Cassady JP, Johnson RK, Pomp D, Rohrer GA, Van Vleck LD, Spiegel EK, et al. Identification of quantitative trait loci affecting reproduction in pigs. J Anim Sci. 2001;79(3):623–33.
CAS
PubMed
Google Scholar
Li K, Ren J, Xing Y, Zhang Z, Ma J, Guo Y, et al. Quantitative trait loci for litter size and prenatal loss in a white Duroc x Chinese Erhualian resource population. Anim Genet. 2009;40(6):963–6.
CAS
PubMed
Google Scholar
Bergfelder-Drüing S, Grosse-Brinkhaus C, Lind B, Erbe M, Schellander K, Simianer H, et al. A genome-wide association study in large white and landrace pig populations for number piglets born alive. PLoS One. 2015;10(3):e0117468.
PubMed
PubMed Central
Google Scholar
Wang Y, Ding X, Tan Z, Xing K, Yang T, Wang Y, et al. Genome-wide association study for reproductive traits in a large white pig population. Anim Genet. 2018;49(3):127–31.
CAS
PubMed
PubMed Central
Google Scholar
Uzzaman MR, Park JE, Lee KT, Cho ES, Choi BH, Kim TH. A genome-wide association study of reproductive traits in a Yorkshire pig population. Livest Sci. 2018;209:67–72.
Google Scholar
Metodiev S, Thekkoot DM, Young JM, Onteru S, Rothschild MF, Dekkers JCM, et al. A whole-genome association study for litter size and litter weight traits in pigs. Livest Sci. 2018;211:87–97.
Google Scholar
Hu ZL, Park CA, Reecy JM. Developmental progress and current status of the animal QTLdb. Nucleic Acids Res. 2016;44(D1):D827–33.
CAS
PubMed
Google Scholar
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC. The transcriptional landscape of the mammalian genome. Science. 2005;309(5740):1559–63.
CAS
PubMed
Google Scholar
Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, et al. DES-ncRNA: a knowledgebase for exploring information about human micro and long noncodingRNAs based on literature-mining. RNA Biol. 2017;14(7):963–71.
PubMed
PubMed Central
Google Scholar
Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009;136(4):629–41.
CAS
PubMed
Google Scholar
Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Pulido TH, Guigo R, Johnson R. LncATLAS database for subcellular localization of long noncoding RNAs. RNA. 2017;23(7):1080–7.
CAS
PubMed
PubMed Central
Google Scholar
Hu G, Niu F, Humburg BA, Liao K, Bendi VS, Callen S, et al. Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis. Oncotarget. 2018;9(26):18648–63.
PubMed
PubMed Central
Google Scholar
Beiki H, Liu H, Huang J, Manchanda N, Nonneman D, Smith TPL, et al. Improved annotation of the domestic pig genome through integration of iso-seq and rna-seq data. BMC Genomics. 2019;20(1):344.
CAS
PubMed
PubMed Central
Google Scholar
Gong QY, Su GF. Roles of miRNAs and long noncoding RNAs in the progression of diabetic retinopathy. Biosci Rep. 2017;37(6):BSR20171157.
CAS
PubMed
PubMed Central
Google Scholar
Van Roosbroeck K, Pollet J, Calin GA. miRNAs and long noncoding RNAs as biomarkers in human diseases. Expert Rev Mol Diagn. 2013;13(2):183–204.
PubMed
Google Scholar
Pradeepa MM, McKenna F, Taylor GC, Bengani H, Grimes GR, Wood AJ, et al. Psip1/p52 regulates posterior Hoxa genes through activation of lncRNA Hottip. PLoS Genet. 2017;13(4):e1006677.
PubMed
PubMed Central
Google Scholar
Yan ZQ, Huang XY, Sun WY, Yang QL, Shi HR, Jiang TT, et al. Analyses of long non-coding RNA and mRNA profiling in the spleen of diarrheic piglets caused by Clostridium perfringens type C. Peer J. 2018;6:e5997.
PubMed
PubMed Central
Google Scholar
Tao H, Zhang JG, Qin RH, Dai C, Shi P, Yang JJ, et al. LncRNA GAS5 controls cardiac fibroblast activation and fibrosis by targeting miR-21 via PTEN/MMP-2 signaling pathway. Toxicology. 2017;386:11–8.
