Divergently expressed gene identification and interaction prediction of long noncoding RNA and mRNA involved in duck reproduction

Whole-genome sequencing identifies potential candidate genes for egg production traits in laying ducks (Anas platyrhynchos)

Egg production traits are economically important in laying ducks. Genetic molecular mechanisms and candidate genes underlying these traits remain unclear. In this study, whole genome variants were identified through whole-genome resequencing using three high-egg producing (HEN) and three low-egg producing (LEN) laying ducks. The gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genome (KEGG) pathways for the genes of common differential variants between HEN and LEN ducks were determined. Frizzled class receptor 6 (FZD6) was further genotyped using the Sequenom MassARRAY iPLEX platform. The association of FZD6 gene polymorphisms with 73 egg production and weight traits in 329 female ducks were estimated. A total of 65,535 single nucleotide polymorphisms (SNPs) and 4,702 indels were identified across the genome. Fourteen GO terms and 14 KEGG pathways were determined for the genes of common differential variants, including MAPK signaling, Wnt signaling, melanogenesis and calcium signaling pathways, which are key functional pathways for poultry egg production reported in previous reports. Further analysis showed that 27 SNPs of FZD6 were associated with three early egg production of duck and egg weight traits, including egg production at 17 weeks (EP17), 18 weeks (EP18) and 19 weeks (EP19) and egg weight at 59 weeks (EW59). The FZD6 should be considered a novel candidate gene for egg production traits in laying ducks.

Differential expression and functional analysis of circRNA in the ovaries of Yili geese at different egg-laying stages

BACKGROUND

Ovarian development is regulated by genes that are expressed dynamically and stage-specifically. Circular RNA (circRNA) has been proven to play a significant role in the regulation of animal reproduction.

OBJECTIVE

Studying the expression characteristics of circRNAs in goose ovaries at various egg-laying stages can provide a reference for the molecular regulation mechanism of ovary development in geese that is mediated by circRNAs.

METHODS

In this study, the expression profiles of circRNAs were compared in ovary tissues from Yili geese in three different breeding periods, namely the prelaying period (KL), laying period (CL), and ceased period (XL), and differentially expressed circRNAs related to ovarian development in Yili geese were screened. The potential biological functions of differential circRNAs were predicted by bioinformatics, and the differential circRNA-miRNA regulatory network was constructed.

RESULTS

The results showed that a total of 4483 circRNAs were identified in 12 ovarian tissue samples from Yili geese at different laying stages. In the KL vs. CL, XL vs. CL, and XL vs. KL groups, 159, 455, and 383 differentially expressed circRNAs were identified, respectively. The host genes of the differential circRNAs were mostly enriched in the signal transduction, metabolism, and other related pathways, such as those for phototransduction, glycerophospholipid metabolism, aminoacyl-tRNA biosynthesis, and retinol metabolism. Finally, we constructed circRNA-miRNA regulation networks. Nine differential circRNAs were randomly selected for qRT-PCR verification, and the expression trends were consistent with the sequencing results.

CONCLUSIONS

Our results indicated that significant differences in the expression profiles of circRNAs in the ovaries of Yili geese at different egg-laying stages. Meanwhile, through analyzing the differential circRNA-miRNA interaction network, core regulators such as circRNA NW_013186107.1:36835|52,574 and gga-miR-34b-5p were screened. This study provides a reference for the further analysis of the molecular regulatory mechanism of the circRNAs regulating goose ovary development and enriches the theory of genetic regulation during goose ovary development.

Comparative liver transcriptome analysis of duck reveals potential genes associated with egg production

BACKGROUND

Molecular studies on egg production in ducks were mostly focused on brain and ovaries as they are directly involved in egg production. Liver plays a vital role in cellular lipid metabolism. It also plays a decisive role in reproductive organ development, including yolk generation in laying ducks at sexual maturity. However, the precise molecular mechanism involved in the liver-blood-ovary axis in ducks remains elusive.

METHODS AND RESULTS

In this study, we analysed the liver transcriptome of laying (LA), immature (IM) and broody (BR) ducks using RNA sequencing to understand the role of genes expressed in the liver. The comparative transcriptome analysis revealed 82 DEGs between LA and IM ducks, 47 DEGs between LA and BR ducks and 51 DEGs between IM and BR ducks. GO analysis of DEGs, showed that DEGs were mainly involved in cellular anatomical entity, intracellular, metabolic process, and binding. Furthermore, pathway analysis indicated the important role of Wnt signaling pathway in egg formation and embryo development. Our study showed several candidate genes including vitellogenin-1, vitellogenin-2, riboflavin binding protein, G protein subunit gamma 4, and fatty acid binding protein 3 that are potentially related to egg production in ducks.

