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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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2
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Abdurahman A, Aierken W, Zhang F, Obulkasim R, Aniwashi J, Sulayman A. miR-1306 induces cell apoptosis by targeting BMPR1B gene in the ovine granulosa cells. Front Genet 2022; 13:989912. [PMID: 36212145 PMCID: PMC9539929 DOI: 10.3389/fgene.2022.989912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/22/2022] [Indexed: 11/15/2022] Open
Abstract
Bone morphogenetic protein receptor type-1B (BMPR1B) is one of the major gene for sheep prolificacy. However, few studies investigated its regulatory region. In this study, we reported that miR-1306 is a direct inhibitor of BMPR1B gene in the ovine granulosa cells (ovine GCs). We detected a miRNA response element of miR-1306 in the 3’ untranslated region of the ovine BMPR1B gene. Luciferase assay showed that the ovine BMPR1B gene is a direct target of miR-1306. qPCR and western blotting revealed that miR-1306 reduces the expression of BMPR1B mRNA and protein in the ovine granulosa cells. Furthermore, miR-1306 promoted cell apoptosis by suppressing BMPR1B expression in the ovine granulosa cells. Overall, our results suggest that miR-1306 is an epigenetic regulator of BMPR1B, and may serve as a potential target to improve the fecundity of sheep.
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Affiliation(s)
- Anwar Abdurahman
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | | | - Fei Zhang
- Animal Diseases Control and Prevention Centre of Xinjiang Uygur Autonomous Region, Urumqi, China
| | | | - Jueken Aniwashi
- College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi, China
| | - Ablat Sulayman
- Institute of Animal Husbandry, Xinjiang Academy of Animal Science, Urumqi, China
- *Correspondence: Ablat Sulayman,
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3
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Gholizadeh M, Esmaeili-Fard SM. Meta-analysis of genome-wide association studies for litter size in sheep. Theriogenology 2021; 180:103-112. [PMID: 34968818 DOI: 10.1016/j.theriogenology.2021.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 12/19/2021] [Accepted: 12/19/2021] [Indexed: 01/01/2023]
Abstract
Litter size and ovulation rate are important reproduction traits in sheep and have important impacts on the profitability of farm animals. To investigate the genetic architecture of litter size, we report the first meta-analysis of genome-wide association studies (GWAS) using 522 ewes and 564,377 SNPs from six sheep breeds. We identified 29 significant associations for litter size which 27 of which have not been reported in individual GWAS for each population. However, we could confirm the role of BMPR1B in prolificacy. Our gene set analysis discovered biological pathways related to cell signaling, communication, and adhesion. Functional clustering and enrichment using protein databases identified epidermal growth factor-like domain affecting litter size. Through analyzing protein-protein interaction data, we could identify hub genes like CASK, PLCB4, RPTOR, GRIA2, and PLCB1 that were enriched in most of the significant pathways. These genes have a role in cell proliferation, cell adhesion, cell growth and survival, and autophagy. Notably, identified SNPs were scattered on several different chromosomes implying different genetic mechanisms underlying variation of prolificacy in each breed. Given the different layers that make up the follicles and the need for communication and transfer of hormones and nutrients through these layers to the oocyte, the significance of pathways related to cell signaling and communication seems logical. Our results provide genetic insights into the litter size variation in different sheep breeds.
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Affiliation(s)
- Mohsen Gholizadeh
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
| | - Seyed Mehdi Esmaeili-Fard
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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4
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Winter E, Cisilotto J, Silva AH, Rosolen D, Fabichak AP, Rode MP, Creczynski-Pasa TB. MicroRNAs: Potential biomarkers for reproduction, diagnosis, prognosis, and therapeutic in domestic animals. Res Vet Sci 2021; 142:117-132. [PMID: 34942556 DOI: 10.1016/j.rvsc.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 11/02/2021] [Accepted: 12/01/2021] [Indexed: 10/19/2022]
Abstract
MicroRNA (miRNAs) are small non-coding RNA molecules involved in a wide range of biological processes through the post-transcriptional regulation of gene expression. Most studies evaluated microRNA expression in human, and despite fewer studies in veterinary medicine, this topic is one of the most exciting areas of modern veterinary medicine. miRNAs showed to be part of the pathogenesis of diseases and reproduction physiology in animals, making them biomarkers candidates. This review provides an overview of the current knowledge regarding miRNAs' role in reproduction and animal diseases, diagnostic and therapy.
