Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size

Whole-genome sequencing identified candidate genes associated with high and low litter size in Chuanzhong black goats

The reproductive performance of goats significantly influences breeding efficiency and economic returns, with litter size serving as a comprehensive indicator. Despite this, research on the genetic control of litter size remains limited. Therefore, we aimed to explore the candidate genes affecting fecundity and compared the whole-genome sequences (WGS) of 15 high-litter (HL) and 15 low-litter (LL) size in Chuanzhong black goats. Then genetic diversity and genomic variation patterns were analyzed by phylogenetic, principal component and population genetic structure analysis, it was found that HL and LL subpopulations diverged. Population evolutionary selection elimination analysis was performed by Fst and θπ resulted in 506 genes were annotated in HL and 528 genes in LL. These genes were mainly related to Hippo signaling pathway, G protein-coupled signaling pathway, G protein-coupled receptor activity, cell surface receptor signaling pathway, gonadal and reproductive structure development. According to the significantly selected genomic regions and important pathways, we found that the g.89172108T > G variant locus in the exon of the AMH gene was significantly associated with litter size (P < 0.05), which could be used as an auxiliary selection gene for the high fertility of Chuanzhong black Goat.

4D label-free quantitative proteomic analysis identifies CRABP1 as a novel candidate gene for litter size in rabbits†

In commercial rabbit breeding, litter size is a crucial reproductive trait. This trait directly determines the reproductive ability of female rabbits and is crucial for evaluating the production efficiency. We here compared differentially expressed proteins of in the ovary tissue from New Zealand female rabbits with high (H) and low (L) litter sizes by using 4D label-free quantitative proteomic technology and identified 92 differential proteins. The biological functions of these proteins were revealed through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Most distributions of GO and KEGG were related to reproduction, growth development, and metabolism. Furthermore, a novel candidate gene cellular retinoic acid binding protein-1 (CRABP1), which was highly expressed in the L group, was selected for further biological function verification. The Cell Counting Kit-8 (CCK-8) assay and flow cytometry analysis revealed that CRABP1 can promote granulosa cell (GC) apoptosis and inhibit GC proliferation. Furthermore, qRT-PCR and western blotting analysis revealed that CRABP1 regulates the genes (HSD17B1, Wnt-10b, FSHR, TAF4B, BMP15, and BMP6) and protein (Wnt-10b) associated with steroid hormone synthesis and follicle development. The PCR product direct sequencing method revealed single nucleotide polymorphisms in the core promoter region of CRABP1. Luciferase activity assays revealed that the transcriptional activity of the GG genotype was significantly higher than that of the TT or TG genotype. Different genotypes are accompanied by changes in transcription factors, which indicates that T-359G polymorphism can regulate CRABP1 expression. In general, we identified litter size-related genes and revealed the mechanism underlying the effect of CRABP1 on litter size. CRABP1 serves as a key factor in the reproductive capacity of rabbits and can act as a molecular biomarker for the breeding of New Zealand rabbits.

2,5-Hexanedione Affects Ovarian Granulosa Cells in Swine by Regulating the CDKN1A Gene: A Transcriptome Analysis

N-hexane, a common industrial organic solvent, causes multiple organ damage owing to its metabolite, 2,5-hexanedione (2,5-HD). To identify and evaluate the effects of 2,5-HD on sows’ reproductive performance, we used porcine ovarian granulosa cells (pGCs) as a vehicle and carried out cell morphology and transcriptome analyses. 2,5-HD has the potential to inhibit the proliferation of pGCs and induce morphological changes and apoptosis depending on the dose. RNA-seq analyses identified 4817 differentially expressed genes (DEGs), with 2394 down-regulated and 2423 up-regulated following 2,5-HD exposure treatment. The DEG, cyclin-dependent kinase inhibitor 1A (CDKN1A), according to the Kyoto Encyclopedia of Genes and Genomes enrichment analysis, was significantly enriched in the p53 signaling pathway. Thus, we evaluated its function in pGC apoptosis in vitro. Then, we knocked down the CDKN1A gene in the pGCs to identify its effects on pGCs. Its knockdown decreased pGC apoptosis, with significantly fewer cells in the G1 phase (p < 0.05) and very significantly more cells in the S phase (p < 0.01). Herein, we revealed novel candidate genes that influence pGCs apoptosis and cell cycle and provided new insights into the role of CDKN1A in pGCs during apoptosis and cell cycle arrest.

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes

Retrotransposons account for more than one-third of the pig reference genome. On account of the genome variability in different breeds, structural variation (SV) caused by retrotranspos-on-generated deletion or insertion (indel) may have a function in the genome. Litter size is one of the most important reproductive traits and significantly impacts profitability in terms of pig production. We used the method of bioinformatics, genetics, and molecular biology to make an analysis among different pig genomes. Predicted 100 SVs were annotated as retrotransposon indel in 20 genes related to reproductive performance. The PCR detection based on these predicted SVs revealed 20 RIPs in 20 genes, that most RIPs (12) were generated by SINE indel, and eight RIPs were generated by the ERV indel. We selected 12 RIPs to make the second round PCR detection in 24 individuals among nine pig breeds. The PCR detection results revealed that the RIP-A1CF-4 insertion in the breed of Bama, Large White, and Meishan only had the homozygous genotype but low to moderately polymorphisms were present in other breeds. We found that RIP-CWH43-9, RIP-IDO2-9, RIP-PRLR-6, RIP-VMP1-12, and RIP-OPN-1 had a rich polymorphism in the breed of Large White pigs. The statistical analysis revealed that RIP-CWH43-9 had a SINE insertion profitable to the reproductive traits of TNB and NBA but was significantly affected (p < 0.01) and (p < 0.05) in the reproductive traits of litter birthweight (LW) in Large White. On the other hand, the SINE insertion in IDO2-9 may be a disadvantage to the reproductive traits of LW, which was significantly affected (p < 0.05) in Large White. These two RIPs are significant in pig genome research and could be useful molecular markers in the breeding system.

