Genome-wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep

A novel nuclear receptor NR1D1 suppresses HSD17B12 transcription to regulate granulosa cell apoptosis and autophagy via the AMPK pathway in sheep

Dominant follicular development and atresia are governed by the proliferation of granulosa cells (GCs), a process influenced by the delicate balance between apoptosis and autophagy. Oxidative stress, a pivotal catalyst of GCs apoptosis, modulates gene expression through epigenetic mechanisms, including chromatin remodeling. Nevertheless, the regulatory mechanisms underpinning GCs functionality in relation to prolificacy remain inadequately elucidated. In this study, we discovered that the chromatin accessibility of nuclear receptor subfamily 1 group D member 1 (NR1D1) was markedly enhanced in dominant follicular GCs from low-prolificacy sheep, as evidenced by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq), which correlated with elevated NR1D1 transcript levels. Remarkably, NR1D1 emerged as a novel regulator of follicular development, exhibiting heightened expression in dominant follicles. The overexpression of NR1D1 induced cell cycle arrest, autophagy activation, and mitochondrial dysfunction via the AMPK pathway, while its knockdown fostered GCs survival and functionality. Furthermore, NR1D1 inhibits the transcription of HSD17B12, thereby contributing to oxidative stress (ROS)-induced apoptosis, as demonstrated by CUT&Tag-qPCR and dual luciferase assays. The downregulation of HSD17B12 partially alleviated the effects of NR1D1 knockdown on GCs functionality. These findings indicate that NR1D1 orchestrates GCs proliferation and apoptosis through the suppression of HSD17B12 and the activation of the AMPK pathway, establishing NR1D1 as a novel transcription factor implicated in follicular development and ovarian function, with significant implications for prolificacy.

β-Nicotinamide Mononucleotide Reduces Oxidative Stress and Improves Steroidogenesis in Granulosa Cells Associated with Sheep Prolificacy via Activating AMPK Pathway

Oxidative stress is a significant factor in the death of granulosa cells (GCs), leading to follicular atresia and consequently limiting the number of dominant follicles that can mature and ovulate within each follicular wave. Follicular fluid contains a diverse array of metabolites that play crucial roles in regulating GCs' proliferation and oocyte maturation, which are essential for follicle development and female fertility. However, the mechanisms behind metabolite heterogeneity and its effects on GCs' function remain poorly understood. Here, we identified elevated nicotinamide levels in the follicular fluid of high-prolificacy sheep, correlated with oxidative stress in GCs, by an integrated analysis. In vitro experiments demonstrated that supplementation with β-nicotinamide mononucleotide (NMN) significantly increased the levels of nicotinamide adenine dinucleotide (NAD+) and adenosine triphosphate (ATP) in GCs. NMN treatment effectively reduced Lipopolysaccharide (LPS)-induced apoptosis and mitigated mitochondrial dysfunction, while also decreasing the production of reactive oxygen species (ROS), thereby enhancing the activity of the antioxidant defense system. Importantly, NMN treatment improved the impairments in steroid hormone levels induced by LPS. Mechanistically, the protective effects of NMN against GCs function were mediated via the AMPK/mTOR pathway. Collectively, our findings elucidate the metabolic characteristics associated with sheep prolificacy and demonstrate that NMN effectively protects GCs from LPS-induced dysfunction and enhances ovarian responsiveness via the AMPK/mTOR pathway. These findings also position NMN as a potential novel metabolic biomarker in enhancing ovarian function.

The Response of the miRNA Profiles of the Thyroid Gland to the Artificial Photoperiod in Ovariectomized and Estradiol-Treated Ewes

The photoperiod has been considered to be a key environmental factor in sheep reproduction, and some studies have shown that the thyroid gland plays an important role in mammalian reproduction, but the molecular mechanism is still unclear. In this study, we used the artificial-light-controlled, ovariectomized, and estradiol-treated model (OVX + E2 model); healthy and consistent 2-3-year-old Sunite multiparous ewes were collected; and thyroids were collected for testing, combined with RNA-seq technology and bioinformatics analysis, to analyze the effects of different photoperiods (long photoperiod treatment for 42 days, LP42; short photoperiod treatment for 42 days, SP42; SP42 transferred to LP42, SPLP42) on the variations in the miRNA profiles of the thyroid gland. A total of 105 miRNAs were differentially expressed in the thyroid gland, most of which were new miRNAs. Through GO and KEGG enrichment analysis, the results showed that the photoperiod response characteristics of Sunite ewes were affected by Olfactory transduction, Wnt signaling pathways, and Apelin signaling pathways. A different illumination time may have a certain influence on the downstream of these pathways, which leads to the change in animal estrus state. In addition, lncRNA-mRNA-miRNA network analysis revealed the target binding sites of identified miRNAs in DE-circRNA and DE-mRNA, such as Novel_369, Novel_370, Novel_461, and so on. The results of this study will provide some new insights into the function of miRNA and the changes in sheep thyroid glands under different photoperiods.

Identification of Functional Variants Between Tong Sheep and Hu Sheep by Whole-Genome Sequencing Pools of Individuals

Tong sheep, known for their superior meat quality and disease resilience, face breeding challenges due to low prolificacy, unlike Hu sheep, which exhibit higher fertility and growth rates. This study identified over 700,000 genetic variants between these breeds through pooled whole-genome sequencing. Functional analysis reveals key differences in pathways related to fat metabolism, insulin signaling, and cell cycle regulation. Notable findings include unique microRNA variants (miR-1185-3p in Tong sheep and miR-487-5p in Hu sheep), with the miR-487-5p mutation potentially regulating KITLG, a fertility-related gene. These results suggest that non-coding RNA mutations contribute to phenotypic differences and provide a genomic foundation for molecular-assisted selection to improve Tong sheep breeding programs.

Identification of the FGB gene polymorphism and analysis of its association with fat deposition traits in Hu sheep

As a crucial economic trait, fat deposition is directly related to carcass quality and feed efficiency in sheep. The purpose of this study was to investigate the polymorphisms of the FGB gene related to fat deposition and detect the expression features of the FGB gene in different adipose tissues of sheep by using Sanger sequencing, MassARRAY® SNP technique, and quantitative real-time PCR (qRT-PCR). Results showed that in the intron region of the FGB gene, a SNP g. 3378953 A > T has been identified, and significant association was found between perirenal fat weight, perirenal fat relative weight, mesenteric fat weight, and mesenteric fat relative weight (P < 0.05). Moreover, qRT-PCR analysis showed that FGB was expressed in all three adipose tissues, and FGB gene expression level in the AA genotype was significantly lower than that in the AT or TT genotypes (P < 0.05). Therefore, the FGB gene can be used as a candidate gene to reduce fat deposition in Hu sheep breeding, and the selection of the AA genotype in Hu sheep in production practice is more conducive to improving production efficiency.

Polymorphism in IGFALS gene and its association with scrotal circumference in Hu lambs

Scrotal circumference is an important reproductive index of breeding rams, which has a high genetic correlation with ejaculation volume and semen quality. In this study, the scrotal circumference of 1353 male Hu sheep at different stages of development was measured and descriptive statistical analysis was performed. The results showed that the coefficient of variation of scrotal circumference at each stage was greater than 10%, and its heritability were moderately to high, ranging from 0.318 to 0.719. We used PCR amplification and Sanger sequencing to scan the polymorphisms of the IGFALS gene, and performed association analysis with the circumference of the scrotum at different stages. We identified a synonymous mutation g.918 G > C in exon 1 of the IGFALS gene, and this mutation was significantly associated with scrotal circumference at 100, 120, 140, 160 and 180 days (p < 0.05). Therefore, IGFALS gene polymorphism can be used as a molecular marker affecting scrotal circumference of Hu sheep, which can provide a reference for future molecular marker-assisted selection of scrotal circumference in sheep.

Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits

The phenotypic diversity resulting from artificial or natural selection of sheep has made a significant contribution to human civilization. Hu sheep are a local sheep breed unique to China with high reproductive rates and rapid growth. Genomic selection signatures have been widely used to investigate the genetic mechanisms underlying phenotypic variation in livestock. Here, we conduct whole-genome sequencing of 207 Hu sheep and compare them with the wild ancestors of domestic sheep (Asiatic mouflon) to investigate the genetic characteristics and selection signatures of Hu sheep. Based on six signatures of selection approaches, we detect genomic regions containing genes related to reproduction (BMPR1B, BMP2, PGFS, CYP19, CAMK4, GGT5, and GNAQ), vision (ALDH1A2, SAG, and PDE6B), nervous system (NAV1), and immune response (GPR35, SH2B2, PIK3R3, and HRAS). Association analysis with a population of 1299 Hu sheep reveals that those missense mutations in the GPR35 (GPR35 g.952651 A>G; GPR35 g.952496 C>T) and NAV1 (NAV1 g.84216190 C>T; NAV1 g.84227412 G>A) genes are significantly associated (P < 0.05) with immune and growth traits in Hu sheep, respectively. This research offers unique insights into the selection characteristics of Hu sheep and facilitates further genetic improvement and molecular investigations.

Analysis of 206 whole-genome resequencing reveals selection signatures associated with breed-specific traits in Hu sheep

As an invaluable Chinese sheep germplasm resource, Hu sheep are renowned for their high fertility and beautiful wavy lambskins. Their distinctive characteristics have evolved over time through a combination of artificial and natural selection. Identifying selection signatures in Hu sheep can provide a straightforward insight into the mechanism of selection and further uncover the candidate genes associated with breed-specific traits subject to selection. Here, we conducted whole-genome resequencing on 206 Hu sheep individuals, each with an approximate 6-fold depth of coverage. And then we employed three complementary approaches, including composite likelihood ratio, integrated haplotype homozygosity score and the detection of runs of homozygosity, to detect selection signatures. In total, 10 candidate genomic regions displaying selection signatures were simultaneously identified by multiple methods, spanning 88.54 Mb. After annotating, these genomic regions harbored collectively 92 unique genes. Interestingly, 32 candidate genes associated with reproduction were distributed in nine genomic regions detected. Out of them, two stood out as star candidates: BMPR1B and GNRH2, both of which have documented associations with fertility, and a HOXA gene cluster (HOXA1-5, HOXA9, HOXA10, HOXA11 and HOXA13) had also been linked to fertility. Additionally, we identified other genes that are related to hair follicle development (LAMTOR3, EEF1A2), ear size (HOXA1, KCNQ2), fat tail formation (HOXA10, HOXA11), growth and development (FAF1, CCNDBP1, GJB2, GJA3), fat deposition (ACOXL, JAZF1, HOXA3, HOXA4, HOXA5, EBF4), immune (UBR1, FASTKD5) and feed intake (DAPP1, RNF17, NPBWR2). Our results offer novel insights into the genetic mechanisms underlying the selection of breed-specific traits in Hu sheep and provide a reference for sheep genetic improvement programs.

Field outcomes of laparoscopic ovum pick-up combined with in vitro embryo production in sheep: Effects of long-acting recombinant ovine FSH pre-stimulation, collection frequency, and donor breed

Laparoscopic ovum pick-up (LOPU) combined with in vitro embryo production (IVEP) is a technology platform that improves the utilization rate of the elite ewe's ovarian oocytes and increases the number of obtained offspring. This study aimed to evaluate the effects of FSH pre-stimulation, serial oocyte collection, and breed on LOPU-IVEP under field conditions. Donors were randomly assigned to five groups (group A: decreasing doses of pituitary FSH (p-FSH); group B: constant doses of p-FSH; group C: two doses of long-acting recombinant ovine FSH (ro-FSH); group D: single administration of a long-acting ro-FSH in; group E: no FSH stimulation). Oocyte yield following LOPU (average recovered oocytes: 20.9 ± 0.5; average viable oocytes: 17.2 ± 0.4) and oocyte developmental competence (average blastocysts: 7.0 ± 0.2) in group C were significantly better than these of group D and group E, and similar to these of groups A and B. Meanwhile, there were no differences in oocyte yield and developmental capacity using repeated LOPU session at 1-, 2-, and 3-month intervals (p > 0.05). Finally, we compared LOPU-IVEP outcomes among five sheep breeds. The results indicated that East Friesian × Chinese Mongolian crossbred sheep and purebred East Friesian sheep had the more recovered oocytes and viable oocytes compared with the Suffolk, Dorper, and Texel breeds, and average number of blastocysts in East Friesian × Chinese Mongolian sheep group was also highest among the groups (8.1 ±0.3, p < 0.05). In summary, the results of this study indicate long-acting ro-FSH pre-stimulation combined with 12 times LOPU sessions over one year maximizes embryo production of elite donor ewes under field conditions.

Polymorphisms of PLIN1 and MOGAT1 genes and their association with feed efficiency in Hu sheep

Feed cost accounts for a high proportion of sheep production, and improving sheep's utilization of feed will reduce production costs and improve economic benefits. The purpose of this study was to investigate the expression characteristics of PLIN1 and MOGAT1 genes and the relationship between their polymorphisms and feed efficiency traits in Hu sheep, and to find molecular Genetic marker that can be used in breeding. The expression levels of PLIN1 and MOGAT1 genes in various tissues were determined using quantitative real-time PCR (qRT-PCR). The results showed that PLIN1 and MOGAT1 genes were widely expressed in heart, liver, spleen, lungs, kidneys, rumen, duodenum, muscle, lymph, and tail fat. The PLIN1 gene had the highest expression level in in the tail fat compared to the other nine tissues. The expression levels of MOGAT1 gene in liver, tail fat, lung and heart was significantly higher than in kidney, muscle and lymph. The expression level of MOGAT1 was lowest in muscle compared to the other tissues (heart, liver, spleen, lung, rumen and tail fat). We recorded the body weight (BW80 and BW180) and feed intake (FI) information of 985 male Hu sheep at 80 and 180 days of age, and calculated the daily average feed intake (ADFI), average daily gain (ADG), and feed conversion rate (FCR) from 80 to 180 days of age. Two intronic mutations, g.18517910 A > G and g.224856118 G > C, were identified in PLIN1 and MOGAT1 genes by PCR amplification and Sanger sequencing. MassARRAY ® SNP detection technology was used to genotype the DNA of 985 Hu sheep and analyze its association with feed efficiency traits. The results showed that the SNP g.18517910 A > G was significantly associated with BW80, BW180, FI, ADFI and FCR (P < 0.05), while SNP g.2248561118 G > C was significantly associated with FCR (P < 0.05). Meanwhile, significant differences were also observed in different combinations of genotypes (P < 0.05). Therefore, these two polymorphic loci can serve as candidate molecular markers for improving feed utilization efficiency in Hu sheep.

Comprehensive analysis of the whole-transcriptome landscape of the ovarian cortex from Mongolian horses that reproduce seasonally

The reproductive cycle of equines tends to be seasonal and is influenced by factors such as light and temperature. The process and methods of regulating the mare oestrous cycle in the anestrus period are still immature. The effects of noncoding RNAs and mRNAs on the oestrous cycle have aroused much interest, but corresponding analyses of seasonal mare ovaries have not been reported. Here, we report a whole transcriptome analysis of the Mongolian horse ovarian cortex collected in anestrus and diestrus periods. In total, 1081 mRNAs, 205 lncRNAs, 54 circRNAs, and 13 miRNAs were upregulated in winter anestrus ovarian cortex (WAO), and 1261 mRNAs, 90 lncRNAs, 29 circRNAs, and 40 miRNAs were upregulated in summer diestrus ovarian cortex (SDO). The GO and KEGG enrichment analysis of differentially expressed mRNAs and target genes of differentially expressed lncRNAs, circRNAs, and miRNAs revealed some key functions and pathways that may be related to follicle and oocyte development. We found that estrogen-related pathways were enriched in different RNAs. Our data were used to generate miRNA, circRNA, lncRNA, and mRNA databases from the Mongolian horse ovary and differential expression profiles between WAO and SDO; these results provide clues for exploring methods of estrus regulation in mares during the anestrus period.

