Transcriptional activity of FIGLA, NEUROG2, and EGR1 transcription factors associated with polymorphisms in the proximal regulatory region of GPR54 gene in cattle

Integrative proteomic and transcriptomic analysis in the female goat ovary to explore the onset of puberty

Puberty is considered a prerequisite for affecting reproductive performance and productivity. Little was known about molecular changes in pubertal goat ovaries. Therefore, we measured and performed a correlation analysis of the mRNA and proteins changes in the pre-pubertal and pubertal goat ovaries. The results showed that only six differentially expressed genes and differentially abundant proteins out of 18,139 genes and 7550 proteins quantified had significant correlations. CNTN2 and THBS1, discovered in the mRNA-mRNA interaction network, probably participated in pubertal and reproductive regulation by influencing GnRH receptor signals, follicular development, and ovulation. The predicted core transcription factors may either promote or inhibit the expression of reproductive genes and act synergistically to maintain normal reproductive function in animals. The interaction between PKM and TIMP3 with other proteins may impact animal puberty through energy metabolism and ovarian hormone secretion. Pathway enrichment analyses revealed that the co-associated key pathways between ovarian genes and proteins at puberty included calcium signalling pathway and olfactory transduction. These pathways were associated with gonadotropin-releasing hormone synthesis and secretion, signal transmission, and cell proliferation. In summary, these results enriched the potential molecules and signalling pathways that affect puberty and provided new insights for regulating and promoting the onset of puberty. SIGNIFICANCE: This study conducted the first transcriptomic and proteomic correlation analysis of pre-pubertal and pubertal goat ovaries and identified six significantly correlated molecules at both the gene and protein levels. Meanwhile, we were drawn to several molecules and signalling pathways that may play a regulatory role in the onset of puberty and reproduction by influencing reproductive-related gene expression, GnRH receptor signals, energy metabolism, ovarian hormone secretion, follicular development, and ovulation. This information contributed to identify potential biomarkers in pubertal goat ovaries, which was vital for predicting the onset of puberty and improving livestock performance.

Ecogroups and maternal haplogroups reveal the ancestral origin of native Chinese goat populations based on the variation of mtDNA D-loop sequences

China is rich in goat breeding resources. Officially recognized local goat breeds are mainly distributed in agro-ecological regions. The population structure and matrilineal origin of native Chinese goats can be used to formulate protection and utilization strategies for these genetic resources. In this study, the genetic structure and maternal origin of native Chinese goats were investigated using mtDNA D-loop sequences. A total of 329 goat samples from 25 Chinese indigenous goat populations and five introduced goat breeds from abroad were collected; these populations were distributed in four ecogroups designated as Southwest, South-central, the North China Plain, and Foreign-ecogroup. A larger average number of nucleotide differences and richer nucleotide diversity were observed in South-central and Foreign-ecogroup, whereas these were lower in Southwest. The 216 haplotypes divided into several haplogroups, of which HapA contained 99 haplotypes distributed in Southwest, the North China Plain, and Foreign-ecogroup with high frequency (0.53-0.77), whereas the frequency of HapA in South-central was <0.09. HapB was mostly found in South-central (0.5538) and was distributed to the North China Plain (0.2667), while it was rare in Southwest (<0.08) and Foreign-ecogroup (<0.07). According to the estimation of kinship and ancestry, HapA had five ancestors (A2, A3, A5, A10, and A12), HapB had a single maternal ancestor (A8), and HapC had two maternal ancestors (A1 and A4). This study showed that native Chinese goat breeds were mainly divided into three haplogroups (HapA, HapB, and HapC) and goat populations have expanded in the ecological regions.

Whole Transcriptome Analysis Identifies the Taxonomic Status of a New Chinese Native Cattle Breed and Reveals Genes Related to Body Size

Wandong (WD) cattle has recently been identified as a new Chinese native cattle breed by the National Commission for Livestock and Poultry Genetic Resources. The population size of this breed is less than 10,000. WD cattle and Dabieshan (DB) cattle are sympatric but are raised in different ecological environments, on mountains and plains, respectively, and the body sizes of these two breeds are markedly different. Blood samples were obtained from 8 adult female WD cattle and 7 adult female DB cattle (24 months old). The total RNA was extracted from leukocyte cells, and sequencing experiments were conducted on the Illumina HiSeq^TM 4000 platform. After the removal of one outlier sample from the WD cattle breed as determined by principal component analysis (PCA), phylogenetic and population structure analyses indicated that WD and DB cattle formed a distinct Central China cattle group and showed evidence of hybridization between Bos. taurus and Bos. indicus. The immune-regulator CD48 (P = 1.3E-6) was associated with breed-specific traits according to loss-of-function variant enrichment analysis. In addition, 113 differentially expressed genes were identified between the two breeds, many of which are associated with the regulation of body growth, which is the major difference between the two breeds. This study showed that WD cattle belong to the group of hybrids between Bos. Taurus and Bos. indicus, and one novel gene associated with breed traits and multiple differentially expressed genes between these two closely related breeds was identified. The results provide insights into the genetic mechanisms that underlie economically important traits, such as body size, in cattle.