Differential MicroRNA Expression in Porcine Endometrium Related to Spontaneous Embryo Loss during Early Pregnancy

Litter size is an important indicator to measure the production capacity of commercial pigs. Spontaneous embryo loss is an essential factor in determining sow litter size. In early pregnancy, spontaneous embryo loss in porcine is as high as 20–30% during embryo implantation. However, the specific molecular mechanism underlying spontaneous embryo loss at the end of embryo implantation remains unknown. Therefore, we comprehensively used small RNA sequencing technology, bioinformatics analysis, and molecular experiments to determine the microRNA (miRNA) expression profile in the healthy and arresting embryo implantation site of porcine endometrium on day of gestation (DG) 28. A total of 464 miRNAs were identified in arresting endometrium (AE) and healthy endometrium (HE), and 139 differentially expressed miRNAs (DEMs) were screened. We combined the mRNA sequencing dataset from the SRA database to predict the target genes of these miRNAs. A quantitative real-time PCR assay identified the expression levels of miRNAs and mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on differentially expressed target genes of DEMs, mainly enriched in epithelial development and amino acids metabolism-related pathways. We performed fluorescence in situ hybridization (FISH) and the dual-luciferase report gene assay to confirm miRNA and predicted target gene binding. miR-205 may inhibit its expression by combining 3′-untranslated regions (3′ UTR) of tubulointerstitial nephritis antigen-like 1 (TINAGL1). The resulting inhibition of angiogenesis in the maternal endometrium ultimately leads to the formation of arresting embryos during the implantation period. This study provides a reference for the effect of miRNA on the successful implantation of pig embryos in early gestation.

Ovarian Transcriptomic Analysis of Ninghai Indigenous Chickens at Different Egg-Laying Periods

Egg production is an essential indicator of poultry fertility. The ovary is a crucial organ involved in egg production; however, little is known about the key genes and signaling pathways involved in the whole egg-laying cycle of hens. In order to explore the mechanism of egg production at different stages of the egg-laying process, ovarian tissues from four chickens were randomly selected for transcriptome analysis at each of the three ages (145 d, 204 d, and 300 d in the early, peak, and late stages of egg laying). A total of 12 gene libraries were constructed, and a total of 8433 differential genes were identified from NH145d vs. NH204d, NH145d vs. NH300d and NH300d vs. NH204d (Ninghai 145-day-old, Ninghai 204-day-old, and Ninghai 300-day-old), with 1176, 1653 and 1868 up-regulated genes, and 621, 1955 and 1160 down-regulated genes, respectively. In each of the two comparison groups, 73, 1004, and 1030 differentially expressed genes were found to be co-expressed. We analyzed the differentially expressed genes and predicted nine genes involved in egg production regulation, including LRP8, BMP6, ZP4, COL4A1, VCAN, INHBA, LOX, PTX3, and IHH, as well as several essential egg production pathways, such as regulation adhesion molecules (CAMs), calcium signaling pathways, neuroactive ligand–receptor interaction, and cytokine–cytokine receptor interaction. Transcriptional analysis of the chicken ovary during different phases of egg-lay will provide a useful molecular basis for study of the development of the egg-laying ovary.

TIMP1 may affect goat prolificacy by regulating biological function of granulosa cells

Tissue inhibitor of metalloproteinase 1 (TIMP1) is associated with animal reproductive processes, such as follicular growth, ovulation, luteinization, and embryo development in mammals. The purposes of this study were to explore the expression and localization of TIMP1 in the ovarian tissues and determine the effect of TIMP1 on the function of granulosa cells and the association of TIMP1 with lambing-related genes of the goats. Immunohistochemical analysis showed that TIMP1 protein was strongly expressed by granulosa cells. Enzyme-linked immunosorbent assay (ELISA) results showed that TIMP1 overexpression promoted the secretion of estradiol of granulosa cells after 12, 24, and 48 h of transfection. Moreover, in vitro experiments indicated that TIMP1 had the ability to promote the cell proliferation and elevate the transcriptional levels of four genes associated with goat prolificacy, including BMPR-1B, BMP15, GDF9, and FSHB, in granulosa cells. In conclusion, TIMP1 could be an important molecule in regulating reproductive performance of the goats by affecting estrogen secretion and cell proliferation, as well as the expression of lambing-related genes of granulosa cells in the goats.

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.

Polymorphism of OPN and AREG Genes in Relation to Transcript Expression of a Panel of 12 Genes Controlling Reproduction Processes and Litter Size in Pigs

The aim of this study was to define the transcript expression of 12 genes, identify new polymorphisms in selected 2 genes and to estimate the association between the level of expression, gene polymorphism and litter size in sows. Two groups of sows were selected: 71 crossbred sows and 328 purebred sows. For transcript analysis endometrial tissue samples were collected, while blood was sampled for the purpose of DNA polymorphism analysis. For all animals data on litter size and weaned piglets were obtained. Transcript analysis of 12 genes was performed in the uterine endometrium of sows in the luteal and follicular phases. Eight out of 12 genes showed higher mRNA expression levels during the luteal phase (AREG, FABP3, IL1A, ITGAV, ITGB3, NMB, OPN, RBP4). In turn, higher expression levels in the follicular phase were observed for 4 genes (IL1B, PPARG, S100A8, SELL). Analysis of six new polymorphic sites within the OPN and AREG genes revealed the highest heterozygosity for OPNe6_Knoll, OPNp3_617 and AREGe2_317 polymorphisms and the lowest heterozygosity in the AREGe3_561 locus. Association analyses concerning transcript expression levels of the 12 genes and the OPN and AREG genotypes in the two groups of sows showed a significant relationship between the IL1A, ITGB3 transcript expression and the OPNe7_603 genotype also between OPNp3_617 genotype and ITGB3 transcript expression. With regard to the litter size and the number of weaned piglets a significant relation with the OPNp3_617, OPNe6_462 and AREGe2_317 genotypes was observed only in the purebred sows. Transcript expression of the genes encoding osteopontin and amphiregulin in the uterus of the sows affect reproductive traits by preparing the uterus for embryo reception.

