Identification and profiling of microRNAs from ovary of estrous Kazakh sheep induced by nutritional status in the anestrous season

The genetic characterization of germplasm and identification of the litter size trait associated candidate genes in Dexin mutton and fine-wool sheep

Xinjiang is a major province of sheep breeding in China, which plays an important role in meeting people's needs for meat products, increasing farmers' income and sustainable development of animal husbandry. However, the genetic differentiation relationship between breeds was not clear, and most sheep had low fecundity, which seriously restricted the efficient development of sheep industry. Therefore, this study used the whole genome resequencing to detect the genetic variation of Dexin mutton and fine-wool sheep, explored the selected regions and important genes of the litter size traits, analyzed the genetic mechanism of reproductive traits, and provided new insights for the high fecundity breeding of sheep. A total of 5,236.338 G genome data and 35,884,037 SNPs were obtained. Furthermore, we identified 39 selection signals spanning candidate genes, 99 genes were significantly associated related to growth, reproduction and immunity, among which, BRIP1, BMPR1B, BMP4, NGF, etc. genes, and MAKP signaling pathway, Fanconi anemia pathway and Thyroid hormone signaling pathway and other signaling pathways were significantly correlated with litter size trait. Among them, we identified NGF, TrKA and BRIP1 genes was the important genes for sheep litter size traits and the mutation frequencies of 9 SNPs in BRIP1 gene were significantly different in domestic sheep in the world. The research provided new insights for the breeding of self-cultivated meat fine-wool sheep.

Cumulus Cell Transcriptome after Cumulus-Oocyte Complex Exposure to Nanomolar Cadmium in an In Vitro Animal Model of Prepubertal and Adult Age

Cadmium (Cd), a highly toxic pollutant, impairs oocyte fertilization, through oxidative damage on cumulus cells (CCs). This study analysed the transcriptomic profile of CCs of cumulus-oocyte complexes (COCs) from adult and prepubertal sheep, exposed to Cd nanomolar concentration during in vitro maturation. In both age-groups, CCs of matured oocytes underwent RNA-seq, data analysis and validation. Differentially expressed genes (DEGs) were identified in adult (n = 99 DEGs) and prepubertal (n = 18 DEGs) CCs upon Cd exposure. Transcriptomes of adult CCs clustered separately between Cd-exposed and control samples, whereas prepubertal ones did not as observed by Principal Component Analysis. The transcriptomic signature of Cd-induced CC toxicity was identified by gene annotation and literature search. Genes associated with previous studies on ovarian functions and/or Cd effects were confirmed and new genes were identified, thus implementing the knowledge on their involvement in such processes. Enrichment and validation analysis showed that, in adult CCs, Cd acted as endocrine disruptor on DEGs involved in hormone biosynthesis, cumulus expansion, regulation of cell signalling, growth and differentiation and oocyte maturation, whereas in prepubertal CCs, Cd affected DEGs involved in CC development and viability and CC-oocyte communications. In conclusion, these DEGs could be used as valuable non-invasive biomarkers for oocyte competence.

Polymorphisms and association of GRM1, GNAQ, and HCRTR1 genes with seasonal reproduction and litter size in three sheep breeds

Litter size is one of the important economic traits of livestock. Seasonal estrus, ovulation, and lambing of sheep have severely restricted the development of sheep farming in Xinjiang China. The purpose of this study was to investigate the polymorphisms and genetic correlation between GRM1, GNAQ, and HCRTR1 genes and the seasonal reproduction and litter size in three sheep breeds. The DNA mixed pool sequencing and PCR-SSCP methods were used to detect single nucleotide polymorphisms (SNPs) of GRM1, GNAQ, and HCRTR1 genes in seasonal estrus (Kazakh and Chinese Merino [Xinjiang Junken type]) and perennial estrus (Hu) sheep breeds. The association between genetic polymorphism and litter size was also analyzed. The results showed that T945C in exon 2 of GRM1 gene, C589T in exon 2 of HCRTR1 gene and A191G in exon 2 of GNAQ gene were identified by Sanger sequencing, and three genotypes were existed in each SNP sites, which all belonged to the synonymous mutation. GRM1 (CC), GNAQ (GA) and HCRTR1 (TC) were the dominant genotypes of seasonal reproduction and litter size in Kazakh sheep and Chinese Merino sheep, respectively. While, in perennial estrus Hu sheep populations, the dominant genotypes were GRM1 (TC), GNAQ (GA) and HCRTR1 (TC) respectively, and association analysis was also confirmed the results. Above results implied that GRM1, GNAQ and HCRTR1 genes are significantly associated with lambing traits in Kazakh, Chinese Merino and Hu sheep. Among them, locus of GRM1 (T945C), GNAQ (A191G) and HCRTR1 (C589T) might be considered as a potential molecular marker which controls seasonal reproduction and litter size in sheep.

Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep

The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.

Comparative Analysis and Identification of Differentially Expressed microRNAs in the Hypothalamus of Kazakh Sheep Exposed to Different Photoperiod Conditions

MicroRNAs (miRNA) plays an important role in several mammalian biological regulatory processes by post-transcriptionally regulating gene expression. However, there is little information on the miRNAs involved in the photoperiodism pathway that controls seasonal activity. To enhance our knowledge on the effect of different photoperiod conditions on miRNA, we divided Kazakh sheep into two groups: one exposed to a long photoperiod (LP, 16L:8D) and another with exposed to a short photoperiod (SP, 8L:16D) under supplemental feeding conditions. Further we compared the related miRNAs and target genes between the two groups. Fifteen differentially expressed miRNAs were identified, which were associated with 310 regulatory pathways covering photoperiodism, reproductive hormones, and nutrition. The miR-136-GNAQ pair was selected and validated as a differentially expressed, and a dual-luciferase reporter assay showed that the negative feedback loop existed between them. Examination of the expression profile revealed that the GNAQ expression was low in the estrous females both under LP and SP conditions, but high expression of GNAQ was observed in the anestrous females under LP conditions. Moreover, functional analysis revealed that KISS1 and GnRH expression was upregulated when GNAQ expression was downregulated in the hypothalamic cells, whereas DIO2 and TSHB expression was downregulated. Thus, miR-136-GNAQ might act as a switch in the regulation of seasonal estrus under different photoperiod conditions. These findings further enrich our understanding of the relationship between miRNAs and seasonal regulation of reproductive activity. Furthermore, our study provides novel insights into the miRNA-mediated regulatory mechanisms for overcoming photoinhibition in the seasonally breeding mammals, such as Kazakh sheep.

Expression and characterization of the serum proteome from yak induced into estrus by improved nutrition

Regulation of estrus plays a crucial role in the livestock industry. It is reported that providing better nutrition can induce early estrus in animals. However, little is known about the major endocrine and physiological mechanisms that could enhance estrus in anestrus animals. Hence in the current research two different groups of yaks, non-breeding season (February-June, NBS) estrus yaks as the experiment group and breeding season (July-September, BS) estrus animals as the control group were compared using the isobaric tags for relative and absolute quantitation (iTRAQ) technique. Study displayed that cold season supplementation significantly improved growth performance, serum biochemical indicators and reproductive hormone concentrations in yaks. We also identified 25 differentially expressed proteins in yak serum using iTRAQ proteomics. Go and KEGG analysis indicated that calcium signaling pathway and beta-alanine metabolism may be candidate pathways for seasonal estrus induced by nutrition. Differential protein expression was validated using parallel reaction monitoring (PRM). The results of this study initially identified A2M, IGF2, A1BG and APOA1 as candidate proteins for seasonal estrus induced by nutrition. Altogether, In conclusion, our results show that providing additional nutrients in the cold season can improve yak productivity and reproductive efficiency, and provide a new reference.