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Affiliation(s)
- Evelyn Winter
- Department of Agriculture, Biodiversity and Forests, Federal University of Santa Catarina, Curitibanos, 89520000, SC, Brazil.
| | - Júlia Cisilotto
- Postgraduate Program in Pharmacy, Federal University of Santa Catarina, Florianopolis, 88040-900, SC, Brazil
| | - Adny Henrique Silva
- Postgraduate Program in Pharmacy, Federal University of Santa Catarina, Florianopolis, 88040-900, SC, Brazil
| | - Daiane Rosolen
- Postgraduate Program in Pharmacy, Federal University of Santa Catarina, Florianopolis, 88040-900, SC, Brazil
| | - Ana Paula Fabichak
- Department of Agriculture, Biodiversity and Forests, Federal University of Santa Catarina, Curitibanos, 89520000, SC, Brazil
| | - Michele Patricia Rode
- Postgraduate Program in Pharmacy, Federal University of Santa Catarina, Florianopolis, 88040-900, SC, Brazil
| | - Tânia Beatriz Creczynski-Pasa
- Postgraduate Program in Pharmacy, Federal University of Santa Catarina, Florianopolis, 88040-900, SC, Brazil; Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianopolis, 88040-900, SC, Brazil
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5
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miRNA Regulatory Functions in Farm Animal Diseases, and Biomarker Potentials for Effective Therapies. Int J Mol Sci 2021; 22:ijms22063080. [PMID: 33802936 PMCID: PMC8002598 DOI: 10.3390/ijms22063080] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small endogenous RNAs that regulate gene expression post-transcriptionally by targeting either the 3′ untranslated or coding regions of genes. They have been reported to play key roles in a wide range of biological processes. The recent remarkable developments of transcriptomics technologies, especially next-generation sequencing technologies and advanced bioinformatics tools, allow more in-depth exploration of messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs), including miRNAs. These technologies have offered great opportunities for a deeper exploration of miRNA involvement in farm animal diseases, as well as livestock productivity and welfare. In this review, we provide an overview of the current knowledge of miRNA roles in major farm animal diseases with a particular focus on diseases of economic importance. In addition, we discuss the steps and future perspectives of using miRNAs as biomarkers and molecular therapy for livestock disease management as well as the challenges and opportunities for understanding the regulatory mechanisms of miRNAs related to disease pathogenesis.
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6
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Pokharel K, Peippo J, Li MH, Kantanen J. Identification and characterization of miRNAs during early pregnancy in domestic sheep. Anim Genet 2020; 51:833-836. [PMID: 32794198 PMCID: PMC7540487 DOI: 10.1111/age.12992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022]
Abstract
MicroRNA resources in sheep are limited compared with those in other domesticated mammalian species. By sequencing small RNAs of sheep corpus luteum and endometrium, we have generated the largest amount of miRNA‐seq data and compiled the most comprehensive list thus far of miRNAs (n = 599) in sheep. Additionally, we observed a highly conserved maternally imprinted cluster of miRNAs on chromosome 18 homologous to that found on chromosome 14 in human and several other eutherian mammals.