CAS
PubMed
Google Scholar
Li Y, Chen X, Sun H, Wang H. Long non-coding RNAs in the regulation of skeletal myogenesis and muscle diseases. Cancer Lett. 2018;417:58–64.
CAS
PubMed
Google Scholar
Song YX, Sun JX, Zhao JH, Yang YC, Shi JX, Wu ZH, et al. Non-coding RNAs participate in the regulatory network of CLDN4 via ceRNA mediated miRNA evasion. Nat Commun. 2017;8(1):289.
PubMed
PubMed Central
Google Scholar
Liang H, Yu T, Han Y, Jiang H, Wang C, You T, et al. LncRNA PTAR promotes EMT and invasion-metastasis in serous ovarian cancer by competitively binding miR-101-3p to regulate ZEB1 expression. Mol Cancer. 2018;17(1):119.
PubMed
PubMed Central
Google Scholar
Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta stone of a hidden RNA language? Cell. 2011;146(3):353–8.
CAS
PubMed
PubMed Central
Google Scholar
Miao XY, Luo QM, Zhao HJ, Qin XY. Ovarian transcriptomic study reveals the differential regulation of miRNAs and lncRNAs related to fecundity in different sheep. Sci Rep. 2016;6:35299.
CAS
PubMed
PubMed Central
Google Scholar
Li MZ, Liu YK, Wang T, Guan JQ, Luo ZG, Chen HS, et al. Repertoire of porcine microRNAs in adult ovary and testis by deep sequencing. Int J Biol Sci. 2011;7(7):1045–55.
CAS
PubMed
PubMed Central
Google Scholar
Huang L, Yin ZJ, Feng YF, Zhang XD, Wu T, Ding YY, et al. Identification and differential expression of microRNAs in theovaries of pigs (Sus scrofa) with high and low litter sizes. Anim Genet. 2016;47(5):543–51.
CAS
PubMed
Google Scholar
Miao XY, Luo QM, Zhao HJ, Qin XY. Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu black goats to explore the regulation of fecundity. Sci Rep. 2016;6:37983.
CAS
PubMed
PubMed Central
Google Scholar
Tang Z, Wu Y, Yang Y, Yang YT, Wang Z, Yuan J, et al. Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expressionpatterns and evolutional conservation in Sus scrofa. Sci Rep. 2017;7:43166.
CAS
PubMed
PubMed Central
Google Scholar
Liu Y, Li M, Bo X, Li T, Ma L, Zhai T, et al. Systematic analysis of long non-coding RNAs and mRNAs in the ovaries of Duroc pigs during different follicular stages using RNA sequencing. Int J Mol Sci. 2018;19(6):E1722.
PubMed
Google Scholar
Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conservedmulti-exonic structure of lincRNAs. Nat Biotechnol. 2010;28(5):503–10.
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, Xue S, Liu X, Liu H, Hu T, Qiu X, et al. Analyses of long non-coding RNA and mRNA profiling using RNA sequencing during the pre-implantation phases in pig endometrium. Sci Rep. 2016;6:20238.
CAS
PubMed
PubMed Central
Google Scholar
Ponjavic J, Oliver PL, Lunter G, Ponting CP. Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet. 2009;5(8):e1000617.
PubMed
PubMed Central
Google Scholar
Rajewsky N. microRNA target predictions in animals. Nat Genet. 2006;38:S8–13.
CAS
PubMed
Google Scholar
Sun XJ, Mei SQ, Tao H, Wang GD, Su Li N, Jiang SW, et al. Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and large white sows. BMC Genomics. 2011;12:111.
CAS
PubMed
PubMed Central
Google Scholar
Zhang X, Huang L, Wu T, Feng Y, Ding Y, Ye P, et al. Transcriptomic analysis of ovaries from pigs with high and low litter size. PLoS One. 2015;10:e0139514.