Polymorphism and expression level of the FADS3 gene and associated with the growth traits in Hu sheep

Growth traits are the economically important traits of sheep, and screening for genes related to growth and development is helpful for the genetic improvement of ovine growth traits. The fatty acid desaturase 3 (FADS3) is one of the important genes affecting the synthesis and accumulation of polyunsaturated fatty acids in animals. In this study, the expression levels of the FADS3 gene and polymorphism of the FADS3 gene associated with growth traits in Hu sheep were detected using quantitative real-time PCR (qRT-PCR), Sanger sequencing, and KAspar assay. The result showed that the expression levels of the FADS3 gene were widely expressed in all tissues, and the expression level of FADS3 in the lung was significantly higher than in other tissues (p < .05). Then, the polymorphism locus g. 2918 A > C was detected in intron 2 of the FADS3 gene, and associated analysis showed that the mutation in the FADS3 gene was associated significantly with growth traits (including body weight, body height, body length, and chest circumference, p < .05). Therefore, individuals with AA genotype showed significantly better growth traits than those with CC genotype, and FADS3 gene could be a candidate gene for improving growth traits in Hu sheep.

CREB1 Is Involved in miR-134-5p-Mediated Endometrial Stromal Cell Proliferation, Apoptosis, and Autophagy

The successful establishment of endometrial receptivity is a key factor in ensuring the fertility of ewes and their economic benefits. Hu sheep have attracted attention due to their high fecundity and year-round estrus. In this study, we found that in the luteal phase, the uterine gland density, uterine coefficient, and number of uterine caruncles of high-fertility Hu sheep were higher than those of low-fertility Hu sheep. Thousands of differentially expressed genes were identified in the endometrium of Hu sheep with different fertility potential using RNA sequencing (RNA-Seq). Several genes involved in endometrial receptivity were screened using bioinformatics analysis. The qRT-PCR analysis further revealed the differential expression of cAMP reactive element binding protein-1 (CREB1) in the Hu sheep endometrium during the estrous cycle. Functionally, our results suggested that CREB1 significantly affected the expression level of endometrial receptivity marker genes, promoted cell proliferation by facilitating the transition from the G1 phase to the S phase, and inhibited cell apoptosis and autophagy. Moreover, we observed a negative linear correlation between miR-134-5p and CREB1 in the endometrium. In addition, CREB1 overexpression prevented the negative effect of miR-134-5p on endometrial stromal cell (ESC) growth. Taken together, these data indicated that CREB1 was regulated by miR-134-5p and may promote the establishment of uterine receptivity by regulating the function of ESCs. Moreover, this study provides new theoretical references for identifying candidate genes associated with fertility.

Mutation of the ETS1 3'UTR interacts with miR-216a-3p to regulate granulosa cell apoptosis in sheep

ETS1, an important member of the ETS transcription factor family, is involved in a variety of physiological processes in living organisms, such as cell development, differentiation, proliferation and apoptosis, and is thought to be associated with embryonic development and reproduction. However, the polymorphism of ETS1 has been rarely studied, and its potential impact on the formation of reproductive traits in sheep remains unclear. Here, we first analyzed polymorphisms of ETS1 in a population of 382 small-tailed Han sheep with a lambing number record using the Kompetitive Allele Specific PCR (KASP) technique. The results showed the presence of a SNP locus rs161611767 (T > C) in the 3'UTR of ETS1. The association analysis showed the lambing number of first, second and third parity in the individuals with the CC genotype (2.51 ± 0.108, 2.51 ± 0.179, 1.27 ± 0.196) was higher than that of individuals with the TT genotype (1.79 ± 0.086, 1.56 ± 0.102, 0.56 ± 0.100) (P < 0.05). Then, molecular biotechnologies were used to investigate the effects of the EST1 rs161611767 mutant locus on host gene expression in sheep and the underlying mechanism of its effect on sheep reproduction. The RT‒qPCR results showed that the expression of ETS1 was higher in individuals with the CC genotype than in those with the TT genotype (P < 0.05). The dual luciferase reporter assay showed that the luciferase activity of ETS1 in sheep with the TT genotype was decreased compared to CC genotype (P < 0.05), confirming the existence of EST1 rs161611767 in the 3'UTR as a functional SNP. Given that the 3'UTR is an important regulatory region of gene transcription and translation, we performed bioinformatics prediction and confirmed that the SNP rs161611767 of ETS1 was a direct functional target of miR-216a-3p using dual luciferase activity assay, and the binding capacity of allele T was stronger than that of allele C. Subsequently, the cell transfection results showed that miR-216a-3p suppressed the endogenous expression of ETS1 in sheep primary granulosa cells (GCs). Finally, CCK-8, EdU, WB detection of marker proteins and flow cytometry were used to detect the effects of miR-216a-3p on GCs viability and proliferation/apoptosis, respectively. The results showed that miR-216a-3p inhibited the proliferation of GCs while promoting apoptosis of GCs. In conclusion, these results demonstrate that the SNP rs161611767 of ETS1 is associated with lambing number in small-tailed Han sheep, and miR-216a-3p can act as a regulatory element binding to the T mutation in rs161611767 to regulate ETS1 expression and affect GCs development, which may indirectly affect the number of lambs in sheep. These studies provide evidence for the involvement of ETS1 polymorphisms in sheep reproduction and are expected to provide new insights to elucidate the molecular genetic mechanisms of lambing traits in sheep.

Identification and analysis of differentially expressed microRNAs in endometrium to explore the regulation of sheep fecundity

BACKGROUND

MicroRNAs (miRNAs) play an important regulatory role in mammalian reproduction. Currently, most studies are primarily concentrated on ovarian miRNAs, ignoring the influence of endometrial miRNAs on the fecundity of female sheep. To uncover potential regulators of sheep fecundity, RNA-seq was used to comparatively analyze miRNA expression profiles of endometrium between high prolificacy sheep (HP, litter size = 3) and low prolificacy sheep (LP, litter size = 1) with FecB genotype.

RESULTS

Firstly, genomic features of miRNAs from endometrium were analyzed. Furthermore, 58 differentially expressed (DE) miRNAs were found in the endometrium of Hu sheep with different litter size. A co-expression network of DE miRNAs and target genes has been constructed, and hub genes related litter size are included, such as DE miRNA unconservative_NC_019472.2_1229533 and unconservative_NC_019481.2_1637827 target to estrogen receptor α (ESR1) and unconservative_NC_019481.2_1637827 targets to transcription factor 7 (TCF7). Moreover, functional annotation analysis showed that the target genes (NRCAM and NEGR1) of the DE miRNAs were significantly enriched in cell adhesion molecules (CAMs) signaling pathway, which was related to uterine receptivity.

CONCLUSION

Taken together, this study provides a new valuable resource for understanding the molecular mechanisms underlying Hu sheep prolificacy.

Comprehensive investigation of milk oligosaccharides in different mammalian species and the effect of breed and lactation period on sheep milk oligosaccharides

Milk oligosaccharides (MOs) have unique health benefits for newborns, and MOs are important components in mammalian milk. The present study was conducted to provide a comprehensive analysis of MOs in important domestic animals, including goats, cows, camels and sheep. The comparison with human MOs was conducted simultaneously. Furthermore, analysis of the relative abundance of sheep MOs among different breeds (Hu sheep, East Friesen sheep, East Friesen-Hu crossbred sheep) and lactation periods (colostrum, mature milk) was performed. In general, 35, 24 19, 26, and 16 MOs were identified in human, goat, bovine, camel and sheep milk, respectively. The type of sheep MOs was not greatly influenced by the breeds and lactation period. Hu sheep colostrum had the highest abundance of MOs among six sheep milks, followed by East Friesen sheep colostrum, while East Friesen-Hu crossbred sheep mature milk had the lowest abundance of MOs. These findings provide evidence for the potential value of MOs from domestic animal milk for the commercial applications.