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Affiliation(s)
- Kisun Pokharel
- Natural Resources Institute of Finland (Luke), Jokioinen, Finland
| | - Jaana Peippo
- Natural Resources Institute of Finland (Luke), Jokioinen, Finland
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Juha Kantanen
- Natural Resources Institute of Finland (Luke), Jokioinen, Finland
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7
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Li J, Hou L, Sun Y, Xing J, Jiang Y, Kang L. Single nucleotide polymorphism rs737028527 (G>A) affect miR-1b-3p biogenesis and effects on chicken egg-laying traits. Anim Reprod Sci 2020; 218:106476. [PMID: 32507256 DOI: 10.1016/j.anireprosci.2020.106476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022]
Abstract
The abundance of miR-1b-3p in the chicken ovary is greater after sexual maturation. In the present study there was assessment of whether a single nucleotine polymorphism (SNP) led to an alteration in expression of reproductive traits. The miR-1b-3p abundance was greatest in ovarian follicles The SNP site of rs737028527 (G > A), located in the 734 bp upstream region of pre-miR-1b-3p, was identified in three different chicken breeds. Results from an association analysis of chicken egg-laying traits indicated the SNP was associated with age at first egg production (AFE) and egg number at 32 and 48 weeks (E32, E48; P < 0.01). Hens with genotype AA had an earlier AFE and greater E32 and E48 than hens with other genotypes. The abundance of mature miR-1b-3p in the hens with the GG genotype was larger than those with the AA genotype (P < 0.01), and the luciferase activity of GG genotype promoter was also greater in birds with the AA than GG genotype (P < 0.05). There was inhibition of the production of the transcription factor bound by the specificity protein 1 (Sp1) as a result of the G-to-A mutation, and the luciferase activity of the GG, but not AA, genotype was markedly increased by Sp1. In conclusion, the SNP, rs737028527 (G> A), affected the abundance of mature miR-1b-3p by Sp1 and was associated with chicken egg-laying traits. Data from the present study allow for an increased understanding of the functions and regulation of miR-1b-3p in ovarian follicle development of hens.
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Affiliation(s)
- Jianbo Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Li Hou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Yi Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Jinyi Xing
- School of Life Science, Linyi University, Linyi 276000, China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China
| | - Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, China.
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8
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Proteomic analysis of sheep uterus reveals its role in prolificacy. J Proteomics 2019; 210:103526. [PMID: 31605788 DOI: 10.1016/j.jprot.2019.103526] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/19/2019] [Accepted: 09/04/2019] [Indexed: 12/23/2022]
Abstract
Small Tail Han sheep have attracted attention for their high fecundity and year-round estrus. However, the molecular mechanisms of this fecundity are unknown. Polymorphism of the FecB gene has been shown to be associated with the ovulation rate and litter size in sheep. In this study, we used tandem mass tag quantitative proteomic techniques to identify the differentially abundant proteins in polytocous and monotocous Small Tail Han sheep (FecB++) uterine tissues in the follicular and luteal phases. In total, 41 and 43 differentially abundant proteins were identified in the follicular and luteal phases, respectively. Correlation analysis between the transcriptome and proteome revealed a positive correlation at the two omics levels of prolificacy. GO and KEGG pathway analyses indicated that the mRNAs and proteins upregulated in the polytocous group relative to the monotocous group are involved in sphingolipid metabolism and amino acid metabolism, and may be important in maintaining uterine functions and increasing the embryo survival rate during the estrus cycle of polytocous sheep. In conclusion, our work provides a prospective understanding of the molecular mechanism underlying the high prolificacy of Small Tail Han sheep. SIGNIFICANCE: Fecundity critically affects the profitability of sheep production, but the genetic mechanism of high-prolificacy is still unclear in sheep. We identified potential signaling pathways and differentially abundant proteins associated with reproductive performance through a combination of sheep uterus tissues proteome and transcriptome analyses. These findings will facilitate a better revealing the mechanism and provide possible targets for molecular design breeding for the formation of polytocous traits in sheep.
