-23b and oar-miR-133 inhibited the proliferation and migration of SDFs by jointly targeting TGFβ2 and NOTCH1, thereby inhibiting the development of superfine wool HFs. Our research provides a molecular marker that can be used to guide the breeding of ultrafine wool sheep.

Background: The Jining grey goat is a renowned local goat breed in China that has exceptional reproductive performance; thereby, it serves as an ideal animal model for studying prolificacy in goats. Recent research on the reproductive traits of Jining grey goats has focused primarily on variations in the expression of key genes, hormone regulatory mechanisms, and breeding techniques, with the aim of enhancing reproductive performance through molecular marker-assisted breeding. Methods: In this study, 8 healthy adult female Jining grey goats of similar age and weight were selected. Ovarian and uterine tissues were collected from Jining grey goats in the high litter size group (HL, high size ≥ 3 in three consecutive litters, n = 4) and the low litter size group (LL, litter size = 1 in three consecutive litters, n = 4) for transcriptome sequencing. Bioinformatics analysis was conducted to investigate key regulatory pathways and candidate genes in ovarian and uterine tissues. Ultimately, 5 pathways (cAMP signalling pathway, neuroactive ligand‒receptor interaction, ABC transporters, cytokine‒cytokine receptor interaction and metabolic pathways) and 10 candidate genes ( 3BHSD , CLSTN2 , BMP5 , DRD1 , CXCL14 , CFAP43 , WNT10B , ENO4 , GABRA1 and the DNAH1 gene) were revealed to be associated with multiple births in Jining grey goats. RT‒qPCR was used to verify the sequencing results, and the relative expression levels of the 10 candidate genes in different tissues were compared. Among them, 3BHSD , CLSTN2 , and GABRA1 were found to be closely related to prolificacy in the Jining grey goat. Conclusion: In this study, key regulatory pathways and candidate genes influencing the prolificacy of Jining Grey goats were investigated through transcriptome analysis, providing in-depth insights into the molecular mechanisms through which the expression of genes related to prolificacy in different tissues affects reproductive performance. These findings provide a theoretical foundation and reference for the selective breeding of Jining grey goats.

Litter size is a vital economic trait in goat production, and previous studies on its regulatory mechanisms mainly focus on ovarian tissues. The genome-wide DNA methylation landscape of the goat uterus and its association with prolificacy remain poorly understood. In this study, we performed whole-genome bisulfite sequencing (WGBS) on uterine tissues from high-prolificacy (HP) and low-prolificacy (LP) Jining Grey Goats to explore epigenetic regulatory mechanisms underlying litter size. A total of 880 differentially methylated regions (DMRs) and 274 differentially methylated genes (DMGs) were identified. Combined with transcriptome data, 21 genes were found to exhibit both differential methylation and differential expression. Three candidate genes (CFAP43, PLPPR1 and TRPC3) and their corresponding DMRs were further verified via bisulfite sequencing PCR (BSP). Integrated analysis highlighted CFAP43, TTC21A, and CROCC as key candidate genes functionally associated with ciliary structure and maintenance, whose methylation and expression patterns correlate with the litter size phenotype. This study establishes the first genome-wide DNA methylation map of the Jining Grey Goat uterus. We demonstrate that DNA methylation modulates the expression of CFAP43, TTC21A and CROCC, and further regulates uterine ciliary function to affect goat prolificacy. Our findings provide novel epigenetic insights into goat reproductive traits and supply candidate molecular markers for goat breeding.