Analysis of pituitary transcriptomics indicates that lncRNAs are involved in the regulation of sheep estrus

Seasonal estrus is a key factor limiting animal fertility, and understanding the molecular mechanisms that regulate animal estrus is important for improving animal fertility. The pituitary gland, which is the most important endocrine gland in mammals, plays an important role in regulating the physiological processes such as growth, development, and reproduction of animals. Here, we used RNA-seq technology to study the expression profile of lncRNAs in the anterior pituitary of sheep during estrus and anestrus. In this study, we identified a total of 995 lncRNAs, of which 335 lncRNAs were differentially expressed in two states (including 38 up-regulated and 297 down-regulated lncRNAs). RT-qPCR verified the expression levels of several lncRNAs. Target predictive analysis revealed that these lncRNAs can act in cis or trans and regulate the expression of genes involved in the regulation of sheep estrus. Target gene enrichment analysis of differentially expressed lncRNAs indicates that these lncRNAs can regulate sheep estrus by regulating hormone metabolism and energy metabolism. Through our research, we provide the expression profile of lncRNAs in the pituitary of sheep, which provides a valuable resource for further understanding of the genetic regulation of seasonal estrus in sheep from the perspective of lncRNAs.

Identification and Profiling of Pituitary microRNAs of Sheep during Anestrus and Estrus Stages

MicroRNAs (miRNAs) are a class of small non-coding RNAs, molecules of 21 to 25 nucleotides in length, that regulate gene expression by binding to their target mRNA and play a significant role in animal development. The expression and role of miRNAs in regulating sheep estrus, however, remain elusive. Transcriptome analysis is helpful to understand the biological roles of miRNAs in the pituitary gland of sheep. A sheep's pituitary gland has a significant difference between estrus and anestrus states. Here, we investigate the expression profiles of sheep anterior pituitary microRNAs (miRNAs) in two states, estrus and anestrus, using Illumina HiSeq-technology. This study identified a total of 199 miRNAs and 25 differentially expressed miRNAs in the estrus and anestrus pituitary gland in sheep. Reverse transcription quantitative-PCR (RT-qPCR) analysis shows six differentially (p < 0.05) expressed miRNAs, that are miR-143, miR-199a, miR-181a, miR-200a, miR-218, and miR-221 in both estrus and anestrus states. miRNAs containing estrus-related terms and pathways regulation are enriched using enrichment analysis from gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Moreover, we also envisioned a miRNA-mRNA interaction network to understand the function of miRNAs involved in the pituitary gland regulatory network. In conclusion, miRNA expression profiles in sheep pituitary gland in the anestrus and estrus deliver a theoretical basis for the study of pituitary gland biology in sheep.

Nutritional status affects the microRNA profile of the hypothalamus of female sheep

Recent studies on the seasonal regulation of the oestrous cycle in sheep have focussed mainly on the responses to photoperiod. However, the brain systems that control reproductive activity also respond to nutritional inputs, although the molecular mechanisms involved are not completely understood. One possibility is that small, non-coding RNAs, such as micro-RNAs (miRNAs), have significant influence. In the present study, the amounts and characteristics of miRNAs in hypothalamus from oestrous and anestrous ewes, fed low- or high-nutrient diets, were compared using Illumina HiSeq sequencing technology. In total, 398 miRNAs, including 261 novel miRNAs, were identified in ewes with an enhanced nutritional status (HEN), whereas 384 miRNAs, including 247 novel miRNAs, were identified in the ewes with a lesser nutritional status (HAN). There were eight conserved and 140 novel miRNAs expressed differentially between the two libraries. Based on quantitative real-time polymerase chain reaction, six miRNAs were assessed to verify the accuracy of the library database. Moreover, the correlation between the miRNA target and several upstream and downstream genes in the oestrus-related pathways were also verified in hypothalamus nerve cells. According to the results, nutritional status plays an important role in oestrous regulation in sheep, and the hypothalamic processes and pathways induced by nutritional signals (folic acid and tyrosine) are different from those induced by photoperiodic regulation of oestrus. We have expanded the repertoire of sheep miRNAs that could contribute to the molecular mechanisms that regulate the initiation of oestrous cycles in anestrous ewes in response to the influence of nutritional status.