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9
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Yang H, Wang F, Li F, Ren C, Pang J, Wan Y, Wang Z, Feng X, Zhang Y. Comprehensive analysis of long noncoding RNA and mRNA expression patterns in sheep testicular maturation. Biol Reprod 2019; 99:650-661. [PMID: 29668837 DOI: 10.1093/biolre/ioy088] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/12/2018] [Indexed: 02/03/2023] Open
Abstract
Long noncoding RNAs (LncRNAs) have been identified as important regulators of testis development; however, their expression patterns and roles in sheep are not yet clear. Thus, we used stranded specific RNA-seq to profile the testis transcriptome (lncRNAs and mRNAs) in premature and mature sheep. Hormone levels and the testis index were examined, and histological analyses were performed at five stages of testis development, 5-day-old (D5), 3-month-old (3M), 6-month-old (6M), 9-month-old (9M), and 2-year-old (2Y), the results of which indicate a significant difference in hormone levels and testis morphometries between the 3M and 9M stages (P < 0.05). Based on the comparison between 3M and 9M samples, we found 1,118 differentially expressed (DE) lncRNAs and 7,253 DE mRNAs in the testes, and qRT-PCR analysis showed that the results correlated well with the transcriptome data. Furthermore, we constructed lncRNA-protein-coding gene interaction networks. Forty-seven DE lncRNA-targeted genes enriched for male reproduction were obtained by cis- and trans-acting; 51 DE lncRNAs and 45 cis-targets, 2 DE lncRNAs and 2 trans-targets were involved in this network. Of these, 5 lncRNAs and their targets, PRKCD, NANOS3, SERPINA5, and CYP19A1, were enriched for spermatogenesis and male gonad development signaling pathways. We further examined the expression levels of 5 candidate lncRNAs and their target genes during testis development. Lastly, the interaction of lncRNA TCONS__00863147 and its target gene PRKCD was validated in vitro in sheep Leydig cells. This study provides a valuable resource for further study of lncRNA function in sheep testis development and spermatogenesis.
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Affiliation(s)
- Hua Yang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Fengzhe Li
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Caifang Ren
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Jing Pang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Yongjie Wan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Ziyu Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Xu Feng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
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10
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Bourdon C, Bardou P, Aujean E, Le Guillou S, Tosser-Klopp G, Le Provost F. RumimiR: a detailed microRNA database focused on ruminant species. Database (Oxford) 2019; 2019:baz099. [PMID: 31608376 PMCID: PMC6790497 DOI: 10.1093/database/baz099] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/07/2019] [Accepted: 07/13/2019] [Indexed: 01/03/2023]
Abstract
The ever-increasing use of next-generation sequencing technologies to explore the genome has generated large quantities of data in recent years. Numerous publications have described several thousand sequences of microRNAs, all species included. A new database (RumimiR) has been created from the literature to provide a detailed description of microRNAs for three ruminant species: cattle, goats and sheep. To date, 2887, 2733 and 5095 unique microRNAs from bovine, caprine and ovine species, respectively, are included. In addition to the most recent reference genomic position and sequence of each microRNA, this database contains details about the animals, tissue origins and experimental conditions mentioned in the publications. Identity to human or mouse microRNA is also indicated. The RumimiR database allows data filtering by selecting microRNAs on the basis of defined criteria such as animal status or tissue origin. For ruminant studies, RumimiR supplements the widely used miRBase database, by using complementary criteria to allow browsing and filtering, and integrates all newly described published sequences. The principal goal of this database is to provide easy access to all the ruminant microRNAs described in the literature.
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Affiliation(s)
- Céline Bourdon
- Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Allée de Vilvert, 78350 Jouy-en-Josas, France
| | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRA, Ecole Nationale Vétérinaire de Toulouse (ENVT), 24 Chemin de Borde Rouge, 31320 Castanet-Tolosan, France
- Sigenae, INRA, 24 Chemin de Borde Rouge, 31320 Castanet-Tolosan, France
| | - Etienne Aujean
- Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Allée de Vilvert, 78350 Jouy-en-Josas, France
| | - Sandrine Le Guillou
- Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Allée de Vilvert, 78350 Jouy-en-Josas, France
| | - Gwenola Tosser-Klopp
- GenPhySE, Université de Toulouse, INRA, Ecole Nationale Vétérinaire de Toulouse (ENVT), 24 Chemin de Borde Rouge, 31320 Castanet-Tolosan, France
| | - Fabienne Le Provost
- Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Allée de Vilvert, 78350 Jouy-en-Josas, France
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11
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Nosrati M, Asadollahpour Nanaei H, Amiri Ghanatsaman Z, Esmailizadeh A. Whole genome sequence analysis to detect signatures of positive selection for high fecundity in sheep. Reprod Domest Anim 2018; 54:358-364. [PMID: 30359467 DOI: 10.1111/rda.13368] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/15/2018] [Indexed: 12/19/2022]
Abstract
Ovulation rate and prolificacy are the most important reproductive traits that have major impact on the efficiency of lamb meat production. Here, we compared the whole genomes of the Romanov sheep, known as one of the high prolific breeds, and four other sheep breeds namely Assaf, Awassi, Cambridge and British du cher, to identify genetic mechanisms underlying prolificacy in sheep. Selection signature analysis revealed 637 and 477 protein-coding genes under positive selection from FST and nucleotide diversity (Pi) statistics, respectively. Further analysis showed that several candidate genes including LEPR, PDGFRL and KLF5 genes are involved in sheep prolificacy. The identified candidate genes in the selected regions are novel and provide new insights into the genetic mechanisms underlying prolificacy in sheep and can be useful in sheep breeding programmes to develop improved breeds for high reproductive efficiency.