EZH2 Gene Knockdown Inhibits Sheep Pituitary Cell Proliferation via Downregulating the AKT/ERK Signaling Pathway

Pituitary gonadotropins perform essential functions in mammalian reproduction by stimulating gametogenesis and steroidogenesis in the ovaries and testicles. EZH2 is a histone methyltransferase that inhibits proliferation and aggravates apoptosis in stem cells subjected to pathological stimuli. However, the expression and molecular mechanisms of EZH2 in pituitary cells in vitro have not been extensively studied. In this study, the relative abundances of EZH2 mRNA (p < 0.01) and protein (p < 0.05) expression were larger in the pituitary cells of Hu sheep with relatively greater fecundity (GF) compared to those with lesser fecundity (LF). Loss-of-function examinations demonstrated that EZH2 gene knockdown led to an earlier induction of apoptosis in sheep pituitary cells (PCs). The relative abundance of CASP3, CASP9, and BAX was increased (p < 0.01), while BCL2's abundance was less decreased (p < 0.01) in PCs where there was EZH2 gene knockdown. Additionally, cell proliferation (p < 0.01) and viability (p < 0.01) were decreased in EZH2-knockdown sheep PCs, and the cell cycle was blocked compared to a negative control (NC). Notably, EZH2 gene knockdown led to reduced abundances of gonadotropin subunit gene transcripts (FSHβ, p < 0.05) and reduced FSH release (p < 0.01) from PCs. EZH2 gene knockdown led to reduced phosphorylation of AKT, ERK, and mTOR (p < 0.01). The results suggest that EZH2 regulates pituitary cell proliferation, apoptosis, and FSH secretion through modulation of the AKT/ERK signaling pathway, providing a foundation for further study of pituitary cell functions.

Identification and characterization of unique and common lncRNAs and mRNAs in the pituitary, ovary, and uterus of Hu sheep with different prolificacy

LncRNAs are regarded as regulators in various animal reproductive physiological processes. However, the regulation of lncRNAs in the reproductive organ development of Hu sheep with different prolificacy remains unknown. Herein, numerous tissue-unique and -common differentially expressed lncRNAs (DELs) and differentially expressed genes (DEGs), and fecundity-unique DELs and DEGs were identified among different comparison groups at horizontal and vertical levels. Moreover, the tissue-unique and -common, and fecundity-unique female reproduction-associated DEGs and DELs were screened, and the interaction networks were constructed. Furthermore, MSTRG.43442.1 was mainly present in the cytoplasm of tested cells. The key genes ADAMTS1 and DCN were mainly localized in the granulosa cells, pituitary cells and/or endometrial epithelial cells of ovary, pituitary and/or uterus. Overall, this study identified large numbers of unique and common DELs and DEGs in the female reproductive organs of Hu sheep with different prolificacy and provided new insights into understanding the regulation of Hu sheep fecundity.

LncRNA-412.25 activates the LIF/STAT3 signaling pathway in ovarian granulosa cells of Hu sheep by sponging miR-346

Although long non-coding RNAs (lncRNAs) are reported to regulate follicular development and reproductive disease pathogenesis, the underlying mechanisms have not been elucidated. In this study, lncRNA expression profiling of different-sized healthy follicles from Hu sheep with different prolificacy revealed 50 613 lncRNAs. Numerous lncRNAs were differentially expressed among different comparison groups. This study characterized one novel transcript, lncRNA-412.25 (from healthy follicles with a diameter of >5 mm), which was predominantly expressed in the high prolificacy group and localized to the cytoplasm of granulosa cells (GCs). LncRNA-412.25 knockdown promoted and inhibited Hu sheep GC apoptosis and proliferation, respectively. Interestingly, lncRNA-412.25 could directly bind to miR-346, which can target the gene of leukemia inhibitory factor (LIF). Knockdown of lncRNA-412.25 promoted GC apoptosis by downregulating LIF expression, where this effect was attenuated by miR-346. Moreover, the miR-346 inhibitor mitigated the lncRNA-412.25 knockdown-induced downregulation of phosphorylated protein of signal transducer and activator of transcription 3 (STAT3), which was validated using immunofluorescence analysis. Our results demonstrated that lncRNA-412.25 regulates GC proliferation and apoptosis in Hu sheep by binding to miR-346 and then activating the LIF/STAT3 pathway. These findings provide novel insights into the mechanisms underlying prolificacy in sheep.

Differential Expression and Functional Prediction of mRNA in the Ovaries of Hanper Sheep of High and Low Fecundity

Hanper ewes that were either monotocous or polytocous provided ovarian follicles of diameter >3 mm in the follicular phase and, in the luteal phase, samples of corpora lutea that had developed from follicles of diameter >3 mm. Differentially expressed mRNAs (monotocous versus polytocous) were then identified and their functions were predicted. Results showed that 1508 mRNAs were differentially expressed in the follicular phase, with 885 being in the luteal tissues. Those which were differentially expressed in the follicular phase were mainly involved in the regulation of the ferroptosis and lysosome signaling pathways whereas, for the luteal tissue, the differentially expressed mRNAs were mainly involved in the regulation of steroid biosynthesis. Based on the results, it was inferred that these pathways could explain variations in the fecundity of sheep.

Ovine RAP1GAP and rBAT gene polymorphisms and their association with tail fat deposition in Hu sheep

Excessive fat deposition in the tail of sheep will affect its feed efficiency, which will increase the feeding cost. The purpose of this study was to identify the single nucleotide polymorphisms (SNPs) of RAP1GAP and rBAT genes by PCR amplification and Sanger sequencing, the SNPs were genotyped by KASP genotyping assays to evaluate their association with tail fat deposition traits. The results showed that two intronic mutations of g.13561 G > A and g.1460 T > C were found in RAP1GAP and rBAT, respectively. There were three genotypes of GG, AG, AA and CC, CT and TT at these two loci, respectively. Association analysis showed that g.13561 G > A of RAP1GAP was associated with tail width, tail fat weight and relative tail fat weight (P < 0.05). The g.1460 T > C of rBAT was associated with tail width and tail fat weight (P < 0.05). Different combinations of genotypes also differed significantly with tail fat deposition traits. In the tail fat tissue, the expression levels of RAP1GAP gene was significantly higher in small-tailed sheep than in big-tailed sheep, and the expression levels of rBAT gene was significantly higher in big-tailed sheep than in small-tailed sheep. In the liver, the expression levels of RAP1GAP and rBAT gene was significantly higher at 6 months than at 0 and 3 months. In conclusion, RAP1GAP and rBAT polymorphisms can be used as a candidate molecular marker to reduce tail fat deposition in sheep.

Comprehensive analysis of differentially expressed profiles of mRNA, lncRNA, and miRNA of Yili geese ovary at different egg-laying stages

Background

The development of the ovaries is an important factor that affects egg production performance in geese. Ovarian development is regulated by genes that are expressed dynamically and stage-specifically. The transcriptome profile analysis on ovarian tissues of goose at different egg laying stages could provide an important basis for screening and identifying key genes regulating ovarian development.

Results

In this study, 4 ovary tissues at each breeding period of pre-laying (PP), laying (LP), and ceased-laying period (CP), respectively, with significant morphology difference, were used for RNA extraction and mRNAs, lncRNAs, and miRNAs comparison in Yili geese. CeRNA regulatory network was constructed for key genes screening. A total of 337, 1136, and 525 differentially expressed DE mRNAs, 466, 925, and 742 DE lncRNAs and 258, 1131 and 909 DE miRNAs were identified between PP and LP, between CP and LP, and between CP and PP groups, respectively. Functional enrichment analysis showed that the differentially expressed mRNAs and non-coding RNA target genes were mainly involved in the cell process, cytokine-cytokine receptor interaction, phagosome, calcium signaling pathway, steroid biosynthesis and ECM-receptor interaction. Differential genes and non-coding RNAs, PDGFRB, ERBB4, LHCGR, MSTRG.129094.34, MSTRG.3524.1 and gga-miR-145–5p, related to reproduction and ovarian development were highly enriched. Furthermore, lncRNA-miRNA-mRNA regulatory networks related to ovary development were constructed.

Conclusions

Our study found dramatic transcriptomic differences in ovaries of Yili geese at different egg-laying stages, and a differential lncRNA-miRNA-mRNA regulatory network related to cell proliferation, differentiation and apoptosis and involved in stromal follicle development were established and preliminarily validated, which could be regarded as a key regulatory pathway of ovarian development in Yili geese.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08774-4.