Differences in gene expression and variable splicing events of ovaries between large and small litter size in Chinese Xiang pigs

BACKGROUND

Although lots of quantitative trait loci (QTLs) and genes present roles in litter size of some breeds, the information might not make it clear for the huge diversity of reproductive capability in pig breeds. To elucidate the inherent mechanisms of heterogeneity of reproductive capability in litter size of Xiang pig, we performed transcriptome analysis for the expression profile in ovaries using RNA-seq method.

RESULTS

We identified 1,419 up-regulated and 1,376 down-regulated genes in Xiang pigs with large litter size. Among them, 1,010 differentially expressed genes (DEGs) were differently spliced between two groups with large or small litter sizes. Based on GO and KEGG analysis, numerous members of genes were gathered in ovarian steroidogenesis, steroid biosynthesis, oocyte maturation and reproduction processes.

CONCLUSIONS

Combined with gene biological function, twelve genes were found out that might be related with the reproductive capability of Xiang pig, of which, eleven genes were recognized as hub genes. These genes may play a role in promoting litter size by elevating steroid and peptide hormones supply through the ovary and facilitating the processes of ovulation and in vivo fertilization.

Comparative transcriptomic analysis of ovaries from high and low egg-laying Lingyun black-bone chickens

Egg‐laying rate is mainly determined by ovarian function and regulated by the hypothalamic‐pituitary‐gonadal axis; however, the mechanism by which the ovary regulates the egg‐laying rate is still poorly understood. The purpose of this study was to compare the differences in the transcriptomes of the ovary of Lingyun black‐bone chickens with relatively high and low egg‐laying rates and screen candidate genes related to the egg‐laying rate. RNA‐sequencing (RNA‐Seq) was conducted to explore the chicken transcriptome from the ovarian tissue of six Lingyun black‐bone chickens with high (group G, n = 3) and low (group D, n = 3) egg‐laying rates. The results showed that 235 differentially expressed genes (DEGs) were identified between the chickens with high and low egg‐laying rates; among them, 209 DEGs were up‐regulated and 26 DEGs were down‐regulated. Gene Ontology analysis showed that the up‐regulated 209 DEGs were enriched in 50 GO terms and the down‐regulated 26 DEGs were enriched in 40 GO terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that up‐regulated DEGs were significantly enriched in 25 pathways and down‐regulated DEGs were significantly enriched in three pathways. Among the pathways, we found the longevity regulating pathway‐multiple species pathway, Estrogen signalling pathway and PPAR signalling pathway may have an essential function in regulating the egg‐laying rate. The results highlighted DEGs in the ovarian tissues of relatively high and low laying Lingyun black‐bone chicken and identified essential candidate genes related to the egg‐laying rate, thereby providing a theoretical basis for improving the egg‐laying rate of Lingyun black‐bone chicken.

The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication

There are wide genomic and phenotypic differences between Asian and European pig breeds, yet the current reference genome is the European Duroc pig genome. A high-quality pig genome is lacking for genetic analysis of agricultural traits in Asian pigs. Here, using a hybrid approach, a high-quality reference genome (MSCAAS v1) for the Asian Meishan breed is assembled with a contig N50 size of 48.05 Mb. MSCAAS v1 outperforms the Duroc genome as a reference genome for Asian breeds. Genomic comparison reveals 49,103 structural variations (SVs) between Meishan and Duroc, 4.02% of which are Asian-specific SVs (AP-SVs). Notably, a 30-Mb hotspot for AP-SVs on chromosome X enriched for genes associated with Asian-pig-specific phenotypes is present in Asian domestic pig breeds, but absent in Asian wild boars, suggesting that Asian domestic breeds share a common ancestor. Interbreed transcriptomics reveals transcriptional suppression roles of AP-SVs in multiple tissues. Finally, transcriptional regulation in the intron of IGF2R is reported, as genomic SV (274-bp deletion) in Tibetan pig limits its growth compared to domestic pig breeds. In summary, this study provides insights regarding the genetic changes underlying pig domestication and presents a benchmark-setting resource for the utilization of agricultural valuable loci in Asian pigs.

Genome-Wide Analyses Reveal Genetic Convergence of Prolificacy between Goats and Sheep

The litter size of domestic goats and sheep is an economically important trait that shows variation within breeds. Strenuous efforts have been made to understand the genetic mechanisms underlying prolificacy in goats and sheep. However, there has been a paucity of research on the genetic convergence of prolificacy between goats and sheep, which likely arose because of similar natural and artificial selection forces. Here, we performed comparative genomic and transcriptomic analyses to identify the genetic convergence of prolificacy between goats and sheep. By combining genomic and transcriptomic data for the first time, we identified this genetic convergence in (1) positively selected genes (CHST11 and SDCCAG8), (2) differentially expressed genes (SERPINA14, RSAD2, and PPIG at follicular phase, and IGF1, GPRIN3, LIPG, SLC7A11, and CHST15 at luteal phase), and (3) biological pathways (genomic level: osteoclast differentiation, ErbB signaling pathway, and relaxin signaling pathway; transcriptomic level: the regulation of viral genome replication at follicular phase, and protein kinase B signaling and antigen processing and presentation at luteal phase). These results indicated the potential physiological convergence and enhanced our understanding of the overlapping genetic makeup underlying litter size in goats and sheep.

Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

Background

Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics.

Results

In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log₂ (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data.

Conclusions

These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.