CONCLUSIONS

The study provides valuable information on the genes responsible for egg production and thus, pave the way for further investigation on the molecular mechanisms of egg production in duck.

LncRNAs in domesticated animals: from dog to livestock species

Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.

Long non-coding RNA profile in banana shrimp, Fenneropenaeus merguiensis and the potential role of lncPV13 in vitellogenesis

The long non-coding RNAs (lncRNAs) have been known to play important roles in several biological processes as well as in reproduction. This study aimed to identify lncRNA in ovary female banana shrimp, Fenneropenaeus merguiensis, and investigate the potential role of lncPV13 in the vitellogenesis. After the in silico identification of the ovarian transcriptome, a total of 24,733 putative lncRNAs were obtained, and only 147 putative lncRNAs were significantly differentially expressed among the ovarian development stages. To validate the in silico identification of lncRNAs, the 16 lncRNAs with the highest differential expression in the transcriptome analysis were evaluated by RT-qPCR. The 6 lncRNAs showed higher expression levels in the mature stage than in the previtellogenic stage and were found in several tissues such as in eyestalks, brains, thoracic ganglia, gills, and muscle. Furthermore, most candidate lncRNAs were amplifiable in Litopenaeus vannamei's and Penaeus monodon's DNA but not in Macrobrachium rosenbergii's DNA, suggesting some lncRNAs are expressed in a species-specific manner among penaeid shrimp. In this study, the lncPV13 was investigated for its vitellogenin regulating function by RNA interference. The result indicates that the lncPV13 expression was suppressed in the ovary on day 7 after the injection of double-stranded RNA specific to lncPV13 (dslncPV13), while vitellogenin (Vg) expression was significantly decreased. In contrast, the gonad inhibiting hormone (GIH) expression was significantly increased in the lncPV13 knockdown shrimp. However, the oocyte proliferation was not significantly different between control and lncPV13 knockdown shrimp. This suggests that lncPV13 regulate Vg synthesis through GIH inhibition. Finally, our findings provide lncRNA information and potential lncRNAs involved in the vitellogenesis of female banana shrimp.

Long noncoding RNAs profiling in ovary during laying and nesting in Muscovy ducks (Cairina moschata)

There are recent reports of the important functions of long noncoding RNAs (lncRNAs) in female reproductive and ovarian development. Studies in which there was characterization of lncRNAs in the ovaries of laying compared with nesting poultry, however, are limited. In this study, RNA libraries were constructed by obtaining sequencing data of ovarian tissues from laying and nesting Muscovy ducks. In the ovarian tissues of Muscovy ducks, a total of 334 differentially abundant mRNA transcripts (DEGs) and 36 differentially abundant lncRNA transcripts were identified in the nesting period, when compared with during the laying period. These results were subsequently validated by qRT-PCR using nine randomly-selected lncRNAs and six randomly-selected DAMTs. Furthermore, the cis- and trans-regulatory target genes of differentially abundant lncRNA transcripts were identified, and lncRNA-gene interaction networks of 34 differentially abundant lncRNAs and 263 DEGs were constructed. A total of 7601 lncRNAs neighboring 10,542 protein-coding genes were identified and found to be enriched in the Wnt signaling pathway and oocyte meiosis pathways associated with follicular development. Overall, only 11 cis-targets and 57 mRNA-mRNA except trans-targets were involved in the lncRNA-gene interaction networks. Based on the interaction networks, nine DEGs were trans-regulated by differentially abundant lncRNAs and 20 differentially abundant lncRNAs were hypothesized to have important functions in the regulation of broodiness in Muscovy ducks. In this study, a predicted interaction network of differentially abundant lncRNAs and DEGs in Muscovy ducks was constructed for the first time leading to an enhanced understanding of lncRNA and gene interactions regulating broodiness.