Integrative analysis of transcriptomics and proteomics of longissimus thoracis of the Hu sheep compared with the Dorper sheep

Meat quality is becoming more important for sheep breeding programs. Meat quality is a complex trait affected by genetic and environmental factors. In the present study, an integrative analysis of the longissimus thoracis tissue transcriptome and proteome was conducted to identify genes, proteins, and pathways related to meat quality in sheep. The sheep breeds Hu and Dorper were considered. These breeds were compared for the differences in muscle fiber structure, chemical composition, and amino acid composition. In the Hu sheep vs. Dorper sheep comparison, 22 DEGs/DEPs showed the same mRNA and protein expression trends. These genes are associated with lipid transport, lipid metabolism, and muscular system development. Moreover, some pathways such as "lipid transport", "lipoprotein metabolic process", "Alanine, aspartate and glutamate metabolism", and "Arginine biosynthesis" were significantly enriched in this study. The reliability of the RNA-Seq results was verified by qRT-PCR. These findings provide new insights into the molecular mechanisms of meat quality in sheep.

Identification of TRAPPC9 and BAIAP2 Gene Polymorphisms and Their Association With Fat Deposition-Related Traits in Hu Sheep

Fat deposition is an important economic trait that is closely related to feed efficiency and carcass performance in livestock. In this study, the fat deposition-related traits of 1,293 Hu sheep were measured and descriptive statistical analysis was conducted. The results showed that the coefficient of variation of all fat deposition-related traits was higher than 24%. In addition, single nucleotide polymorphisms and the expression characteristics of TRAPPC9 (encoding trafficking protein particle complex subunit 9) and BAIAP2 (encoding brain-specific Angiogenesis inhibitor 1-associated protein 2) genes in Hu sheep were detected using PCR amplification, Sanger sequencing, KASPar genotyping, and quantitative real-time reverse transcription PCR (qRT-PCR). The associations between SNPs and fat deposition-related traits were also analyzed. Two intronic mutations, TRAPPC9 g.57654 A > G and BAIAP2 g.46061 C > T, were identified in Hu sheep. The result of association analysis showed that TRAPPC9 g.57654 A > G and BAIAP2 g.46061 C > T were both significantly associated with the weight of tail fat, tail fat relative weight (body weight), and tail fat relative weight (carcass) (P < 0.05). Comprehensive effects analysis showed that there were significant differences between the combined genotypes and tail fat and perirenal fat deposition. Moreover, qRT-PCR analysis showed that TRAPPC9 and BAIAP2 are widely expressed, and their expression levels were significantly higher in the small-tail group compared with those in the big-tail group (P < 0.01). These results provided important candidate molecular markers that could be used in strategies to reduce tail fat deposition in Hu sheep.

Whole genome sequencing of Luxi Black Head sheep for screening selection signatures associated with important traits

Objective

Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH.

Methods

We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (H_P), fixation index (F_ST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (θ_π) ratio.

Results

The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected.

Conclusion

The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

Comparative analysis of long noncoding RNA and mRNA expression provides insights into adaptation to hypoxia in Tibetan sheep

Tibetan sheep have lived on the Qinghai-Tibetan Plateau for thousands of years and have good adaptability to the hypoxic environment and strong disease resistance. However, the molecular mechanism by which Tibetan sheep adapt to this extreme environment, especially the role of genetic regulation, is still unknown. Emerging evidence suggests that long noncoding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. To explore the potential lncRNAs involved in the adaptation to high-altitude hypoxia of Tibetan sheep, we analysed the expression profile of lncRNAs and mRNAs in the liver and lung tissues of sheep using comparative transcriptome analysis between four Tibetan sheep populations (high altitude) and one Hu sheep population (low altitude). The results showed a total of 7848 differentially expressed (DE) lncRNA transcripts, and 22,971 DE mRNA transcripts were detected by pairwise comparison. The expression patterns of selected mRNAs and lncRNAs were validated by qRT-PCR, and the results correlated well with the transcriptome data. Moreover, the functional annotation analysis based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases showed that DE mRNAs and the target genes of the lncRNAs were significantly enriched in organ morphogenesis, response to stimulus, haem binding, the immune system, arginine and proline metabolism, and fatty acid biosynthesis. The prediction of mRNA–mRNA and lncRNA–mRNA interaction networks further revealed transcripts potentially involved in adaptation to high-altitude hypoxia, and the hub genes DDX24, PDCD11, EIF4A3, NDUFA11, SART1, PRPF8 and TCONS_00306477, TCONS_00306029, TCONS_00139593, TCONS_00293272, and TCONS_00313398 were selected. Additionally, a set of target genes, PIK3R1, IGF1R, FZD6, IFNB2, ATF3, MB, CYP2B4, PSMD13, and TGFB1, were also identified as candidate genes associated with high-altitude hypoxia adaptation. In conclusion, a collection of novel expressed lncRNAs, a set of target genes and biological pathways known to be relevant for altitude adaptation were identified by comparative transcriptome analysis between Tibetan sheep and Hu sheep. Our results are the first to identify the characterization and expression profile of lncRNAs between Tibetan sheep and Hu sheep and provide insights into the genetic regulation mechanisms by which Tibetan sheep adapt to high-altitude hypoxic environments.

The Novel Competing Endogenous Long Noncoding RNA SM2 Regulates Gonadotropin Secretion in the Hu Sheep Anterior Pituitary by Targeting the Oar-miR-16b/TGF-β/SMAD2 Signaling Pathway

Pituitary gonadotropins play a pivotal role in reproduction. Long noncoding RNAs (lncRNAs) have been identified as important regulators in the hypothalamic−pituitary−ovarian (HPO) axis associated with reproduction. However, the contributions of lncRNAs to pituitary gonadotropin secretion remain largely unknown. Therefore, this work was performed to uncover the functional mechanisms of the novel lncRNA TCONS_00083279 (lncRNA SM2) and its potential targeting pathway oar-miR-16b/TGF-beta/SMAD2, which is associated with gonadotropin secretion in sheep pituitary cells. In the present study, the lncRNA SM2 showed high expression levels in the sheep pituitary gland, and it was located in both the nucleus and the cytoplasm of pituitary cells. lncRNA SM2 knockdown inhibited pituitary cell proliferation and FSH and LH secretion. The function of the lncRNA SM2 was sponged by oar-miR-16b, and this regulated the growth and gonadotropin secretion of pituitary cells by modulating SMAD2, as shown by the dual-luciferase reporter assay. FSH and LH levels were both upregulated by SMAD2 overexpression. Moreover, the levels of the lncRNA SM2, SMAD2 and TGFR1, as well as FSH and LH, in sheep pituitary cells increased significantly under gonadotropin-releasing hormone (GnRH) stimulation (p < 0.05). This work illustrates that the lncRNA SM2 regulates gonadotropin secretion in the Hu sheep anterior pituitary by targeting the oar-miR-16b/TGF-β/SMAD2 signaling pathway, providing a valuable resource for understanding the molecular mechanisms underlying sheep reproduction.

Immunocastration with gene vaccine (KISS1) induces a cell-mediated immune response in ram testis: A transcriptome evaluation

Immunocastration vaccines achieve their effects through neutralization of the endogenous hormone by the humoral antibody produced against the immunized genes. But there is little information regarding cell-mediated immune response on the gonadal function of the immunized model is available. In this study, we used ram as a model animal to identify the cellular immune response in testicular tissues of rams immunized with intranasal KISS1 gene vaccine. The immune castration model was evaluated by sexual behaviors, spermatogenesis, and serum hormone profiles after the KISS1 gene immunization. Transcriptome analysis of testicular tissues was carried out to identify the expressions of protein-coding genes involved in cellular immunity. The results showed that we successfully constructed the KISS1 immune castration ram model, in which testicular growth and development, testosterone and kisspeptin-54 levels, and sexual function were suppressed in immunized rams (P <0.05). Using HiseqTM 2000 high sequencing for ram testicular, we identified 21 differentially expressed genes (DEGs) related to cellular immunity, of which, 14 genes were up-regulated and seven genes were down-regulated in the testis of the immunized group (P<0.05). The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment showed that these differentially expressed genes were enriched in the antigen presentation process mediated by MHC class I and the cytotoxic pathway mediated by natural killer cells. It is concluded that KISS1 gene vaccine induced the cell-mediated immune response in testicular tissue to suppress reproductive activities in rams.