Ovarian transcriptomic analysis and follicular development of Leizhou black duck

This study investigated the factors that caused the differences in egg production during the development of ovarian follicles in Leizhou black ducks. Leizhou black ducks population was divided into 2 groups as high-yield group (HG) and low-yield group (LG). The number of eggs (NE), age at first egg (AFE), weight at first egg, and egg weight (EW) of both groups were recorded, and differences were analyzed using the t test. The logistic model was used to simulate the egg production curves to analyze the production rules. The ovarian follicles of both duck groups were collected to count the number of different grades sized follicles, weigh the ovaries, and observe follicular sections to analyze the developmental differences. Ovarian transcriptomic sequencing was performed to investigate differentially expressed genes and signal pathways in both duck groups. The results revealed a significant difference (P < 0.01) in the NE laid, AFE, and EW between both groups. Comparatively, HG had significantly more (P < 0.01) large yellow follicles (LYF) than LG. The density of medullary layer cells of the follicle section was greater in HG than LG ducks. Transcriptome sequencing revealed a total of 1,027 differentially expressed genes between the HG and LG ducks of which 495 genes were upregulated, and 532 genes were downregulated. Fifty genes were related to reproduction and reproductive processes. Kyoto Encyclopedia of Genes and Genomes–enriched signaling pathways revealed 274 signal pathways enriched in these differentially expressed genes of which the steroid biosynthesis pathway was significantly enriched. Analysis (Q < 0.05) showed that HSD3β → gonadotropin-releasing hormone (GnRH) and estrogen receptor (ESR) → LHβ/ERK1/2 were enriched in the steroid biosynthesis signal pathway. Follicle-stimulating hormone signal pathway mediated by HSD3β → GnRH and ESR → LHβ/ERK1/2 may be involved in ovarian follicle development to regulate LYF reserve process and affect its ovulation cycle, which in turn influence the egg production of Leizhou black ducks.

Identification of Ovarian Circular RNAs and Differential Expression Analysis between MeiShan and Large White Pigs

MeiShan and Large White pigs differ in their female fecundity. However, the mechanisms behind the gene expression and regulation that cause these differences remain unclear. In this study, we profiled circRNAs and identified 5,879 circRNAs from the ovaries of MeiShan and Large White pigs. Eighty-five circRNAs were differentially expressed between the two pig breeds. Of these, 37 were up-regulated and 48 were down-regulated in MeiShan pigs. Gene ontology enrichment analysis suggested that the differentially expressed circRNA were involved in the hormone-mediated signaling pathway. We verified that circSCIN and its parent gene, scinderin (SCIN), were differentially expressed by reverse transcription and quantitative PCR (RT-qPCR). Luciferase assays demonstrated that circSCIN can target and sponge miR-133 and miR-148a/b. The identification of differentially expressed circRNAs (DECs) and their regulatory functions increased our understanding of the differences in reproductive efficiency between MeiShan and Large White pigs.

Ovarian Circular RNAs Associated with High and Low Fertility in Large White Sows during the Follicular and Luteal Phases of the Estrous Cycle

In this study, the ovarian tissues of Large White pigs were mined for novel circular RNAs (circRNAs), following which, their molecular characteristics and potential mechanisms for fertility regulation were examined. RNA sequencing was used for transcriptome analysis of ovarian follicles and corpora lutea in Large White sows with high (H) and low (L) fertility during the follicular (F) and luteal (L) phases of the estrous cycle. In total, 21,386 circRNA derived from 4535 host genes were identified. Differentially expressed circRNAs were detected in the LH vs. LL (1079) and in the FH vs. FL (1077) comparisons, and their host genes were enriched in steroid biosynthesis and forkhead box O (FOXO), thyroid hormone, cell cycle, and tumor growth factor (TGF)-beta signaling pathways. Protein–protein interaction networks were constructed on the basis of the host genes that were significantly enriched in pathways related to reproductive processes, with AKT3 and PP2CB serving as the hub genes in the networks of the LH vs. LL and FH vs. FL comparisons, respectively. The microRNA (miRNA) binding sites of the differentially expressed circRNAs were predicted, and 128 (LH vs. LL) and 113 (FH vs. FL) circRNA–miRNA pairs were identified. Finally, circRNA–miRNA negative regulatory networks were established on the basis of the gene expression profiles and bioinformatic analyses. In the current study, differentially expressed circRNAs were observed in ovarian tissues between the H and L fertility groups in both F and L phases of the estrous cycle, which suggested roles in pig fertility regulation. These findings provide new clues for elucidating fertility differences in pigs.

Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

Background

Fertility is an important economic trait in the production of meat goat, and follicular development plays an important role in fertility. Although many mRNAs and microRNAs (miRNAs) have been found to play critical roles in ovarian biological processes, the interaction between mRNAs and miRNAs in follicular development is not yet completely understood. In addition, less attention has been given to the study of single follicle (dominant or atretic follicle) in goats. This study aimed to identify mRNAs, miRNAs, and signaling pathways as well as their interaction networks in the ovarian follicles (large follicles and small follicles) of uniparous and multiple Chuanzhong black goats at estrus phase using RNA-sequencing (RNA-seq) technique.

Results

The results showed that there was a significant difference in the number of large follicles between uniparous and multiple goats (P < 0.05), but no difference in the number of small follicles was observed (P > 0.05). For the small follicles of uniparous and multiple goats at estrus phase, 289 differentially expressed mRNAs (DEmRNAs) and 16 DEmiRNAs were identified; and for the large follicles, 195 DEmRNAs and 7 DEmiRNAs were identified. The functional enrichment analysis showed that DE genes in small follicles were significantly enriched in ovarian steroidogenesis and steroid hormone biosynthesis, while in large follicles were significantly enriched in ABC transporters and steroid hormone biosynthesis. The results of quantitative real-time polymerase chain reaction were consistent with those of RNA-seq. Analysis of the mRNA-miRNA interaction network suggested that CD36 (miR-122, miR-200a, miR-141), TNFAIP6 (miR-141, miR-200a, miR-182), CYP11A1 (miR-122), SERPINA5 (miR-1, miR-206, miR-133a-3p, miR-133b), and PTGFR (miR-182, miR-122) might be related to fertility, but requires further research on follicular somatic cells.