LncRNA lnc_13814 promotes the cells apoptosis in granulosa cells of duck by acting as apla-miR-145-4 sponge

Follicle development is a vital factor which determines the reproductive performance of poultry. Long noncoding RNAs (lncRNAs) have been reported to maintain animal reproductive function and play key roles in ovarian development and hormone secretion. But the regulatory mechanism of lncRNAs in duck follicle development has seldom been reported. In this study, to better explore the molecular mechanism of follicle development in ducks, the follicular lncRNA was sequenced and analyzed. A total of 9,551 lncRNAs were predicted in the duck follicles. Four hundred and forty-five lncRNAs were differentially expressed between the white follicles and yellow follicles. The results of our studies showed that lnc_13814 promoted cell apoptosis in duck GCs. Furthermore, the bioinformatics analysis results demonstrated that lnc_13814 was involved in a lncRNA-miRNA-mRNA coexpression network and it was observed to sponge two follicle-related miRNAs by a luciferase activity assay. Moreover, we found that overexpression of lnc_13814 significantly increased DNA damage inducible transcript 3 (DDIT3) expression and downregulated GCs apoptosis. Finally, we found that lnc_13814 directly binds to and inhibits apla-mir-145-4; then, lnc_13814 increases the expression of DDIT3 and up-regulates GCs apoptosis. Taken together, our findings demonstrate that lncRNAs have potential effects on duck ovarian follicles and lncRNAs may represent a new approach to understand follicular development.

Comparative Transcriptome Profiling of mRNA and lncRNA of Ovaries in High and Low Egg Production Performance in Domestic Pigeons (Columba livia)

Egg production performance is one of the most important economic traits in pigeon industry. However, little is known regarding how egg production performance is regulated by long non-coding RNAs (lncRNAs) in pigeons. To evaluate the lncRNAs and mRNAs in ovaries associated with egg production performance in domestic pigeons, high-throughput RNA sequencing of ovaries between high and low egg production performance groups were performed and analyzed in this study. A total of 34,346 mRNAs and 24,601 lncRNAs were identified, including 14,525 known lncRNAs and 10,076 novel lncRNAs, of which 811 mRNAs and 148 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the groups of high and low egg production performance. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to cell differentiation, ATP binding and methylation. Moreover, we found that FOXK2, a target gene of lncRNA MSTRG.7894.4, was involved in regulating estrogen receptors. Our study provided a catalog of lncRNAs and mRNAs associated with egg production performance, and they deserve further study to deepen the understanding of biological processes in the ovaries of pigeons.

Transcriptome Analysis of Long Noncoding RNAs and mRNAs in Granulosa Cells of Jinghai Yellow Chickens Illuminated With Red Light

Jinghai Yellow chickens are a new indigenous breed with a dual purpose in China, but their egg laying performance is limited. Compared with white light (WL), exposure to red light (RL) can improve the egg laying performance of hens. Herein, to elucidate the molecular mechanism by which RL affects the egg laying performance, RNA sequencing was used to analyze long noncoding RNAs (lncRNAs) and mRNAs from granulosa cells of small yellow follicles from Jinghai Yellow chickens in RL and WL groups. A total of 12,466 lncRNAs were identified among the assembled transcripts, of which 168 lncRNAs were significantly different between the RL and WL groups (101 downregulated and 67 upregulated). Additionally, 1182 differentially expressed mRNAs were identified (958 downregulated and 224 upregulated). Integrated network analysis demonstrated that numerous differential mRNAs were involved in follicular development through steroid hormone synthesis, oocyte meiosis, and the PI3K-Akt signaling pathway. The impact of lncRNAs on cis and trans target mRNAs indicates that some lncRNAs play important roles in follicular development of small yellow follicles. The results provide a starting point for studies aimed at understanding the molecular mechanisms by which monochromatic light affects follicular development and egg production in hens.

Identification of differentially expressed genes and signalling pathways in the ovary of higher and lower laying ducks

1. Ovarian transcriptomic profiling between birds showing high egg number (HEN) and birds of low egg number (LEN) in Longyan Shan-ma ducks at 71 weeks of age was carried out using Illumina Hiseq 2500 technology. 2. A total of 343 differentially expressed genes (DEGs, 269 upregulated and 74 downregulated) were identified between HEN and LEN ovaries. These DEGs were enriched in 30 Gene Ontology terms. Pathway functional analysis found that the DEGs were enriched in 10 metabolic pathways (P < 0.05), one of which was regulation of the actin cytoskeleton pathway (Q < 0.05). 3. Three integrin family genes, ITGB2, ITGB5 and ITGA8 were differentially expressed in the RNA-seq and qPCR experiments. 4. The DEGs and signalling pathways identified in ovarian tissue in this study provide new insights into high egg production in Longyan Shan-ma duck.