Genome-Wide Identification of mRNAs, lncRNAs, and Proteins, and Their Relationship With Sheep Fecundity

The exploration of multiple birth-related genes has always been a significant focus in sheep breeding. This study aimed to find more genes and proteins related to the litter size in sheep. Ovarian specimens of Small Tail Han sheep (multiple births) and Xinji Fine Wool sheep (singleton) were collected during the natural estrus cycle. Transcriptome and proteome of ovarian specimens were analyzed. The transcriptome results showed that "steroid hormone biosynthesis" and "ovarian steroidogenesis" were significantly enriched, in which HSD17B1 played an important role. The proteome data also confirmed that the differentially expressed proteins (DEPs) were enriched in the ovarian steroidogenesis pathway, and the CYP17A1 was the candidate DEP. Furthermore, lncRNA MSTRG.28645 was highly expressed in Small Tailed Han sheep but lowly expressed in Xinji fine wool sheep. In addition, MSTRG.28645, a hub gene in the co-expression network between mRNAs and lncRNAs, was selected as one of the candidate genes for subsequent verification. Expectedly, the overexpression and interference of HSD17B1 and MSTRG.28645 showed a significant effect on hormone secretion in granulosa cells. Therefore, this study confirmed that HSD17B1 and MSTRG.28645 might be potential genes related to the fecundity of sheep. It was concluded that both HSD17B1 and MSTRG.28645 were critical regulators in the secretion of hormones that affect the fecundity of the sheep.

Integrative Genome-Wide DNA Methylome and Transcriptome Analysis of Ovaries from Hu Sheep with High and Low Prolific

DNA methylation plays an important role in biological processes by affecting gene expression. However, how DNA methylation regulates phenotypic variation in Hu sheep remains unclear. Therefore, we generated genome-wide DNA methylation and transcriptomic profiles in the ovaries of Hu sheep with different prolificacies and genotypes (FecBB and FecB+). Results showed that ovary DNA methylome and transcriptome were significantly different between high prolificacy and low prolificacy Hu sheep. Comparative methylome analyses identified 10,644, 9,594, and 12,214 differentially methylated regions and 87, 1,121, and 2,375 genes, respectively, showing differential expression levels in three different comparison groups. Female reproduction-associated differentially methylated regions-related genes and differentially expressed genes were enriched, thereby the respective interaction networks were constructed. Furthermore, systematical integrative analyses revealed a negative correlation between DNA methylation around the transcriptional start site and gene expression levels, which was confirmed by testing the expression of integrin β2 subunit (ITGB2) and lysosome-associated protein transmembrane-4 beta (LAPTM4B) in vivo and in vitro. These findings demonstrated that DNA methylation influences the propensity for prolificacy by affecting gene expression in the ovaries, which may contribute to a greater understanding of the epigenome and transcriptome that will be useful for animal breeding.

Expression of ovine CTNNA3 and CAP2 genes and their association with growth traits

Growth traits is a critical economic trait for animal husbandry. In this study, the SNPs of CTNNA3 and CAP2 genes were investigated to check whether they are associated with growth traits (body weight, body height, body length and chest circumference) in Hu sheep. The result of the association analysis indicated that the mutation in CTNNA3 (g.2018018 A > G) were associated significantly with body weight, body height, body length and chest circumference (P < 0.05), the mutation in CAP2 (g.8588 T > C) were associated significantly with body height at 140, 160, 180 days (P < 0.05), AA and CC of CTNNA3 and CAP2 were the dominant genotypes associated with growth traits in Hu sheep. Moreover, combined effect analyses indicated that the growth traits with combined genotypes AA^CTNNA3-CC^CAP2 and AA^CTNNA3-CT^CAP2 were higher than those with genotype GG^CTNNA3-CT^CAP2. RT-qPCR indicated that CTNNA3 expression levels were significantly higher in liver and lung than in other nine tissues (P < 0.05), CAP2 expression levels were significantly higher in bone, heart, liver, lung and duodenum than in other six tissues (P < 0.05). In conclusion, CTNNA3 and CAP2 polymorphisms could be used as genetic markers for improving growth traits in Hu sheep husbandry.

Follicular development in livestock: Influencing factors and underlying mechanisms

Livestock farming development has become increasingly important in recent years. It not only provides us with meat nutrition and pet feeding but also increases the economic value by providing numerous employment opportunities, which improves our life quality. The livestock farming development depends on successful animal reproduction. As a vital process in animal reproduction, folliculogenesis and its influencing factors as well as their underlying mechanisms need to be understood thoroughly. This review is aimed at summarizing the factors such as cellular processes, gene regulation, noncoding RNAs and other endocrine or paracrine regulatory factors that affect follicular development, and their underlying mechanisms of action in livestock in order to provide novel insights for future studies. The above factors were found as significant determinants influencing the follicular development in livestock through various signaling pathways.

Cathepsin D knockdown regulates biological behaviors of granulosa cells and affects litter size traits in goats

Cathepsin D (CTSD), the major lysosomal aspartic protease that is widely expressed in different tissues, potentially regulates the biological behaviors of various cells. Follicular granulosa cells are responsive to the increase of ovulation number, hence indirectly influencing litter size. However, the mechanism underlying the effect of CTSD on the behaviors of goat granulosa cells has not been fully elucidated. This study used immunohistochemistry to analyze CTSD localization in goat ovarian tissues. Moreover, western blotting was applied to examine the differential expression of CTSD in the ovarian tissues of monotocous and polytocous goats. Subsequently, the effects of CTSD knockdown on cell proliferation, apoptosis, cell cycle, and the expression of candidate genes of the prolific traits, including bone morphogenetic protein receptor IB (BMPR-IB), follicle-stimulating hormone (FSHR), and inhibin α (INHA), were determined in granulosa cells. Results showed that CTSD was expressed in corpus luteum, follicle, and granulosa cells. Notably, CTSD expression in the monotocous group was significantly higher than that in the polytocous group. In addition, CTSD knockdown could improve granulosa cell proliferation, inhibit cell apoptosis, and significantly elevate the expression of proliferating cell nuclear antigen (PCNA) and B cell lymphoma 2 (Bcl-2), but it lowered the expression of Bcl-2-associated X (Bax) and caspase-3. Furthermore, CTSD knockdown significantly reduced the ratios of cells in the G0/G1 and G2/M phases but substantially increased the ratio of cells in the S phase. The expression levels of cyclin D2 and cyclin E were elevated followed by the obvious decline of cyclin A1 expression. However, the expression levels of BMPR-IB, FSHR, and INHA clearly increased as a result of CTSD knockdown. Hence, our findings demonstrate that CTSD is an important factor affecting the litter size trait in goats by regulating the granulosa cell proliferation, apoptosis, cell cycle, and the expression of candidate genes of the prolific trait.

Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep

The tail fat of sheep is the most typical deposited fat, and it can be widely used in human daily life, such as diet, cosmetics, and industrial raw materials. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6, 18, and 30 months. A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep. Based on functional analysis, we found that fat-related DEGs were mainly expressed at 6 months of age and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their transregulators. Further, we obtained several fat-related differentially expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Finally, we concluded that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process.

Identification of Photoperiod-Induced LncRNAs and mRNAs in Pituitary Pars Tuberalis of Sheep

The pituitary pars tuberalis (PT) is the regulating center of seasonal reproduction, which can sense the melatonin signal and eventually cause downstream changes of GnRH secretion through TSHβ. Recently, lncRNAs have been identified in animal reproductive-related tissues, and they play important roles in reproductive regulation. Therefore, in this study, we expect to identify photoperiod-induced lncRNAs and genes in pituitary PT of sheep by comparison of expression profiles between short photoperiod (SP) and long photoperiod (LP). Through RNA-Seq, a total of 55,472 lncRNAs were identified in pituitary PT of Sunite ewes. The number of differentially expressed (DE) genes and lncRNAs between SP and LP increased gradually with the extension of LP (from LP7 to LP42). The notable LP-induced candidate genes included EYA3, TSHB, SIX1, DCT, VMO1, AREG, SUV39H2, and EZH2, and SP-induced genes involved ENSOARG00000012585, CHGA, FOS, SOCS3, and TH. In enriched pathways for DE genes and lncRNA target genes between SP and LP, the reproduction- and circadian-related pathways were highlighted. In addition, the interactome analysis of lncRNAs and their targets implied that MSTRG.209166 and its trans-target TSHB, MSTRG.288068 and its cis-target SIX1, and ENSOARG00000026131 and its cis-target TH might participate in regulation of seasonal reproduction. Together, these results will help to determine important photoperiod-induced lncRNAs and genes and give us some new insights into the epigenetic regulation of seasonal reproduction in sheep.

