Dataset Information

Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity.

ABSTRACT: Goat fecundity is important for agriculture and varies depending on the genetic background of the goat. Two excellent domestic breeds in China, the Jining Grey and Laiwu Black goats, have different fecundity and prolificacies. To explore the potential miRNAs that regulate the expression of the genes involved in these prolific differences and to potentially discover new miRNAs, we performed a genome-wide analysis of the miRNAs in the ovaries from these two goats using RNA-Seq technology. Thirty miRNAs were differentially expressed between the Jining Grey and Laiwu Black goats. Gene Ontology and KEGG pathway analyses revealed that the target genes of the differentially expressed miRNAs were significantly enriched in several biological processes and pathways. A protein-protein interaction analysis indicated that the miRNAs and their target genes were related to the reproduction complex regulation network. The differential miRNA expression profiles found in the ovaries between the two distinctive breeds of goats studied here provide a unique resource for addressing fecundity differences in goats.

SUBMITTER: Miao X

PROVIDER: S-EPMC5126701 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity.

Miao Xiangyang X Luo Qingmiao Q Zhao Huijing H Qin Xiaoyu X

Scientific reports 20161129

Goat fecundity is important for agriculture and varies depending on the genetic background of the goat. Two excellent domestic breeds in China, the Jining Grey and Laiwu Black goats, have different fecundity and prolificacies. To explore the potential miRNAs that regulate the expression of the genes involved in these prolific differences and to potentially discover new miRNAs, we performed a genome-wide analysis of the miRNAs in the ovaries from these two goats using RNA-Seq technology. Thirty m ...[more]

PMID: 27897262

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Project description:Understanding the molecular mechanism of mammalian reproduction (puberty and prolificacy) will play a part in improving animal reproductive performance. GLUD1 (glutamate dehydrogenase 1) is important for mammalian reproduction, as shown in previous studies; however, its roles in puberty and prolificacy have rarely been reported. In this study, we designed seven pairs of primers (P1 to P7) for cloning and sequencing genomic DNA of Jining Grey goats and Liaoning Cashmere goats. Primer 8 (P8) was designed to detect single nucleotide polymorphism (SNP) of the GLUD1 in both sexually precocious and high-fecundity breeds (Jining Grey, Nanjiang Brown and Matou goats) and sexually late-maturing and low-fecundity breeds (Liaoning Cashmere, Inner Mongolia Cashmere and Taihang goats) by PCR-RFLP (restriction fragment length polymorphism). The real-time quantitative polymerase chain reaction (RT-qPCR) technique was used to detect the expression of GLUD1 in a variety of tissues. The results showed that the A197C mutation was only found in the amplification product of P6. For this SNP locus, only two genotypes (AA and AC) were detected in Nanjiang Brown goats, while three genotypes (AA, AC and CC) were detected in the other five breeds. In Jining Grey goats, the frequency of genotypes AA, AC and CC was 0.69, 0.26 and 0.05, respectively. In Jining Grey goats, AA genotype had 0.54 (P<0.05) and 0.3 (P<0.05) more kids than the CC and AC genotype, respectively, and no significant difference (P>0.05) was found in kidding number between the AC and CC genotype. GLUD1 was expressed in five tissues of different developmental stages. The expression level of GLUD1 in the hypothalamus was higher than that in the other four tissues except during puberty of Liaoning Cashmere goats. In puberty in goats, GLUD1 expression was significantly higher in ovaries than that in the juvenile period (P<0.01). RT-qPCR results showed that the expression of GLUD1 in ovaries may relate to the puberty of goats. The present study preliminarily indicated that there might be an association between the 197 locus of GLUD1 and sexual precocity in goats, and allele A of GLUD1 was a potential DNA marker for improving kidding number in Jining Grey goats.

Project description:BackgroundExploring the physiological and molecular mechanisms underlying goat sexual maturation can enhance breeding practices and optimize reproductive efficiency and is therefore substantially important for practical breeding purposes. As an essential neuroendocrine organ in animals, the hypothalamus is involved in sexual development and other reproductive processes in female animals. Although microRNAs (miRNAs) have been identified as significant regulators of goat reproduction, there is a lack of research on the molecular regulatory mechanisms of hypothalamic miRNAs that are involved in the sexual development of goats. Therefore, we examined the dynamic changes in serum hormone profiles and hypothalamic miRNA expression profiles at four developmental stages (1 day (neonatal, D1, n = 5), 2 months (prepubertal, M2, n = 5), 4 months (sexual maturity, M4, n = 5), and 6 months (breeding period, M6, n = 5)) during sexual development in Jining grey goats.ResultsTranscriptome analysis revealed 95 differentially expressed miRNAs (DEMs) in the hypothalamus of goats across the four developmental stages. The target genes of these miRNAs were significantly enriched in the GnRH signalling pathway, the PI3K-Akt signalling pathway, and the Ras signalling pathway (P < 0.05). Additionally, 16 DEMs are common among the M2 vs. D1, M4 vs. D1, and M6 vs. D1 comparisons, indicating that the transition from D1 to M2 represents a potentially critical period for sexual development in Jining grey goats. The bioinformatics analysis results indicate that miR-193a/miR-193b-3p-Annexin A7 (ANXA7), miR-324-5p-Adhesion G protein-coupled receptor A1 (ADGRA1), miR-324-3p-Erbb2 receptor tyrosine kinase 2 (ERBB2), and miR-324-3p-Rap guanine nucleotide exchange factor 3 (RAPGEF3) are potentially involved in biological processes such as hormone secretion, energy metabolism, and signal transduction. In addition, we further confirmed that miR-324-3p targets the regulatory gene RAPGEF3.ConclusionThese results further enrich the expression profile of hypothalamic miRNAs in goats and provide important insights for studying the regulatory effects of hypothalamic miRNAs on the sexual development of goats after birth.