PubMed
PubMed Central
Google Scholar
Shen Y, Mao H, Huang M, Chen L, Chen J, Cai Z, et al. Long noncoding RNA and mRNA expression profiles in the thyroid gland of two phenotypically extreme pig breeds using Ribo-zero RNA sequencing. Genes. 2016;7(7):34.
PubMed Central
Google Scholar
Zhao W, Mu Y, Ma L, Wang C, Tang Z, Yang S, et al. Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development. Sci Rep. 2015;5:8957.
CAS
PubMed
PubMed Central
Google Scholar
Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, et al. An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res. 2015;43(D1):D174–80.
CAS
PubMed
Google Scholar
Kang L, Cui X, Zhang Y, Yang C, Jiang Y. Identification of miRNAs associated with sexual maturity in chicken ovary by Illumina small RNA deep sequencing. BMC Genomics. 2013;14:352.
CAS
PubMed
PubMed Central
Google Scholar
Hsueh AJ, Kawamura K, Cheng Y, Fauser BC. Intraovarian control of early Folliculogenesis. Endocr Rev. 2015;36(1):1–24.
CAS
PubMed
Google Scholar
Li N, Guo XR, Liu L, Wang L, Cheng R. Molecular mechanism of miR-204 regulates proliferation, apoptosis and autophagy of cervical cancer cells by targeting ATF2. Artif Cells. 2019;47:2529–35.
Google Scholar
Yang L, Du X, Liu L, Cao Q, Pan Z, Li Q. miR-1306 mediates the feedback regulation of the TGF-β/SMAD signaling pathway in Granulosa cells. Cells. 2019;8:E298.
PubMed
Google Scholar
Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014;505(7483):344–52.
CAS
PubMed
PubMed Central
Google Scholar
Fang BJ, Li GL, Xu CF, Hui YZ, Li G. MicroRNA miR-1249 downregulates adenomatous polyposis coli 2 expression and promotes glioma cells proliferation. Am J Transl Res. 2018;10(5):1324–36.
CAS
PubMed
PubMed Central
Google Scholar
Fagerlind M, Stalhammar H, Olsson B, Klinga-Levan K. Expression of miRNAs in bull spermatozoa correlates with fertility rates. Reprod Domest Anim. 2015;50(4):587–94.
CAS
PubMed
Google Scholar
McDaneld TG, Kuehn LA, Thomas MG, Snelling WM, SmithE TP, Pollak EJ, et al. Genome wide association study of reproductive efficiency in female cattle. J Anim Sci. 2014;92(5):1945–57.
CAS
PubMed
Google Scholar
Sahu DK, Panda SP, Meher PK, Das P, Routray P, Sundaray JK, et al. Construction, De-novo assembly and analysis of Transcriptome for identification of reproduction-related genes and pathways from Rohu, Labeo rohita (Hamilton). PLoS One. 2015;10(7):e0132450.
PubMed
PubMed Central
Google Scholar
Buaas FW, Lee K, Edelhoff S, Disteche C, Braun RE. Cloning and characterization of the mouse interleukin enhancer binding factor 3 (Ilf3) homolog in a screen for RNA binding proteins. Mamm Genome. 1999;10(5):451–6.
CAS
PubMed
Google Scholar
Groh KJ, Nesatyy VJ, Segner H, Eggen RI, Suter MJ. Global proteomics analysis of testis and ovary in adult zebrafish (danio rerio). Fish Physiol Biochem. 2011;37(3):619–47.
CAS
PubMed
PubMed Central
Google Scholar
Groh KJ, Schönenberger R, Eggen RI, Segner H, Suter MJ. Analysis of protein expression in zebrafish during gonad differentiation by targeted proteomics. Gen Comp Endocrinol. 2013;193:210–20.
CAS
PubMed
Google Scholar
Li HS, Wang D, Shen Q, Schonemann MD, Gorski JA, Jones KR, et al. Inactivation of numb and numblike in embryonic dorsal forebrain impairs neurogenesis and disrupts cortical morphogenesis. Neuron. 2003;40(6):1105–18.
CAS
PubMed
Google Scholar
Jing J, Jiang X, Chen J, Yao X, Zhao M, Li P, et al. Notch signaling pathway promotes the development of ovine ovarian follicular granulosa cells. Anim Reprod Sci. 2017;181:69–78.