Conclusions

This study was used for the first time to reveal the DEmRNAs and DEmiRNAs as well as their interaction in the follicles of uniparous and multiple goats at estrus phase using RNA-seq technology. Our findings provide new clues to uncover the molecular mechanisms and signaling networks of goat reproduction that could be potentially used to increase ovulation rate and kidding rate in goat.

Transcriptional analysis of deoxynivalenol-induced apoptosis of sow ovarian granulosa cell

Litter size is one of the most important economic traits in pig production. Recent studies identified that deoxynivalenol (DON), a widespread toxin in fodder, was associated with animal prolificacy. However, the underlying mechanisms have not yet been completely elucidated. Here, we used porcine ovary granulosa cells (pGCs) as a vector to establish DON concentration-time models and performed cell morphology and transcriptome analysis to identify and analyse the effects of DON on reproductive performance in swine. The results showed that DON can induce morphological changes and apoptosis of pGCs, while inhibiting cell proliferation. Moreover, these effects of DON on pGCs were dose-dependent. After treatment of pGCs with different concentrations of DON, the percentage of cells in S phase and G2/M phase increased. RNA-seq analyses revealed 5,937 differentially expressed genes, of which 1995 were down-regulated and 3,942 were up-regulated after DON treatment. KEGG enrichment analysis indicated important metabolic pathways such as IL-17 signalling pathway, eukaryotic ribosome synthesis pathway, RNA transport pathway and RNA degradation. Based on our results, we speculate that the effects of DON are related to the DNA damage process. Our study provides novel insights and a foundation to further understand the effect of DON on swine prolificacy.

Genome-Wide Differential Expression Profiling of Ovarian circRNAs Associated With Litter Size in Pigs

Circular RNAs (circRNAs) have been emerging as an important regulator in mammalian reproduction via acting as miRNA sponges. However, the circRNAs in porcine ovaries related with litter size remains largely unknown. In this study, porcine ovaries with smaller or larger litter size (LLS) were subjected to high-throughput RNA sequencing. In total, 38,722 circRNAs were identified, of which 1,291 circRNAs were commonly expressed in all samples. There were 56 circRNAs significantly down-regulated and 54 circRNAs up-regulated in LLS pig (|log2 (fold change) | > 1, FDR < 0.05). Bioinformatics predicted that most of circRNAs harbored miRNA binding sites, and the expression patterns of circRNAs and their putative binding miRNAs were validated by qPCR. Moreover, the expression of circ-TCP11/miR-183 was significantly reversely correlated and their direct interaction was confirmed by dual-luciferase assay. Our study indicates that circRNAs may play potential effects on modulating porcine litter size.

Serial gene co-expression network approach to mine biological meanings from integrated transcriptomes of the porcine endometrium during estrous cycle

The estrous cycle is a complex process regulated by several hormones. To understand the dynamic changes in gene expression that takes place in the swine endometrium during the estrous cycle relative to the day of estrus onset, we performed RNA-sequencing analysis on days 0, 3, 6, 9, 12, 15, and 18, resulting in the identification of 4495 differentially expressed genes (DEGs; Q ≤ 0.05 and |log₂FC| ≥ 1) at various phases in the estrous cycle. These DEGs were integrated into multiple gene co-expression networks based on different fold changes and correlation coefficient (R²) thresholds and a suitable network, which included 899 genes (|log2FC| ≥ 2 and R² ≥ 0.99), was identified for downstream analyses based on the biological relevance of the Gene Ontology (GO) terms enriched. The genes in this network were partitioned into 6 clusters based on the expression pattern. Several GO terms including cell cycle, apoptosis, hormone signaling, and lipid biosynthetic process were found to be enriched. Furthermore, we found 15 significant KEGG pathways, including cell adhesion molecules, cytokine-cytokine receptor signaling, steroid biosynthesis, and estrogen signaling pathways. We identified several genes and GO terms to be stage-specific. Moreover, the identified genes and pathways extend our understanding of porcine endometrial regulation during estrous cycle and will serve as a good resource for future studies.

Combined microRNAome and transcriptome analysis of follicular phase and luteal phase in porcine ovaries

The aim of this study was to explore the expression difference of miRNAs and mRNAs between the follicular phase (FP) and luteal phase (LP) in porcine ovaries and provide a theoretical basis for the research on mammalian reproductive regulation. RNA-Seq and miRNA-Seq were used to identify differentially expressed genes (DEGs) and miRNAs (DEMs) between the FP and LP in ovaries of six sows (3-year-old Yorkshire pigs with similar weights and same parities). Bioinformatic analysis was used to screen potential genes and miRNAs related to porcine ovarian function. Real-time qualitative PCR was used to validate the sequencing results. RNA-Seq results showed that 3,078 genes were up-regulated, and 1,444 genes were down-regulated in the LP compared with the FP, and DEGs were significantly enriched in 242 Gene Ontology (GO) terms and 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. miRNA-Seq identified 112 DEMs, of which 25 were up-regulated and 87 were down-regulated in the LP compared with the FP. We obtained 186 intersection genes (IGs) between the 4,522 DEGs and 2,444 target genes predicted from the 112 DEMs. After constructing a miRNA-gene-pathway network, we identified key miRNAs and genes including miR-17-3p, miR-214, miR-221-5p, miR-125b, FGF1, YWHAG, YWHAZ, FDFT1 and DHCR24, which are enriched in Hippo and PI3K-Akt signalling pathways, and various metabolic pathways. These results indicate that these key genes and miRNAs may play important roles in the developmental transition from FP to LP in porcine ovaries and represent candidate targets for further study.