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Affiliation(s)
- Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.,Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.,Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
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12
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Yao Y, Niu J, Sizhu S, Li B, Chen Y, Li R, Yangzong Q, Li Q, Xu Y. microRNA-125b Regulates Apoptosis by Targeting Bone Morphogenetic Protein Receptor 1B in Yak Granulosa Cells. DNA Cell Biol 2018; 37:878-887. [PMID: 30260685 DOI: 10.1089/dna.2018.4354] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The intronic microRNA, miR-125b, plays a vital role in promyelocytic and hematopoietic stem cells, and in the development and apoptosis of cancer cells. In this study, we showed that miR-125b regulates granulosa cell (GC) apoptosis in the yak ovary. Bioinformatic analyses and luciferase reporter assays demonstrated that bone morphogenetic protein receptor type 1B (BMPR1B) is an miR-125b target. miR-125b overexpression induced apoptosis in yak GC, and affected the mRNA and protein expression of BMPR1B and the ratio of Bcl2/Bax. Silencing of miR-125b decreased the rate of yak GC apoptosis and increased the ratio of Bcl2/Bax. In addition, the effects of an miR-125b inhibitor were overturned by cotransfection with siRNA-BMPR1B2 (siRNA-299) in yak GC. Together, these results demonstrated that miR-125b regulates GC apoptosis in the yak ovary by targeting BMPR1B.
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Affiliation(s)
- Yilong Yao
- 1 Department of Animal Science, Tibet Agricultural and Animal Husbandry College , Nyingzhi, Tibet, P.R. China .,2 Department of Animal Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu, P.R. China
| | - Jiaqiang Niu
- 1 Department of Animal Science, Tibet Agricultural and Animal Husbandry College , Nyingzhi, Tibet, P.R. China
| | - Suolang Sizhu
- 1 Department of Animal Science, Tibet Agricultural and Animal Husbandry College , Nyingzhi, Tibet, P.R. China
| | - Bojiang Li
- 2 Department of Animal Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu, P.R. China
| | - Yun Chen
- 2 Department of Animal Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu, P.R. China
| | - Rongyang Li
- 2 Department of Animal Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu, P.R. China
| | - Qiangba Yangzong
- 1 Department of Animal Science, Tibet Agricultural and Animal Husbandry College , Nyingzhi, Tibet, P.R. China
| | - Qifa Li
- 1 Department of Animal Science, Tibet Agricultural and Animal Husbandry College , Nyingzhi, Tibet, P.R. China
| | - Yefen Xu
- 1 Department of Animal Science, Tibet Agricultural and Animal Husbandry College , Nyingzhi, Tibet, P.R. China
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Comparative mRNA and miRNA expression in European mouflon (Ovis musimon) and sheep (Ovis aries) provides novel insights into the genetic mechanisms for female reproductive success. Heredity (Edinb) 2018; 122:172-186. [PMID: 29784930 PMCID: PMC6327046 DOI: 10.1038/s41437-018-0090-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/20/2018] [Accepted: 04/18/2018] [Indexed: 01/09/2023] Open
Abstract
Prolific breeds of domestic sheep (Ovis aries) are important genetic resources due to their reproductive performance, which is characterized by multiple lambs per birth and out-of-season breeding. However, the lack of a comprehensive understanding of the genetic mechanisms underlying the important reproductive traits, particularly from the evolutionary genomics perspective, has impeded the efficient advancement of sheep breeding. Here, for the first time, by performing RNA-sequencing we built a de novo transcriptome assembly of ovarian and endometrial tissues in European mouflon (Ovis musimon) and