Genome-Wide Analysis and Function Prediction of Long Noncoding RNAs in Sheep Pituitary Gland Associated with Sexual Maturation

Long noncoding RNA (lncRNA) plays a crucial role in the hypothalamic-pituitary-testis (HPT) axis associated with sheep reproduction. The pituitary plays a connecting role in the HPT axis. However, little is known of their expression pattern and potential roles in the pituitary gland. To explore the potential lncRNAs that regulate the male sheep pituitary development and sexual maturation, we constructed immature and mature sheep pituitary cDNA libraries (three-month-old, TM, and nine-month-old, NM, respectively, n = 3) for lncRNA and mRNA high-throughput sequencing. Firstly, the expression of lncRNA and mRNA were comparatively analyzed. 2417 known lncRNAs and 1256 new lncRNAs were identified. Then, 193 differentially expressed (DE) lncRNAs and 1407 DE mRNAs were found in the pituitary between the two groups. Moreover, mRNA-lncRNA interaction network was constructed according to the target gene prediction of lncRNA and functional enrichment analysis. Five candidate lncRNAs and their targeted genes HSD17B12, DCBLD2, PDPK1, GPX3 and DLL1 that enriched in growth and reproduction related pathways were further filtered. Lastly, the interaction of candidate lncRNA TCONS_00066406 and its targeted gene HSD17B12 were validated in in vitro of sheep pituitary cells. Our study provided a systematic presentation of lncRNAs and mRNAs in male sheep pituitary, which revealed the potential role of lncRNA in male reproduction.

Transcriptome profiling of the liver among the prenatal and postnatal stages in chickens

The liver is an important organ that has pivotal functions in the synthesis of several vital proteins, the metabolism of various biologically useful materials, the detoxification of toxic substances, and immune defense. Most liver functions are not mature at a young age and many changes happen during postnatal liver development, which lead to differential functions of the liver at different developmental stages. However, the transcriptome details of what changes occur in the liver after birth and the molecular mechanisms for the regulation of the developmental process are not clearly known in chickens. Here, we used RNA-sequencing to analyze the transcriptome of chicken liver from the prenatal (at an embryonic day of 13) to the postnatal stages (at 5 wk and 42 wk of age). A total of approximately 161.17 Gb of raw data were obtained, with 4,127 putative and 539 differentially expressed lncRNAs, and with 13,949 putative and 6,370 differentially expressed mRNAs. Coexpression of lncRNAs-mRNAs in hepatic transcriptome analysis showed that the liver plays important roles in providing energy for organisms through the mitochondrial respiratory chain in chickens, meanwhile, acting as a crucial part of antioxidant stress. The developmental transcriptome date revealed that antioxidant defenses are likely to act on chicken embryo development and that significant functional changes during postnatal liver development are associated with the liver maturation of chickens. These results provide a timeline for the functional transcriptome transition from the prenatal to adult stages in chickens and will be helpful to reveal the underlying molecular mechanisms of liver development.

Differentially Expressed lncRNAs After the Activation of Primordial Follicles in Mouse

The activation of primordial follicles is critical to ovarian follicle development, which directly influences female fertility and reproductive life span. Several studies have suggested a role for long noncoding RNAs (lncRNAs) in ovarian function. However, the precise involvement of lncRNAs in the initiation of primordial follicles is still unknown. Here, an in vitro culture model was used to investigate the roles of lncRNAs in primordial follicle activation. We found that primordial follicles in day 3 mouse ovaries were activated after culturing for 8 days in vitro, as indicated by ovarian morphology changes, increases in primary follicle number, and downregulation of mammalian Sterile 20-like kinase messenger RNA (mRNA) and upregulation of growth differentiation factor 9 mRNA. We next examined lncRNA expression profiles by RNA sequencing at the transcriptome level and found that among 60 078 lncRNAs, 6541 lncRNA were upregulated and 2135 lncRNA were downregulated in 3-day ovaries cultured for 8 days in vitro compared with ovaries from day 3 mice. We also found that 4171 mRNAs were upregulated and 1795 were downregulated in the cultured ovaries. Gene ontology and pathway analyses showed that the functions of differentially expressed lncRNA targets and mRNAs were closely linked with many processes and pathways related to ovary development, including cell proliferation and differentiation, developmental processes, and other signaling transduction pathways. Additionally, many novel identified lncRNAs showed inducible expression, suggesting that these lncRNAs may be good candidates for investigating mouse primordial follicle activation. This study provides a foundation for further exploring lncRNA-related mechanisms in the initiation of mouse primordial follicles.