Transcriptome analysis of the endometrium from Chinese Erhualian sows that differ in calcium ion concentration and litter size

Embryonic survival rate, an important factor in the fecundity of sows, is affected by endometrium-secreting histotroph. A higher concentration of calcium ion has been observed in the uterus of highly prolific Erhualian sows (EH) compared with those of less prolific (EL) sows. This suggests that EH sows have better establishment and maintenance of pregnancies, thus increasing embryonic survival rate during the peri-implantation period. To understand the mechanisms of how the endometrium-secreting histotroph affects embryonic survival rate during the Erhualian peri-implantation period, the expression patterns of endometrial mRNA in the EH and EL sows on day 12 of gestation were analyzed using RNA sequencing technology. A total of 164 differentially expressed genes (DEGs) were identified (P_adj  < 0.05, |log₂ (FC)| ≥ 1), including 46 upregulated and 118 downregulated genes in EH compared to EL. Gene Ontology enrichment indicated that a subset of DEGs was involved in calcium ion binding and cell adhesion. Solute carrier family 8 member A3 and solute carrier family 24 member 4, identified as upregulated genes (P_adj  < 0.05) in EH, were considered key candidate genes expressed in the endometrium affecting embryonic survival rate during the peri-implantation period. The results improve understanding of the genetic mechanism underlying the variation in litter size of Erhualian pigs during the peri-implantation period.

Filtered reproductive long non-coding RNAs by genome-wide analyses of goat ovary at different estrus periods

Background

The goat is an important farm animal. Reproduction is an important process of goat farming. The ovary is the most important reproductive organ for goats. In recent years, an increasing number of long non-coding RNAs (lncRNAs) have been implicated in the regulation of mammal reproduction. However, there are few studies on the function of lncRNAs in reproduction, particularly lncRNAs in the ovary.

Results

The sequencing of goat ovaries generated 1,122,014,112 clean reads, and 4926 lncRNAs and 1454 TUCPs (transcripts of uncertain coding potential) were identified for further analysis by using the coding potential analysis software, CNCI, CPC and Pfam-sca. There were 115 /22 differential lncRNAs /TUCPs transcripts between the ovaries of the luteal phase and the follicular phase. We predicted the related genes of lncRNA /TUCP based on co-expression and co-localization methods. In total, 2584 /904 genes were predicted by co-expression, and 326/73 genes were predicted by co-localization. The functions of these genes were further analyzed with GO and KEGG analysis. The results showed that lncRNAs /TUCPs, which are highly expressed in goat ovaries in the luteal phase, are mainly associated with the synthesis of progesterone, and we filtered the lncRNAs /TUCPs, such as XR_001918177.1 and TUCP_001362, which may regulate the synthesis of progesterone; lncRNAs /TUCPs, which are highly expressed in goat ovaries in the follicular phase, are mainly associated with oogenesis and the maturation of oocytes, and we filtered the lncRNAs /TUCPs that may regulate the oogenesis and maturation of oocyte, such as XR_001917388.1 and TUCP_000849.

Conclusion

The present study provided the genome expression profile of lncRNAs /TUCPs in goat ovaries at different estrus periods and filtered the potential lncRNAs /TUCPs associated with goat reproduction. These results are helpful to further study the molecular mechanisms of goat reproduction.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5268-7) contains supplementary material, which is available to authorized users.

MicroRNA-21 and microRNA-214 play important role in reproduction regulation during porcine estrous

Normal estrous cycle is crucial for porcine reproduction, and microRNA is closely related to regulation of estrous cycle in porcine ovaries. In this study, we found that the expression of miR-214 in porcine ovaries was higher than in many other tissues, and miR-21 expression in ovaries was significantly higher than in the uterus and pituitary. Meanwhile, miR-21 was upregulated and miR-214 was downregulated in the ovaries of high litter size (YH) pigs compared with low litter size (YL) pigs. Moreover, the lowest expression of miR-21 and miR-214 occurred on Days 14 and 7 of the estrous cycle and was expressed at greater levels in the granulosa cells of subordinate follicles than in dominant follicles on Day 3 of the estrous cycle. Bioinformatics analysis showed that miR-21 and miR-214 might target several genes that involved in the mTOR signaling, apoptosis, and steroid biosynthesis pathways, and they play important roles in maintaining the porcine estrous cycle. The qPCR and western blot analysis indicated that miR-214 inhibited the expression of SCARB1 gene in the transcriptional level, but not affected the SCARB1 gene's protein level. Our research findings indicated that miR-21 and miR-214 played important roles in reproduction regulation during porcine estrous.

Transcriptome analysis reveals candidate genes involved in splay leg syndrome in piglets

Splay leg is frequently observed in newborn piglets and leads to economic loss as well as welfare concerns. However, the etiology and pathogenesis of splay leg syndrome in piglets are still poorly understood. The aims of this paper were to characterize changes in the transcriptome of splay leg piglets and identify candidate genes responsible for this disease. We chose three splay leg piglets and their healthy full sibs, and constructed six RNA libraries using skeletal muscle samples from both groups and identified the differentially expressed genes between the two groups using RNA-seq. A total of 555 differentially expressed genes were identified, of which 216 were up-regulated and 339 genes were down-regulated in the splay leg group relative to the healthy group. In addition, 321 significantly enriched GO terms and 12 significantly enriched KEGG pathways were identified. FBXO32 is one of the ten most differentially expressed genes in our experiment, and it is regulated by the significantly enriched pathway (PI3K-Akt). The overexpression of FBXO32 which leads to the process of muscle atrophy might be responsible for congenital splay leg in piglets. The result of this study could help improve understanding of the molecular mechanism of congenital splay leg syndrome.