CAS
PubMed
Google Scholar
Lin YT, Barske L, DeFalco T, Capel B. Numb regulates somatic cell lineage commitment during early gonadogenesis in mice. Development. 2017;144(9):1607–18.
CAS
PubMed
PubMed Central
Google Scholar
Knapczyk-Stwora K, Grzesiak M, Witek P, Duda M, Koziorowski M, Slomczynska M. Neonatal exposure to agonists and antagonists of sex steroid receptors induces changes in the expression of oocyte-derived growth factors and their receptors in ovarian follicles in gilts. Theriogenology. 2019;134:42–52.
CAS
PubMed
Google Scholar
Li EL, Xie XH, Xu YF, Xie Z, Chen L, Liu HL, et al. Relationship between the mRNA expression level of TGF-β receptor genes in tissues and ovulation rate in Hu sheep. Agric Sci China. 2010;9:1659–66.
CAS
Google Scholar
Atli MO, Guzeloglu A, Dinc DA. Expression of wingless type (WNT) genes and their antagonists at mRNA levels in equine endometrium during the estrous cycle and early pregnancy. Anim Reprod Sci. 2011;125(1–4):94–102.
CAS
PubMed
Google Scholar
Zavareh S, Gholizadeh Z, Lashkarbolouki T. Evaluation of changes in the expression of Wnt/β-catenin target genes in mouse reproductive tissues during estrous cycle: an experimental study. Int J Reprod Biomed (Yazd). 2018;16(2):69–76.
CAS
Google Scholar
Shi B, Liu X, Thomas P, Pang Y, Xu Y, Li X, et al. Identification and characterization of a progestin and adipoQ receptor (PAQR) structurally relatedto Paqr7 in the ovary of Cynoglossus semilaevis and its potential role in regulating oocytematuration. Gen Comp Endocrinol. 2016;237:109–20.
CAS
PubMed
Google Scholar
Haouzi D, Assou S, Monzo C, Vincens C, Dechaud H, Hamamah S. Altered gene expression profile in cumulus cells of mature MII oocytes from patients with polycystic ovary syndrome. Hum Reprod. 2012;27(12):3523–30.
CAS
PubMed
Google Scholar
Hu HY, Jia Q, Zhou B, Zhang J, Li ZQ, Liu ZW. Comparative analysis of the ovarian transcriptome reveals novel insights into fertility differences in large white sows. Genes Genom. 2020;42(7):715–25.
CAS
Google Scholar
Hu HY, Xi JZ, Zhou B, Zhang J, Li ZQ, Liu ZW, et al. Ovarian circular RNAs associated with high and low fertility in large white sows during the follicular and luteal phases of the estrous cycle. Animals. 2020;10(4):696.
PubMed Central
Google Scholar
Soede NM, Langendijk P, Kemp B. Reproductive cycles in pigs. Anim ReprodSci. 2011;124(3–4):251–8.
CAS
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621–8.
CAS
PubMed
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
CAS
PubMed
PubMed Central
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
PubMed
PubMed Central
Google Scholar
Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, et al. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol. 2008;26(4):407–15.
PubMed
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–504.
CAS
PubMed
PubMed Central
Google Scholar
Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, et al. CPC: assess the protein-codingpotential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007;35:W345–9.
PubMed
PubMed Central
Google Scholar
Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C, et al. Utilizing sequenceintrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 2013;41(17):e166.
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W. CPAT: coding-potential assessment tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013;41(6):e74.
CAS
PubMed
PubMed Central
Google Scholar
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, et al. The Pfam protein families database. Nucleic Acids Res. 2002;30:276–80.
CAS
PubMed
PubMed Central
Google Scholar
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15(8):1034–50.
CAS
PubMed
PubMed Central
Google Scholar
Carmona S, Lin B, Chou T, Arroyo K, Sun S. LncRNA Jpx induces Xist expression in mice using both trans and cis mechanisms. PLoS Genet. 2018;14(5):e1007378.
PubMed
PubMed Central
Google Scholar
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C (T)) method. Methods. 2001;25(4):402–8.
CAS
PubMed
Google Scholar