performed an mRNA–miRNA integrated expression profiling analysis of the wild species and a highly prolific domestic sheep breed, the Finnsheep. We identified several novel genes with differentially expressed mRNAs (e.g., EREG, INHBA, SPP1, AMH, TDRD5, and ZP2) between the wild and domestic sheep, which are functionally involved in oocyte and follicle development and fertilization, and are significantly (adjusted P-value < 0.05) enriched in the Gene Ontology (GO) terms of various reproductive process, including the regulation of fertilization, oogenesis, ovarian follicle development, and sperm–egg recognition. Additionally, we characterized 58 differentially expressed miRNAs and 210 associated target genes that are essential for the regulation of female reproduction cycles through specific regulatory networks [e.g., (miR-136, miR-374a, miR-9-5p)-(EREG, INHBA)]. Furthermore, our integrated mRNA and miRNA expression profiling analysis elucidated novel direct and indirect miRNA/mRNA causal regulatory relationships related to the reproductive traits of the Ovis species. This study provides in-depth insights into the genomic evolution underlying the reproductive traits of the Ovis species and valuable resources for ovine genomics.
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14
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Yao Y, Reheman A, Xu Y, Li Q. miR-125b Contributes to Ovarian Granulosa Cell Apoptosis Through Targeting BMPR1B, a Major Gene for Sheep Prolificacy. Reprod Sci 2018; 26:295-305. [DOI: 10.1177/1933719118770544] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Yilong Yao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Anwaier Reheman
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yefei Xu
- Department of Animal Science, College of Tibet Agricultural and Animal Husbandry, Nyingzhi, People’s Republic of China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, People’s Republic of China
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15
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Xu SS, Gao L, Xie XL, Ren YL, Shen ZQ, Wang F, Shen M, Eyϸórsdóttir E, Hallsson JH, Kiseleva T, Kantanen J, Li MH. Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds. Front Genet 2018; 9:118. [PMID: 29692799 PMCID: PMC5902979 DOI: 10.3389/fgene.2018.00118] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/23/2018] [Indexed: 12/11/2022] Open
Abstract
Reproduction is an important trait in sheep breeding as well as in other livestock. However, despite its importance the genetic mechanisms of litter size in domestic sheep (Ovis aries) are still poorly understood. To explore genetic mechanisms underlying the variation in litter size, we conducted multiple independent genome-wide association studies in five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) using the Ovine Infinium HD BeadChip, respectively. We identified different sets of candidate genes associated with litter size in different breeds: BMPR1B, FBN1, and MMP2 in Wadi; GRIA2, SMAD1, and CTNNB1 in Hu; NCOA1 in Icelandic; INHBB, NF1, FLT1, PTGS2, and PLCB3 in Finnsheep; ESR2 in Romanov and ESR1, GHR, ETS1, MMP15, FLI1, and SPP1 in Texel. Further annotation of genes and bioinformatics analyses revealed that different biological pathways could be involved in the variation in litter size of females: hormone secretion (FSH and LH) in Wadi and Hu, placenta and embryonic lethality in Icelandic, folliculogenesis and LH signaling in Finnsheep, ovulation and preovulatory follicle maturation in Romanov, and estrogen and follicular growth in Texel. Taken together, our results provide new insights into the genetic mechanisms underlying the prolificacy trait in sheep and other mammals, suggesting targets for selection where the aim is to increase prolificacy in breeding projects.