MicroRNAs in ovarian follicular atresia and granulosa cell apoptosis

MicroRNAs (miRNAs) are short, noncoding RNAs that posttranscriptionally regulate gene expression. In the past decade, studies on miRNAs in ovaries have revealed the key roles of miRNAs in ovarian development and function. In this review, we first introduce the development of follicular atresia research and then summarize genome-wide studies on the ovarian miRNA profiles of different mammalian species. Differentially expressed miRNA profiles during atresia and other biological processes are herein compared. In addition, current knowledge on confirmed functional miRNAs during the follicular atresia process, which is mostly indicated by granulosa cell (GC) apoptosis, is presented. The main miRNA families and clusters, including the let-7 family, miR-23-27-24 cluster, miR-183-96-182 cluster and miR-17-92 cluster, and related pathways that are involved in follicular atresia are thoroughly summarized. A deep understanding of the roles of miRNA networks will not only help elucidate the mechanisms of GC apoptosis, follicular development, atresia and their disorders but also offer new diagnostic and treatment strategies for infertility and other ovarian dysfunctions.

Gonadal transcriptome analysis of hybrid triploid loaches (Misgurnus anguillicaudatus) and their diploid and tetraploid parents

Hybrid triploid loaches (Misgurnus anguillicaudatus) were generated from natural tetraploid and diploid loaches. We studied the gonads of parents and offspring from direct and reciprocal crosses through histological and transcriptome analyses. The triploid offspring had inferior ability to form sperm and egg cells compared with diploid forms. After sequencing the transcriptomes, 655,109,158 clean reads were obtained, and 62,821 unigenes and 178,962 transcripts were assembled. Of these unigenes, 23,189 were annotated in the GO database, 18,525 in the KEGG database and 24,661 in the KOG database. 36 fertility-related genes were found to be differentially expressed between the direct cross (2n × 4n) progenies and their parents, while 53 fertility-related genes between the reciprocal cross (4n × 2n) progenies and their parents. Following protein-protein interaction network analyses, 54 differentially expressed genes, including PLCB4, cyp17a1 and Pla2g4d, were mined, yielding candidate genes involved in the poor fertility of hybrid triploid loaches. This is the first report of transcriptomes of gonads of hybrid triploid loaches and their parents, offering a substantial contribution to sequence resources for this species and providing a deep insight into the molecular mechanism controlling the fertility of hybrid triploid fish.

Comparative Profiling of MicroRNAs Reveals the Underlying Toxicological Mechanism in Mice Testis Following Carbon Ion Radiation

This study investigated the toxicity of heavy ion radiation to mice testis by microRNA (miRNA) sequencing and bioinformatics analyses. Testicular indices and histology were measured following enterocoelia irradiation with a 2 Gy carbon ion beam, with the testes exhibiting the most serious injuries at 4 weeks after carbon ion radiation (CIR) exposure. Illumina sequencing technology was used to sequence small RNA libraries of the control and irradiated groups at 4 weeks after CIR. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses implicated differential miRNAs in the regulation of target genes involved in metabolism, development, and reproduction. Here, 8 miRNAs, including miR-34c-5p, miR-138, and 6 let-7 miRNA family members previously reported in testis after radiation, were analyzed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) to validate miRNA sequencing data. The differentially expressed miRNAs described here provided a novel perspective for the role of miRNAs in testis toxicity following CIR.

Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries)

Sheep are small ruminants, and their long intestines exhibit high digestive and absorptive capacity in many different rearing conditions; however, the genetic bases of this characteristic remains unclear. MicroRNAs (miRNAs) play a major role in maintaining both intestinal morphological structure as well as in regulating the physiological functions of this organ. However, no study has reported on the miRNA expression profile in the intestinal tissues of sheep. Here, we analyzed and identified the miRNA expression profile of three different intestinal tissues (i.e., duodenum, cecum, and colon) of sheep (Ovis aries) using high-throughput sequencing and bioinformatic methods. In total, 106 known miRNAs were identified, 458 conserved miRNAs were detected, 192 unannotated novel miRNAs were predicted, and 195 differentially expressed miRNAs were found between the different tissues. Additionally, 3,437 candidate target genes were predicted, and 17 non-redundant significantly enriched GO terms were identified using enrichment analysis. A total of 99 candidate target genes were found to significantly enriched in 4 KEGG biological pathways. A combined regulatory network was constructed based on 92 metabolism-related candidate target genes and 65 differentially expressed miRNAs, among which 7 miRNAs were identified as hub miRNAs. Via these mechanisms, miRNAs may play a role in maintaining intestinal homeostasis and metabolism. This study helps to further explain the mechanisms that underlie differences in tissue morphology and function in three intestinal segments of sheep.