Whole-Transcriptome Analysis of LncRNAs Mediated ceRNA Regulation in Granulosa Cells Isolated From Healthy and Atresia Follicles of Chinese Buffalo

Granulosa cells (GCs) are the main supporting cells in follicles and play an important role in the regulation of oocyte maturation and follicular atresia. Accumulating evidence indicates that non-coding RNAs participate in regulation of the physiological function of GCs. However, whole-transcriptome analysis for GCs of buffalo has yet to be reported. In this study, healthy follicles (HFs) and atretic follicles (AFs) were defined according to the apoptosis rate of GCs and the hormone level in follicular fluid. GCs were collected from HFs and AFs (n = 15, 5 < n < 8 mm) for whole-transcriptome analysis using second-generation high-throughput sequencing. A total of 1,861 and 1,075 mRNAs, 159 and 24 miRNAs, and 123 and 100 lncRNAs, were upregulated and downregulated between HFs and AFs, respectively. Enrichment of functions and signaling pathways of these differentially expressed (DE) genes showed that most of DEmRNAs and targets of DEmiRNAs were annotated to the categories of ECM–receptor interaction and focal adhesion, as well as PI3K-AKT, mTOR, TGF-beta, Rap1, and estrogen signaling pathways. The competing endogenous RNA (CeRNA) network was also constructed based on the ceRNA theory which further revealed regulatory roles of these DERNAs in GCs of buffalo follicles. Finally, we validated that lnc4040 regulated the expression of Hif1a as miR-709 sponge in a ceRNA mechanism, suggesting their critical functions in GCs of buffalo follicles. These results show that lncRNAs are dynamically expressed in GCs of HFs and AFs, and interacting with target genes in a ceRNA manner, suggesting their critical functions in buffalo follicular development and atresia.

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep

Simple Summary

Litter size is an important trait affecting reproductive capacity and breeding economics in meat sheep. Consequently, revealing its molecular mechanism helps us understand multiple lambs from the genetic perspective. In this study, we provide a genome-wide expression profile of circular RNAs (circRNAs) expression in Hanper sheep, which is a new breed of meat sheep raised by cross and self-group breeding for 15 years. In this study, ovarian circular RNAs and miRNAs associated with high and low fertility Hanper sheep are identified during the follicular and luteal phases of the estrous cycle, and their potential biological functions are predicted through Gene Ontology (GO), KEGG, GSEA, STEM, WGCNA analysis.

Abstract

Litter size is a considerable quality that determines the production efficiency of mutton sheep. Therefore, revealing the molecular regulation of high and low fertility may aid the breeding process to develop new varieties of mutton sheep. CircRNAs are the important factors regulating follicular development, but their mechanism role in the regulation of litter size in Hanper sheep is not clear. In the present study, ovarian tissues from the follicular (F) or luteal phase (L) of Hanper sheep that were either consecutive monotocous (M) or polytocous were collected. Then, we performed transcriptome sequencing to screen for differentially expressed circRNAs (DE-circRNAs) and elucidate their function. In total, 4256 circRNA derived from 2184 host genes were identified in which 183 (146 were upregulated, while 37 were downregulated) were differentially expressed in monotocous sheep in the follicular phase versus polytocous sheep in the follicular phase (MF vs. PF). Moreover, 34 circRNAs (14 were upregulated, while 20 were downregulated) were differentially expressed in monotocous sheep in the luteal phase versus polytocous sheep in the luteal sheep (ML vs. PL). This was achieved through DE-circRNAs function enrichment annotation analysis by GESA, GO, and KEGG, which function through the EGF-EGFR-RAS-JNK, TGF-β and thyroid hormone signaling pathway to affect the litter size of Hanper sheep in MF vs. PF and ML vs. PL. STEM results showed that MAPK signaling pathways play a key role in MF vs. PF and ML vs. PL. Through WGCNA analysis, AKT3 was a core gene in MF vs. PF and ML vs. PL. Moreover, competitive endogenous RNA (ceRNA) network analysis revealed the target binding sites for miRNA such as oar-miR-27a, oar-miR-16b, oar-miR-200a/b/c, oar-miR-181a, oar-miR-10a/b, and oar-miR-432 in the identified DE-cirRNAs.

Transcriptome Analysis Reveals Differentially Expressed Genes and Long Non-coding RNAs Associated With Fecundity in Sheep Hypothalamus With Different FecB Genotypes

Small-tailed Han sheep, with different FecB genotypes, manifest distinct ovulation rates and fecundities, which are due to differences in reproductive hormones secreted by the hypothalamic-pituitary-ovarian axis. Nevertheless, the function of the hypothalamus against a FecB mutant background on increasing ovulation rate is rarely reported. Therefore, we determined the expression profiles of hypothalamus tissue collected from six wild-type (WW) and six FecB mutant homozygous (BB) ewes at the follicular and luteal phases by whole-transcriptome sequencing. We identified 53 differentially expressed mRNAs (DEGs) and 40 differentially expressed long non-coding RNAs (DELs) between the two estrus states. Functional annotation analysis revealed that one of the DEGs, PRL, was particularly enriched in the hypothalamic function, hormone-related, and reproductive pathways. The lncRNA-target gene interaction networks and KEGG analysis in combination suggest that the lncRNAs LINC-676 and WNT3-AS cis-acting on DRD2 and WNT9B in different phases may induce gonadotropin-releasing hormone (GnRH) secretion. Furthermore, there were differences of regulatory elements and WNT gene family members involved in the follicular-luteal transition in the reproductive process between wild-type (WNT7A) and FecB mutant sheep (WNT9B). We combined the DEG and DEL data sets screened from different estrus states and genotypes. The overlap of these two sets was identified to select the mRNAs and lncRNAs that have major effects on ovulation. Among the overlapping molecules, seven DEGs and four DELs were involved in the follicular-luteal transition regulated by FecB mutation. Functional annotation analysis showed that two DEGs (FKBP5 and KITLG) were enriched in melanogenesis, oxytocin, and GnRH secretion. LINC-219386 and IGF2-AS were highly expressed in the BB ewes compared with WW ewes, modulating their target genes (DMXL2 and IGF2) to produce more GnRH during follicular development, which explains why mutated ewes produced more mature follicles. These results from expression profiling of the hypothalamus with the FecB mutation at different estrus states provide new insights into how the hypothalamus regulates ovulation under the effect of the FecB mutation.

Profiling and integrated analysis of whole-transcriptome changes in uterine caruncles of pregnant and non-pregnant buffaloes

Improved reproductive performance in buffaloes can be achieved by understanding the basic mechanism governing the embryonic attachment and feto-maternal communication. Considering this, trascriptomic profiling and integrative analysis of long intergenic non-coding RNAs were carried out in the uterine caruncles of pregnant and non-pregnant buffaloes. Transcriptome data of pregnant and non-pregnant uterine caruncles after quality control was used to perform the analysis. Total of 86 novel lincRNAs expressed in uterine caruncular tissues were identified and characterized. Differential expression analysis revealed that 447 mRNAs and 185 mRNAs were up- and down- regulated, respectively. The number of up- and down- regulated lincRNAs were 114 and 13, respectively. Of the identified 86 novel lincRNAs, six novel lincRNAs were up-regulated in the pregnant uterine caruncles. GO terms (biological process) and PANTHER pathways associated with reproduction and embryogenesis were over-represented in differentially expressed genes. Through miRNA interaction analysis, interactions of 16 differentially expressed lincRNAs with mi-RNAs involved in reproduction were identified. This study has provided a catalogue of differentially expressed genes and novel regions previously unknown to play a significant role in buffalo reproduction. The results from the current study extends the buffalo uterine lncRNAs database and provides candidate regulators for future molecular genetic studies on buffalo uterine physiology to improve the embryo implantation and successful completion of pregnancy.