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Affiliation(s)
- Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Emma Eyϸórsdóttir
- Faculty of Natural Resources and Environmental Sciences, Agricultural University of Iceland, Borgarnes, Iceland
| | - Jón H. Hallsson
- Faculty of Natural Resources and Environmental Sciences, Agricultural University of Iceland, Borgarnes, Iceland
| | - Tatyana Kiseleva
- All-Russian Research Institute of Genetics and Farm Animal Breeding, Russian Academy of Sciences, Moscow, Russia
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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16
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Pokharel K, Peippo J, Honkatukia M, Seppälä A, Rautiainen J, Ghanem N, Hamama TM, Crowe MA, Andersson M, Li MH, Kantanen J. Integrated ovarian mRNA and miRNA transcriptome profiling characterizes the genetic basis of prolificacy traits in sheep (Ovis aries). BMC Genomics 2018; 19:104. [PMID: 29378514 PMCID: PMC5789708 DOI: 10.1186/s12864-017-4400-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 12/19/2017] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The highly prolific breeds of domestic sheep (Ovis aries) are globally valuable genetic resources for sheep industry. Genetic, nutritional and other environmental factors affect prolificacy traits in sheep. To improve our knowledge of the sheep prolificacy traits, we conducted mRNA-miRNA integrated profiling of ovarian tissues from two pure breeds with large (Finnsheep) vs. small (Texel) litter sizes and their F1 crosses, half of which were fed a flushing diet. RESULTS Among the samples, 16,402 genes (60.6% known ovine genes) were expressed, 79 novel miRNAs were found, and a cluster of miRNAs on chromosome 18 was detected. The majority of the differentially expressed genes between breeds were upregulated in the Texel with low prolificacy, owing to the flushing diet effect, whereas a similar pattern was not detected in the Finnsheep. F1 ewes responded similarly to Finnsheep rather than displaying a performance intermediate between the two pure breeds. CONCLUSIONS The identification and characterization of differentially expressed genes and miRNAs in the ovaries of sheep provided insights into genetic and environmental factors affecting prolificacy traits. The three genes (CST6, MEPE and HBB) that were differentially expressed between the group of Finnsheep and Texel ewes kept in normal diet appeared to be candidate genes of prolificacy traits and will require further validation.
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Affiliation(s)
- Kisun Pokharel
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
| | - Jaana Peippo
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
| | - Mervi Honkatukia
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
| | - Arja Seppälä
- Eastman Chemical Company, Tammasaarenkatu 1, Helsinki, Finland
| | | | - Nasser Ghanem
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Tuula-Marjatta Hamama
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
| | - Mark A. Crowe
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Magnus Andersson
- Department of Production Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute of Finland (Luke), Myllytie 1, Jokioinen, Finland
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17
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Kang L, Yang C, Wu H, Chen Q, Huang L, Li X, Tang H, Jiang Y. miR-26a-5p Regulates TNRC6A Expression and Facilitates Theca Cell Proliferation in Chicken Ovarian Follicles. DNA Cell Biol 2017; 36:922-929. [PMID: 28876086 DOI: 10.1089/dna.2017.3863] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ovarian theca cells play an indispensable role in ovarian follicular development and hormone secretion. miR-26a-5p was reported to be differentially expressed in mature and immature chicken ovaries in our previous study; however, the role of miR-26a-5p in regulating ovarian follicle function is still unclear. In this study, we demonstrated that the expression dynamics of TNRC6A mRNA in either chicken ovaries or follicles showed an opposite trend compared with that of chicken miR-26a-5p expression. miR-26a-5p inhibited TNRC6A mRNA expression by directly targeting its 3'-untranslated region in cultured chicken theca cells. Overexpression of miR-26a-5p promoted chicken follicular theca cell proliferation in vitro. Furthermore, overexpression of miR-26a-5p and knockdown of TNRC6A significantly upregulated the antiapoptotic BCL-2 gene. Taken together, this study revealed the expression dynamics of miR-26a-5p and TNRC6A in chicken ovaries and ovarian follicles and the relationship between the expression of miR-26a-5p and TNRC6A in chicken ovarian theca cells. These results suggest that miR-26a-5p facilitates chicken ovarian theca cell proliferation by targeting the TNRC6A gene.
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Affiliation(s)
- Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University , Taian, People's Republic of China
| | - Chunhong Yang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University , Taian, People's Republic of China
| | - Haizhen Wu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University , Taian, People's Republic of China
| | - Qiuyue Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University , Taian, People's Republic of China
| | - Libo Huang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University , Taian, People's Republic of China
| | - Xianyao Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University , Taian, People's Republic of China
| | - Hui Tang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University , Taian, People's Republic of China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University , Taian, People's Republic of China
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