Comparative transcriptomic analysis of high and low egg-producing duck ovaries

The egg-laying rate is an important indicator of egg production of laying ducks. Egg production directly impacts the economic benefits of the duck industry. In order to obtain better insight into the molecular mechanisms associated with the process of egg production, comparative transcriptomic analysis of the ovaries of Jinding ducks with high and low egg production was performed using the Illumina HiSeq 2500 system. A total of 843 differentially expressed genes (DEGs) was identified, 367 that were down-regulated and 476 that were up-regulated in high egg production (HEP) ovaries, as compared with low egg production (LEP) ovaries. Some genes, such as MC5R, APOD, ORAI1, and DYRK4, were more active in HEP ovaries, indicating that these genes may play important roles in regulation of egg production. Among these 843 DEGs, 685 were assigned to gene ontology (GO) categories. Of these, 25 genes were related to reproduction, and 30 were related to the reproductive process, including some associated with ovarian follicle development, circadian regulation of gene expression, circadian rhythm, and estrogen receptor binding. Furthermore, some important functional pathways were revealed, such as the steroid biosynthesis pathway, the endocrine and other factor-regulated calcium reabsorption pathways, circadian rhythm, the neuroactive ligand-receptor interaction pathway, fatty acid biosynthesis, and the calcium-signaling pathway, which appear to be much more active in the HEP group, as compared to those of the LEP group. The results of this study provide very useful information that may contribute to future functional studies of genes involved in bird reproduction.

Genome-wide DNA methylation profiles of porcine ovaries in estrus and proestrus

DNA methylation is an important epigenetic modification involved in the estrous cycle and the regulation of reproduction. Here, we investigated the genome-wide profiles of DNA methylation in porcine ovaries in proestrus and estrus using methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in intergenic and intron regions. The methylation levels of coding regions were higher than those of the 5'- and 3'-flanking regions of genes. There were 4,813 differentially methylated regions (DMRs) of CpG islands in the estrus vs. proestrus ovarian genomes. Additionally, 3,651 differentially methylated genes (DMGs) were identified in pigs in estrus and proestrus. The DMGs were significantly enriched in biological processes and pathways related to reproduction and hormone regulation. We identified 90 DMGs associated with regulating reproduction in pigs. Our findings can serve as resources for DNA methylome research focused on porcine ovaries and further our understanding of epigenetically regulated reproduction in mammals.

Differential gene expression of Eph-ephrin A1 and LEPR-LEP with high or low number of embryos in pigs during implantation

The objective of this study was to ascertain whether mRNA and protein expressions of implantation-related genes (erythropoietin-producing hepatocellular receptor-ligand A1, Eph-ephrin A1 and leptin receptor-leptin, LEPR-LEP) differed between pigs with high and low number of embryos, and whether these differences in gene expression might affect embryo implantation. Experimental pig groups (n = 24) for high and low number of embryos were prepared by altering the number of eggs ovulated in pre-pubertal gilts treated with 1.5 × (High) or 1.0 × (Low) PG600 ([400 IU PMSG + 200 IU hCG]/dose, AKZO-NOBEL). Gilts expressing oestrus were artificially inseminated twice and maintained in breeding and gestation until the reproductive tract was collected on day 22 of pregnancy. At slaughter, the reproductive tracts from each pregnant gilt from each treatment were immediately processed to collect samples for RNA and protein analysis. Within each gilt, three conceptus points were sampled, one from each horn and then a random conceptus within the tract. At each conceptus point, endometrial attachment site, chorion-allantois and embryo were collected and immediately frozen in liquid nitrogen. Number of corpus luteum (CL) (35.4 vs. 12.6) and total embryo number (18.8 vs. 10.2) were greater in the high-embryo compared to the low-embryo group, respectively (p < .05). Real-time qPCR results showed that Eph-ephrin A1 mRNA expression was less in the high-embryo (p < .05) compared to the low-embryo group. In addition, Western blotting analysis indicated that Eph-ephrin A1 and LEP protein expression at endometrial attachment site in high-embryo was less (p < .05) compared to low-embryo group. It was also noted that mRNA expression of Eph-ephrin A1 and LEPR-LEP was greater in pregnant than non-pregnant gilts (p < .05). Moreover, mRNA expression of Eph-ephrin A1 (p < .05) and LEPR-LEP was greatest at endometrial attachment site among all three tissues. There was a positive correlation between expressions of Eph-ephrin A1, LEPR-LEP and embryo length with the correlation coefficient 0.31-0.59. For Eph-ephrin A1, the highest correlation coefficient appeared between Eph A1 expression and normal embryo number, between ephrin A1 expression and embryo length. For LEPR-LEP, the highest correlation coefficient appeared between LEPR-LEP expression and ovary weight (0.79 for both, p < .05), followed by embryo length and weight. The results of this study suggest that low expression of Eph-ephrin A1 and LEPR-LEP is somehow related to increased embryo number during implantation and that endometrial attachment site might be the main target tissue of these gene products. Yet, the increased expression of Eph-ephrin A1 and LEPR-LEP appeared associated with increased embryo growth (length and weight) and ovary weight, Eph-ephrin A1 and LEPR-LEP might play roles in the regulation of embryo implantation in pigs.

Integrated transcriptomes throughout swine oestrous cycle reveal dynamic changes in reproductive tissues interacting networks

Female fertility is a highly regulated process involving the synchronized activities of multiple tissues. The underlying genomic regulation of the tissue synchronization is poorly understood. To understand this better we investigated the transcriptomes of the porcine ovary, endometrium, and oviduct at days 0, 3, 6, 9, 12, 15, or 18 of the oestrous cycle. We analysed the transcriptome profiles of the individual tissues and focus on the bridging genes shared by two or more tissues. The three tissue-networks were connected forming a triangular shape. We identified 65 bridging genes with a high level of connectivity to all other genes in the network. The expression levels showed negative correlations between the ovary and the other two tissues, and low correlations between endometrium and oviduct. The main functional annotations involved biosynthesis of steroid hormones, cell-to-cell adhesion, and cell apoptosis, suggesting that regulation of steroid hormone synthesis and tissue viability are major regulatory mechanisms.

Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P ≤ 0.05, |log2  Ratio| ≥ 1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

Effect of dietary chitosan oligosaccharide supplementation on the pig ovary transcriptome

Fecundity improvement is one of the most important economic traits for the swine industry. In this study, we identified 486 differentially expressed genes associated with sow prolificacy from COS administrated sow ovaries by RNA-seq.