Project description:A normal estrus cycle is essential for the breeding of goats, and the luteal phase accounts for most of the estrus cycle. The corpus luteum (CL) formed during the luteal phase is a transient endocrine gland that is crucial for the reproductive cycle and pregnancy maintenance, and is controlled by many regulatory factors. However, the molecular mechanism of the hypothalamus effect on the reproductive performance of different litter sizes during the luteal phase of goats has not been elucidated. In this study, RNA-sequencing was used to analyze the mRNA and miRNA expression profiles of the hypothalamic tissues with the high-fecundity goats during the luteal phase (LP-HF) and low-fecundity goats during the luteal phase (LP-LF). The RNA-seq results found that there were 1963 differentially expressed genes (DEGs) (890 up-regulated and 1073 down-regulated). The miRNA-seq identified 57 differentially expressed miRNAs (DEMs), including 11 up-regulated and 46 down-regulated, of which 199 DEGs were predicted to be potential target genes of DEMs. Meanwhile, the functional enrichment analysis identified several mRNA-miRNA pairs involved in the regulation of the hypothalamic activity, such as the common target gene MEA1 of novel-miR-972, novel-miR-125 and novel-miR-403, which can play a certain role as a related gene of the reproductive development in the hypothalamic-pituitary-gonadal (HPG) axis and its regulated network, by regulating the androgen secretion. While another target gene ADIPOR2 of the novel-miR-403, is distributed in the hypothalamus and affects the reproductive system through a central role on the HPG axis and a peripheral role in the gonadal tissue. An annotation analysis of the DE miRNA-mRNA pairs identified targets related to biological processes, such as anion binding (GO:0043168) and small molecule binding (GO: 0036094). Subsequently, the KEGG(Kyoto Encyclopedia of Genes and Genomes) pathways were performed to analyze the miRNA-mRNA pairs with negatively correlated miRNAs. We found that the GnRH signaling pathway (ko04912), the estrogen signaling pathway (ko04915), the Fc gamma R-mediated phagocytosis (ko04666), and the IL-17 signaling pathway (ko04657), etc., were directly and indirectly associated with the reproductive process. These targeting interactions may be closely related to the reproductive performance of goats. The results of this study provide a reference for further research on the molecular regulation mechanism for the high fertility in goats.

Project description:Compared to high-yield commercial laying hens, Chinese indigenous chicken breeds have poor egg laying capacity due to the lack of intensive selection. However, as these breeds have not undergone systematic selection, it is possible that there is a greater abundance of genetic variations related to egg laying traits. In this study, we assessed 5 egg number (EN) traits at different stages of the egg-laying period: EN1 (from the first egg to 23 wk), EN2 (from 23 to 35 wk), EN3 (from 35 to 48 wk), EN4 (from the first egg to 35 wk), and EN5 (from the first egg to 48 wk). To investigate the molecular mechanisms underlying egg number traits in a Chinese local chicken breed, we conducted a genome-wide association study (GWAS) using data from whole-genome sequencing (WGS) of 399 Laiwu Black chickens. We obtained a total of 3.01 Tb of raw data with an average depth of 7.07 × per individual. A total of 86 genome-wide suggestive or significant single-nucleotide polymorphisms (SNP) contained within a set of 45 corresponding candidate genes were identified and found to be associated with stages EN1-EN5. The genes vitellogenin 2 (VTG2), lipase maturation factor 1 (LMF1), calcium voltage-gated channel auxiliary subunit alpha2delta 3 (CACNA2D3), poly(A) binding protein cytoplasmic 1 (PABPC1), programmed cell death 11 (PDCD11) and family with sequence similarity 213 member A (FAM213A) can be considered as the candidate genes associated with egg number traits, due to their reported association with animal reproduction traits. Noteworthy, results suggests that VTG2 and PDCD11 are not only involved in the regulation of EN3, but also in the regulation of EN5, implies that VTG2 and PDCD11 have a significant influence on egg production traits. Our study offers valuable genomic insights into the molecular genetic mechanisms that govern egg number traits in a Chinese indigenous egg-laying chicken breed. These findings have the potential to enhance the egg-laying performance of chickens.

Dataset Information

Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity.

Publications

Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity.

Similar Datasets

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