Photoperiod induced the pituitary differential regulation of lncRNAs and mRNAs related to reproduction in sheep

The pituitary is a vital endocrine organ that regulates animal seasonal reproduction by controlling the synthesis and secretion of the hormone. The change of photoperiod is the key factor affecting the function of the pituitary in animals, but the mechanism is unclear. Here, we studied the transcriptomic variation in pars distalis (PD) of the pituitary between short photoperiod (SP) and long photoperiod (LP) using RNA sequencing based on the OVX+E₂ sheep. 346 differentially expressed (DE) lncRNAs and 186 DE-mRNA were found in the PD. Moreover, function annotation analysis indicated that the reproductive hormones and photoperiod response-related pathways including aldosterone synthesis and secretion, insulin secretion, thyroid hormone synthesis, and circadian entrainment were enriched. The interaction analysis of mRNA-lncRNA suggested that MSTRG.240648, MSTRG.85500, MSTRG.32448, and MSTRG.304959 targeted CREB3L1 and DUSP6, which may be involved in the photoperiodic regulation of the PD. These findings provide resources for further study on the seasonal reproductive in ewes.

Shared Ancestry and Signatures of Recent Selection in Gotland Sheep

Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (~50%), Karakul (~30%), Romanov (~20%), and Fjällnäs (~10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation F_ST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the F_ST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep.

Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages

Ovary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.

lncRNA FDNCR promotes apoptosis of granulosa cells by targeting the miR-543-3p/DCN/TGF-β signaling pathway in Hu sheep

Long non-coding RNAs (lncRNAs) regulate the development of follicles and reproductive diseases, but the mechanisms by which lncRNAs regulate ovarian functions and fertility remain elusive. We profiled the expression of lncRNAs in ovarian tissues of Hu sheep with different prolificacy and identified 21,327 lncRNAs. Many of the lncRNAs were differentially expressed in different groups. We further characterized an lncRNA that was predominantly expressed in the ovaries of the low prolificacy Fec^B+ (LPB+) group and mainly present in granulosa cells (GCs), and the expression of this lncRNA decreased during follicular development, which we named follicular development-associated lncRNA (FDNCR). Next, we found that FDNCR directly binds miR-543-3p, and decorin (DCN) was identified as a target of miR-543-3p. FDNCR overexpression promoted GC apoptosis through increased expression of DCN, which could be attenuated by miR-543-3p. Furthermore, miR-543-3p increased and FDNCR reduced the expression of transforming growth factor-β (TGF-β) pathway-related genes, including TGF-β1 and inhibin beta A (INHBA), which were upregulated upon DCN silencing. Our results demonstrated that FDNCR sponges miR-543-3p in GCs and prevents miR-543-3p from binding to the DCN 3′ UTR, resulting in DCN transactivation and TGF-β pathway inhibition and promotion of GC apoptosis in Hu sheep. These findings provide insights into the mechanisms underlying prolificacy in sheep.

Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

BACKGROUND

Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecB^BB (MM) and FecB⁺⁺ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified.

RESULTS

Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included.

CONCLUSION

All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

Differential expression and prediction of function of lncRNAs in the ovaries of low and high fecundity Hanper sheep

Litter size is an important trait that determines the production efficiency of sheep bred for meat. Its detailed investigation can reveal the molecular mechanisms that control the fecundity of sheep and possibly accelerate the breeding process of new varieties of sheep that have high prolificacy. Long non-coding RNAs (lncRNAs) have proven to be an important factor in the regulation of follicular development. However, the mechanisms by which lncRNAs regulate litter size in sheep remain unclear. In the present study, ovarian tissues from the follicular (F) or luteal phase (L) of Hanper sheep that were either monotocous (M) or polytocous (P; FM, FP, LM and LP groups) were collected and sequenced to identify differentially expressed lncRNAs and predict their function. The results indicate that the number of up- and down-regulated lncRNAs in the follicular phase (FM vs. FP) was 95 and 111 and 109 and 49, respectively, in the luteal phase (LM vs. LP). The functional enrichment of the different lncRNAs coexpressed with mRNA was analysed. The results demonstrated that the KISS1-GnRH-LH/FSH-E2 and EGF-EGFR-RAS-PI3K signalling pathways promoted the initiation of the primordial period, follicular development and ovulation in the follicular phase (FM vs. FP). During the luteal phase (LM vs. LP), the production and development of the corpus luteum in ewes was influenced by the KITLG-KIT/FGF-FGFR/HGF-MET-RAS-ERK signalling pathway. STEM clustering functional enrichment analysis of the differentially expressed lncRNAs indicated that profile11 was principally enriched in the Cytokine-Jak-STAT, PDGF-PDGFR-PI3K and KITLG-KIT-RAS-ERK signalling pathways. By analysis of the differential expression of the lncRNAs and their expression in each group, lncRNAs Xist (loc101112291) and Gtl2 (loc101123329) were found to be highly expressed, suggesting that regulation of follicular development was mediated through methylation processes.

Transcriptome analysis of long noncoding RNAs ribonucleic acids from the livers of Hu sheep with different residual feed intake

Long noncoding RNAs (LncRNAs), as key regulators, have vital functions in various biological activities. However, in sheep, little has been reported concerning the genetic mechanism of LncRNA regulation of feed efficiency. In the present study, we explored the genome-wide expression of LncRNAs and transcripts of uncertain coding potential (TUCPs) in the livers of sheep with extreme residual feed intake (RFI) using RNA sequencing. We identified 1 523 TUCPs and 1 996 LncRNAs, among which 10 LncRNAs and 16 TUCPs were identified as being differentially expressed between the High-RFI and Low-RFI groups. Co-expression and co-localization methods were used to search for LncRNA and TUCP target genes, which identified 970/1 538 and 23/27 genes, respectively. Ontology and pathways analysis revealed that the LncRNAs/TUCPs that were highly expressed in the Low-RFI group are mostly concentrated in energy metabolism pathways. For example, LNC_000890 and TUCP_000582 might regulate liver tissue metabolic efficiency. The LncRNAs/TUCPs that were highly expressed in the High-RFI group are mostly enriched in immune function pathways. For example, TUCP_000832 might regulate animal health, thereby affecting feed efficiency. Subsequently, a co-expression network was established by applying the expression information of both the differentially expressed LncRNAs and TUCPs and their target mRNAs. The network indicated that differentially expressed genes targeted by the upregulated LncRNAs and TUCPs were mainly related to energy metabolism, while those genes targeted by the downregulated LncRNAs and TUCPs were mainly related to immune response. These results provide the basis for further study of LncRNA/TUCP-mediated regulation of feed efficiency.

Long non-coding RNA366.2 controls endometrial epithelial cell proliferation and migration by upregulating WNT6 as a ceRNA of miR-1576 in sheep uterus

Long non-coding RNAs (lncRNAs) play an important regulatory role in mammalian fecundity. Currently, most studies are primarily concentrated on ovarian lncRNAs, ignoring the influence of uterine lncRNAs on the fecundity of female sheep. In this study, we found a higher density of uterine glands and endometrial microvessel density (MVD) in high prolificacy group of Hu sheep compared to low prolificacy groups (p < 0.05) as well as an increased level of serum placental growth factor (PLGF). Hundreds of differentially expressed (DE) lncRNAs were identified in Hu sheep with different fecundity by RNA sequencing (RNA-seq), and their targets were enriched in some signaling pathways involved in endometrial functions, such as the estrogen signaling pathway, nuclear factor kappa B (NF-κB) signaling pathway, oxytocin signaling pathway, and Wnt signaling pathway. Furthermore, the underlying mechanisms of competitive endogenous RNA (ceRNA) of lncRNA366.2-miR-1576- WNT6 were determined by bioinformatics analysis. Functionally, our results indicated that lncRNA366.2 promoted endometrial epithelial cell (EEC) proliferation, migration, and growth factor expression by sponging miR-1576 to upregulate WNT6 expression and activate the Wnt/β-catenin pathway. Taken together, our research indicated the regulatory mechanism of the lncRNA366.2-miR-1576-WNT6 in EEC proliferation and migration. Furthermore, this study provides a new theoretical reference for the identification of candidate genes related to fecundity.