To understand how genes precisely regulate lactation physiological activity and the molecular genetic mechanisms underlying mammary gland involution, this study investigated the transcriptome characteristics of goat mammary gland tissues at the late gestation (LG), early lactation (EL), peak lactation (PL), late lactation (LL), dry period (DP), and involution (IN) stages. A total of 13,083 differentially expressed transcripts were identified by mutual comparison of mammary gland tissues at six developmental stages. Genes related to cell growth, apoptosis, immunity, nutrient transport, synthesis, and metabolism make adaptive transcriptional changes to meet the needs of mammary lactation. Notably, platelet derived growth factor receptor beta (PDGFRB) was screened as a hub gene of the mammary gland developmental network, which is highly expressed during the DP and IN. Overexpression of PDGFRB in vitro could slow down the G1/S phase arrest of goat mammary epithelial cell cycle and promote cell proliferation by regulating the PI3K/Akt signaling pathway. In addition, PDGFRB overexpression can also affect the expression of genes related to apoptosis, matrix metalloproteinase family, and vascular development, which is beneficial to the remodeling of mammary gland tissue during involution. These findings provide new insights into the molecular mechanisms involved in lactation and mammary gland involution.

Background: Rabbit wool traits are important in fiber production and for model organism research on hair growth, but their genetic architecture remains obscure. In this study, we focused on wool characteristics in Angora rabbits, a breed well-known for the quality of its wool. Considering the cost to generate population-scale sequence data and the biased detection of variants using chip data, developing an effective genotyping strategy using low-coverage whole-genome sequencing (LCS) data is necessary to conduct genetic analyses. Results: Different genotype imputation strategies (BaseVar + STITCH, Bcftools + Beagle4, and GATK + Beagle5), sequencing coverages (0.1X, 0.5X, 1.0X, 1.5X, and 2.0X), and sample sizes (100, 200, 300, 400, 500, and 600) were compared. Our results showed that using BaseVar + STITCH at a sequencing depth of 1.0X with a sample size larger than 300 resulted in the highest genotyping accuracy, with a genotype concordance higher than 98.8% and genotype accuracy higher than 0.97. We performed multivariate genome-wide association studies (GWAS), followed by conditional GWAS and estimation of the confidence intervals of quantitative trait loci (QTL) to investigate the genetic architecture of wool traits. Six QTL were detected, which explained 0.4 to 7.5% of the phenotypic variation. Gene-level mapping identified the fibroblast growth factor 10 ( FGF10 ) gene as associated with fiber growth and diameter, which agrees with previous results from functional data analyses on the FGF gene family in other species, and is relevant for wool rabbit breeding. Conclusions: We suggest that LCS followed by imputation can be a cost-effective alternative to array and high-depth sequencing for assessing common variants. GWAS combined with LCS can identify new QTL and candidate genes that are associated with quantitative traits. This study provides a cost-effective and powerful method for investigating the genetic architecture of complex traits, which will be useful for genomic breeding applications.

The ovary is a crucial reproductive organ in mammals, and its development directly influences an individual’s sexual maturity and reproductive capacity. To comprehensively describe ovarian sexual maturation in goats, we integrated phenotypic, hormonal, metabolomic, and transcriptomic data from four specific time points: after birth (D1), at 2 months old (M2), at 4 months old (M4), and at 6 month old (M6). The study showed that during the early stage (D1–M2), ovarian growth was the most rapid, with weight and morphology increasing by 284% and 65%, respectively, and hormone levels rose significantly, with estradiol increasing by 57%. Metabolomic analysis identified 1231 metabolites, primarily lipids, lipid molecules, and organic acids, which can support hormone balance and follicle development by providing energy and participating in signaling transduction. Transcriptomic analysis identified 543 stage-specific differentially expressed genes, mainly enriched in steroid biosynthesis, amino acid metabolism, and the PI3K/AKT pathway, which are key factors influencing ovarian cell proliferation, apoptosis, hormone secretion, and metabolism. The integrated analysis revealed the key processes in the ovarian steroid hormone biosynthesis pathway and gene/metabolite networks associated with ovarian phenotypes and hormone levels, ultimately highlighting scavenger receptor class B type 1 (SCARB1), Cytochrome P450 Family 1 Subfamily A Member 1 (CYP11A1), 3beta-hydroxysteroid dehydrogenase (3BHSD), progesterone, estradiol, and L-phenylalanine as key regulators of ovarian morphological and functional changes at different developmental stages. This study is the first to reveal the metabolic changes and molecular regulatory mechanisms during ovarian sexual maturation in goats, providing valuable insights for understanding reproductive system development and optimizing reproductive performance and breeding efficiency.

Background: Goat milk has gained global attention for its unique nutritional properties and potential health benefits. Advancements in functional genomic technologies have significantly progressed genetic research on milk composition traits in dairy goats. Results: This review summarizes various research methodologies applied in this field. Genome-wide association studies (GWAS) have identified genomic regions associated with major milk components, with the diacylglycerol acyltransferase 1 (DGAT1) gene and casein gene cluster consistently linked to milk composition traits. Transcriptomics has revealed gene expression patterns in mammary tissue across lactation stages, while the role of non-coding RNAs (such as miRNAs and circRNAs) in regulating milk composition has been confirmed. Proteomic and metabolomic studies have not only helped us gain a more comprehensive understanding of goat milk composition characteristics but have also provided crucial support for the functional validation of genes related to milk components. The integration of multi-omics data has emerged as an effective strategy for elucidating complex regulatory networks from a systems biology perspective. Conclusions: Despite progress, challenges remain, including refining reference genomes, collecting large-scale phenotypic data, and conducting functional validations. Future research should focus on improving reference genomes, expanding study populations, investigating functional milk components, exploring epigenetic regulation and non-coding RNAs, and studying microbiome–host genome interactions. These efforts will inform more precise genomic and marker-assisted selection strategies, advancing genetic improvements in milk composition traits in dairy goats.

As a vital metabolic and immune organ in animals, the liver plays an important role in protein synthesis, detoxification, metabolism, and immune defense. The primary research purpose of this study was to reveal the effect of breast-feeding, weaning transition, and weaning on the gene expression profile in the goat kid liver and to elucidate the transcriptome-level signatures associated with liver metabolic adaptation. Therefore, transcriptome sequencing was performed on liver tissues, which was collected at 1 day (D1), 2 weeks (W2), 4 weeks (W4), 8 weeks (W8), and 12 weeks (W12) after birth in Laiwu black goats at five different time-points, with five goats at each time point. From 25 libraries, a total of 37497 mRNAs were found to be expressed in goat kid livers, and 1271 genes were differentially expressed between at least two of the five time points. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that these genes were annotated as an extracellular region fraction, exhibiting monooxygenase activity, positive regulation of T cell activation, mitotic spindle mid-region assembly, cytokinesis, cytoskeleton-dependent cytokinesis, regulation of cytokinesis, regulation of lymphocyte proliferation, and so on. In addition, it mainly deals with metabolism, endocrine, cell proliferation and apoptosis, and immune processes. Finally, a gene regulatory network was constructed, and a total of 14 key genes were screened, which were mainly enriched for cell growth and development, endocrine, immune, and signal transduction-related pathways. Our results provide new information on the molecular mechanisms and pathways involved in liver development, metabolism, and immunity of goats.