Differentially expressed genes in the caecal and colonic mucosa of Landrace finishing pigs with high and low food conversion ratios

The feed conversion ratio (FCR) is an essential economic trait for pig production, and is directly related to feed efficiency. Studies identifying the differential expression of functional genes involved in biological and molecular mechanisms in the intestine in relation to growth performance are rare. In this study, RNA-Seq was used to identify transcriptomes in caecal and colonic mucosal tissues in order to determine the differential expression of genes from two full-sibling pairs and two half-sibling pairs of Landrace finishing pigs with opposing FCR phenotypes. In total, 138 (comparison of high and low FCR in caecal mucosa), 64 (comparison of high and low FCR in colonic mucosa), and 165 (contrast between the caecal and colonic mucosa) differentially expressed genes were identified. Some of these genes were functionally related to energy and lipid metabolism, particularly short chain fatty acids metabolism, as well as gastrointestinal peristalsis and ion transport. Functional annotation were performed to identify differentially expressed genes, such as GUCA2A, GUCA2B, HSP70.2, NOS2, PCK1, SLCs, and CYPs, which may positively influence feed efficiency in Landrace pigs. These differentially expressed genes need to be further tested for candidate genes that are related to feed efficiency.

Ovarian transcriptomic analysis of Shan Ma ducks at peak and late stages of egg production

Objective

To assess the differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production, and to obtain new transcriptomic data of these egg-producing ducks.

Methods

The Illumina HiSeq 2000 system was used for high throughput sequencing of ovarian transcriptomes from Shan Ma ducks at their peak or late stages of egg production.

Results

Greater than 93% of the sequencing data had a base quality score (Q score) that was not less than 20 (Q20). From ducks at their peak stage of egg production, 42,782,676 reads were obtained, with 4,307,499,083 bp sequenced. From ducks at their late stage of egg production, 45,316,166 reads were obtained, with 4,562,063,363 bp sequenced. A comparison of the two datasets identified 2,002 differentially expressed genes, with 790 upregulated and 1,212 downregulated. Further analysis showed that 1,645 of the 2,002 differentially expressed genes were annotated in the non-redundant (NR) database, with 646 upregulated and 999 downregulated. Among the differentially expressed genes with annotations in the NR database, 696 genes were functionally annotated in the clusters of orthologous groups of proteins database, involving 25 functional categories. One thousand two hundred four of the differentially expressed genes with annotations in the NR database were functionally annotated in the gene ontology (GO) database, and could be divided into three domains and 56 categories. The three domains were cellular component, molecular function, and biological process. Among the genes identified in the GO database, 451 are involved in development and reproduction. Analysis of the differentially expressed genes with annotations in the NR database against the Kyoto encyclopedia of genes and genomes database revealed that 446 of the genes could be assigned to 175 metabolic pathways, of which the peroxisome proliferator-activated receptor signaling pathway, insulin signaling pathway, fructose and mannose metabolic pathways, gonadotropin releasing hormone signaling pathway and transforming growth factor beta signaling pathway were significantly enriched.

Conclusion

The differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production were elucidated, which greatly enriched the ovarian transcriptomic information of egg-producing ducks.

Using RNA-Seq SNP data to reveal potential causal mutations related to pig production traits and RNA editing

RNA-Seq technology is widely used in quantitative gene expression studies and identification of non-annotated transcripts. However this technology also can be used for polymorphism detection and RNA editing in transcribed regions in an efficient and cost-effective way. This study used SNP data from an RNA-Seq assay to identify genes and mutations underlying production trait variations in an experimental pig population. The hypothalamic and hepatic transcriptomes of nine extreme animals for growth and fatness from an (Iberian × Landrace) × Landrace backcross were analyzed by RNA-Seq methodology, and SNP calling was conducted. More than 125 000 single nucleotide variants (SNVs) were identified in each tissue, and 78% were considered to be potential SNPs, those SNVs segregating in the context of this study. Potential informative SNPs were detected by considering those showing a homozygous or heterozygous genotype in one extreme group and the alternative genotype in the other group. In this way, 4396 and 1862 informative SNPs were detected in hypothalamus and liver respectively. Out of the 32 SNPs selected for validation, 25 (80%) were confirmed as actual SNPs. Association analyses for growth, fatness and premium cut yields with 19 selected SNPs were carried out, and four potential causal genes (RETSAT, COPA, RNMT and PALMD) were identified. Interestingly, new RNA editing modifications were detected and validated for the NR3C1:g.102797 (ss1985401074) and ACSM2B:g.13374 (ss1985401075) positions and for the COG3:g3.4525 (ss1985401087) modification previously identified across vertebrates, which could lead to phenotypic variation and should be further investigated.

Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare

In the past years, there has been a remarkable development of high-throughput omics (HTO) technologies such as genomics, epigenomics, transcriptomics, proteomics and metabolomics across all facets of biology. This has spearheaded the progress of the systems biology era, including applications on animal production and health traits. However, notwithstanding these new HTO technologies, there remains an emerging challenge in data analysis. On the one hand, different HTO technologies judged on their own merit are appropriate for the identification of disease-causing genes, biomarkers for prevention and drug targets for the treatment of diseases and for individualized genomic predictions of performance or disease risks. On the other hand, integration of multi-omic data and joint modelling and analyses are very powerful and accurate to understand the systems biology of healthy and sustainable production of animals. We present an overview of current and emerging HTO technologies each with a focus on their applications in animal and veterinary sciences before introducing an integrative systems genomics framework for analysing and integrating multi-omic data towards improved animal production, health and welfare. We conclude that there are big challenges in multi-omic data integration, modelling and systems-level analyses, particularly with the fast emerging HTO technologies. We highlight existing and emerging systems genomics approaches and discuss how they contribute to our understanding of the biology of complex traits or diseases and holistic improvement of production performance, disease resistance and welfare.