{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T20:19:44Z","timestamp":1790885984651,"version":"4.1.0"},"reference-count":97,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2020,8,25]],"date-time":"2020-08-25T00:00:00Z","timestamp":1598313600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2015\/22276-3"],"award-info":[{"award-number":["2015\/22276-3"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2017\/14707-0"],"award-info":[{"award-number":["2017\/14707-0"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2014\/07566-2"],"award-info":[{"award-number":["2014\/07566-2"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and\/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.<\/jats:p>","DOI":"10.3390\/genes11090997","type":"journal-article","created":{"date-parts":[[2020,8,25]],"date-time":"2020-08-25T10:48:24Z","timestamp":1598352504000},"page":"997","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0649-7033","authenticated-orcid":false,"given":"P\u00e2mela A.","family":"Alexandre","sequence":"first","affiliation":[{"name":"Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil"},{"name":"Commonwealth Scientific and Industrial Research Organization, Agriculture &amp; Food, St. Lucia, Brisbane, QLD 4067, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Reverter","sequence":"additional","affiliation":[{"name":"Commonwealth Scientific and Industrial Research Organization, Agriculture &amp; Food, St. Lucia, Brisbane, QLD 4067, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberta B.","family":"Berezin","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laercio R.","family":"Porto-Neto","sequence":"additional","affiliation":[{"name":"Commonwealth Scientific and Industrial Research Organization, Agriculture &amp; Food, St. Lucia, Brisbane, QLD 4067, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela","family":"Ribeiro","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miguel H. A.","family":"Santana","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Bento S.","family":"Ferraz","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heidge","family":"Fukumasu","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,8,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Salviano-Silva, A., Lobo-Alves, S., Almeida, R., Malheiros, D., and Petzl-Erler, M. (2018). Besides pathology: Long non-coding RNA in cell and tissue homeostasis. Non-Coding RNA, 4.","DOI":"10.3390\/ncrna4010003"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1111\/age.12493","article-title":"Mining long noncoding RNA in livestock","volume":"48","author":"Weikard","year":"2017","journal-title":"Anim. Genet."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/s10142-016-0524-x","article-title":"Long noncoding RNA (lincRNA), a new paradigm in gene expression control","volume":"17","author":"Deniz","year":"2017","journal-title":"Funct. Integr. Genom."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nrg.2015.10","article-title":"Unique features of long non-coding RNA biogenesis and function","volume":"17","author":"Quinn","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1016\/j.cell.2013.02.012","article-title":"Long noncoding RNAs: Cellular address codes in development and disease","volume":"152","author":"Batista","year":"2013","journal-title":"Cell"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"11061","DOI":"10.3168\/jds.2018-14900","article-title":"Integrated analysis of long noncoding RNA and mRNA expression profiles reveals the potential role of long noncoding RNA in different bovine lactation stages","volume":"101","author":"Zheng","year":"2018","journal-title":"J. Dairy Sci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1780","DOI":"10.1111\/febs.14783","article-title":"A novel long non-coding RNA regulates the immune response in MAC\u2014T cells and contributes to bovine mastitis","volume":"286","author":"Wang","year":"2019","journal-title":"FEBS J."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Tong, C., Chen, Q., Zhao, L., Ma, J., Ibeagha-Awemu, E.M., and Zhao, X. (2017). Identification and characterization of long intergenic noncoding RNAs in bovine mammary glands. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3858-4"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2835","DOI":"10.1016\/j.bbamcr.2016.08.014","article-title":"The developmental transcriptome sequencing of bovine skeletal muscle reveals a long noncoding RNA, lncMD, promotes muscle differentiation by sponging miR-125b","volume":"1863","author":"Sun","year":"2016","journal-title":"Biochim. Biophys. Acta. Mol. Cell Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1080\/10495398.2018.1521337","article-title":"Identification and analysis of differentially expressed long non-coding RNAs of Chinese Holstein cattle responses to heat stress","volume":"31","author":"Li","year":"2020","journal-title":"Anim. Biotechnol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/s11259-020-09769-w","article-title":"Genome-wide identification and characterization of novel long non-coding RNA in Ruminal tissue affected with sub-acute Ruminal acidosis from Holstein cattle","volume":"44","author":"Mahmoudi","year":"2020","journal-title":"Vet. Res. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"646","DOI":"10.3389\/fgene.2019.00646","article-title":"Analysis of Long Non-Coding RNA and mRNA expression profiling in immature and mature bovine (Bos taurus) testes","volume":"10","author":"Gao","year":"2019","journal-title":"Front. Genet."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Tizioto, P.C., Coutinho, L.L., Decker, J.E., Schnabel, R.D., Rosa, K.O., Oliveira, P.S., Souza, M.M., Mour\u00e3o, G.B., Tullio, R.R., and Chaves, A.S. (2015). Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes. BMC Genom., 16.","DOI":"10.1186\/s12864-015-1464-x"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3331","DOI":"10.2527\/jas.2015-8975","article-title":"Transcriptomic analysis by RNA sequencing reveals that hepatic interferon-induced genes may be associated with feed efficiency in beef heifers","volume":"93","author":"Paradis","year":"2015","journal-title":"J. Anim. Sci."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1111\/j.1365-2052.2011.02182.x","article-title":"Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake","volume":"42","author":"Chen","year":"2011","journal-title":"Anim. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0152274","article-title":"Identification of Gene networks for residual feed intake in Angus cattle using genomic prediction and RNA-seq","volume":"11","author":"Weber","year":"2016","journal-title":"PLoS ONE"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"189","DOI":"10.3389\/fgene.2020.00189","article-title":"Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses","volume":"11","author":"Koltes","year":"2020","journal-title":"Front. Genet."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Koufariotis, L.T., Chen, Y.-P.P.P., Chamberlain, A., Vander Jagt, C., and Hayes, B.J. (2015). A catalogue of novel bovine long noncoding RNA across 18 tissues. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0141225"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1016\/j.tig.2016.08.004","article-title":"Computational approaches for functional prediction and characterisation of long noncoding RNAs","volume":"32","author":"Signal","year":"2016","journal-title":"Trends Genet."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.3389\/fgene.2019.01130","article-title":"Biological network approach for the identification of regulatory long non-coding RNAs associated with metabolic efficiency in cattle","volume":"10","author":"Nolte","year":"2019","journal-title":"Front. Genet."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Nolte, W., Weikard, R., Brunner, R.M., Albrecht, E., Hammon, H.M., Reverter, A., and K\u00fchn, C. (2020). Identification and annotation of potential function of regulatory antisense long non-coding RNAs related to feed efficiency in bos taurus bulls. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21093292"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Porto-Neto, L.R., Sonstegard, T.S., Liu, G.E., Bickhart, D.M., Da Silva, M.V.B., Machado, M.A., Utsunomiya, Y.T., Garcia, J.F., Gondro, C., and Van Tassell, C.P. (2013). Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. BMC Genom., 14.","DOI":"10.1186\/1471-2164-14-876"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1111\/age.12836","article-title":"Genomic clues of the evolutionary history of Bos indicus cattle","volume":"50","author":"Utsunomiya","year":"2019","journal-title":"Anim. Genet."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/s12711-020-00546-6","article-title":"Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB","volume":"52","author":"Cardoso","year":"2020","journal-title":"Genet. Sel. Evol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"230","DOI":"10.3389\/fgene.2019.00230","article-title":"Systems biology reveals NR2F6 and TGFB1 as key regulators of feed efficiency in beef cattle","volume":"10","author":"Alexandre","year":"2019","journal-title":"Front. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"486","DOI":"10.2527\/jas1963.222486x","article-title":"Efficiency of feed use in beef cattle","volume":"22","author":"Koch","year":"1963","journal-title":"J. Anim. Sci."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Alexandre, P.A., Kogelman, L.J.A., Santana, M.H.A., Passarelli, D., Pulz, L.H., Fantinato-Neto, P., Silva, P.L., Leme, P.R., Strefezzi, R.F., and Coutinho, L.L.L. (2015). Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle. BMC Genom., 16.","DOI":"10.1186\/s12864-015-2292-8"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1543","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: Ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1007\/978-1-4939-3167-5_18","article-title":"Analysis of RNA-Seq data using TopHat and cufflinks","volume":"1374","author":"Ghosh","year":"2016","journal-title":"Methods Mol. Biol."},{"key":"ref_31","unstructured":"Trapnell, C. (2020, April 29). Tracking Transfrags through Multiple Samples. Available online: http:\/\/cole-trapnell-lab.github.io\/cufflinks\/cuffcompare\/#tracking-transfrags-through-multiple-samples-outprefixtracking."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","article-title":"EMBOSS: The European molecular biology open software suite","volume":"16","author":"Rice","year":"2000","journal-title":"Trends Genet."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1261\/rna.029520.111","article-title":"Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3\u2032 UTRs","volume":"18","author":"Niazi","year":"2012","journal-title":"RNA"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10.","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"W12","DOI":"10.1093\/nar\/gkx428","article-title":"CPC2: A fast and accurate coding potential calculator based on sequence intrinsic features","volume":"45","author":"Kang","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nbt.2450","article-title":"Differential analysis of gene regulation at transcript resolution with RNA-seq","volume":"31","author":"Trapnell","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"D308","DOI":"10.1093\/nar\/gkx1107","article-title":"NONCODEV5: A comprehensive annotation database for long non-coding RNAs","volume":"46","author":"Fang","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2003-5-1-r1","article-title":"MicroRNA targets in drosophila","volume":"5","author":"Enright","year":"2003","journal-title":"Genome Biol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3429","DOI":"10.1093\/nar\/gkg599","article-title":"Vienna RNA secondary structure server","volume":"31","author":"Hofacker","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: A Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"C\u00e1novas, A., Reverter, A., DeAtley, K.L., Ashley, R.L., Colgrave, M.L., Fortes, M.R.S., Islas-Trejo, A., Lehnert, S., Porto-Neto, L., and Rinc\u00f3n, G. (2014). Multi-Tissue omics analyses reveal molecular regulatory networks for puberty in composite beef cattle. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0102551"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/nrg2538","article-title":"A census of human transcription factors: Function, expression and evolution","volume":"10","author":"Vaquerizas","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Heberle, H., Meirelles, V.G., da Silva, F.R., Telles, G.P., and Minghim, R. (2015). InteractiVenn: A web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics, 16.","DOI":"10.1186\/s12859-015-0611-3"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1093\/bioinformatics\/btq051","article-title":"Regulatory impact factors: Unraveling the transcriptional regulation of complex traits from expression data","volume":"26","author":"Reverter","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Hudson, N.J., Dalrymple, B.P., and Reverter, A. (2012). Beyond differential expression: The quest for causal mutations and effector molecules. BMC Genom., 13.","DOI":"10.1186\/1471-2164-13-356"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"D871","DOI":"10.1093\/nar\/gks1150","article-title":"Animal QTLdb: An improved database tool for livestock animal QTL\/association data dissemination in the post-genome era","volume":"41","author":"Hu","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"2491","DOI":"10.1093\/bioinformatics\/btn482","article-title":"Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks","volume":"24","author":"Reverter","year":"2008","journal-title":"Bioinformatics"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"W110","DOI":"10.1093\/nar\/gkw345","article-title":"MiEAA: MicroRNA enrichment analysis and annotation","volume":"44","author":"Backes","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/BF00818163","article-title":"Fast folding and comparison of RNA secondary structures","volume":"125","author":"Hofacker","year":"1989","journal-title":"Mon. Chem. Chem. Mon."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"W741","DOI":"10.1093\/nar\/gki475","article-title":"WebGestalt: An integrated system for exploring gene sets in various biological contexts","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Kosinska-Selbi, B., Mielczarek, M., and Szyda, J. (2020). Review: Long non-coding RNA in livestock. Animal, 1\u201311.","DOI":"10.1017\/S1751731120000841"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Kern, C., Wang, Y., Chitwood, J., Korf, I., Delany, M., Cheng, H., Medrano, J.F., Van Eenennaam, A.L., Ernst, C., and Ross, P. (2018). Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genom., 19.","DOI":"10.1186\/s12864-018-5037-7"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s13059-020-1931-9","article-title":"The deep genome project","volume":"21","author":"Lloyd","year":"2020","journal-title":"Genome Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"7303","DOI":"10.1038\/s41598-018-25605-3","article-title":"Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle","volume":"8","author":"Mukiibi","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Salleh, M.S., Mazzoni, G., H\u00f6glund, J.K., Olijhoek, D.W., Lund, P., L\u00f8vendahl, P., and Kadarmideen, H.N. (2017). RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3622-9"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2141","DOI":"10.2527\/jas.2012-6053","article-title":"Intestinal integrity, endotoxin transport and detoxification in pigs divergently selected for residual feed intake","volume":"91","author":"Mani","year":"2013","journal-title":"J. Anim. Sci."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1038\/s41598-017-19072-5","article-title":"Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs","volume":"8","author":"Ballester","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1111\/asj.12159","article-title":"Analysis of biological networks and biological pathways associated with residual feed intake in beef cattle","volume":"85","author":"Karisa","year":"2014","journal-title":"Anim. Sci. J."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.livsci.2012.02.012","article-title":"Feed efficiency and its correlations with carcass traits measured by ultrasound in Nellore bulls","volume":"145","author":"Santana","year":"2012","journal-title":"Livest. Sci."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.livsci.2012.09.012","article-title":"Feedlot performance, feed efficiency reranking, carcass traits, body composition, energy requirements, meat quality and calpain system activity in Nellore steers with low and high residual feed intake","volume":"150","author":"Gomes","year":"2012","journal-title":"Livest. Sci."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"189","DOI":"10.4141\/A02-065","article-title":"Residual feed intake and body composition in young growing cattle","volume":"83","author":"Basarab","year":"2003","journal-title":"Can. J. Anim. Sci."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.2527\/jas.2008-0914","article-title":"Relationships among measures of growth performance and efficiency with carcass traits, visceral organ mass, and pancreatic digestive enzymes in feedlot cattle","volume":"87","author":"Mader","year":"2009","journal-title":"J. Anim. Sci."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1007\/s00281-011-0280-x","article-title":"Interactions between coagulation and complement\u2014Their role in inflammation","volume":"34","author":"Oikonomopoulou","year":"2012","journal-title":"Semin. Immunopathol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"39493","DOI":"10.1038\/srep39493","article-title":"Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake","volume":"6","author":"Tizioto","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"11953","DOI":"10.1038\/srep11953","article-title":"Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs","volume":"5","author":"Jing","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"650","DOI":"10.3389\/fgene.2020.00650","article-title":"Genome regulation and gene interaction networks inferred from muscle transcriptome underlying feed efficiency in pigs","volume":"11","author":"Carmelo","year":"2020","journal-title":"Front. Genet."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Fukumasu, H., Santana, M.H., Alexandre, P.A., and Ferraz, J.B.S. (2016). Systems Biology Application in Feed Efficiency in Beef Cattle, Springer.","DOI":"10.1007\/978-3-319-43332-5_4"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Gondret, F., Vincent, A., Hou\u00e9e-Bigot, M., Siegel, A., Lagarrigue, S., Causeur, D., Gilbert, H., and Louveau, I. (2017). A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3639-0"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1210\/en.2002-220983","article-title":"Translational control of protein synthesis in muscle and liver of growth hormone-treated pigs","volume":"144","author":"Bush","year":"2003","journal-title":"Endocrinology"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"928","DOI":"10.2527\/jas.2006-373","article-title":"Growth, carcass quality, and protein and energy metabolism in beef cattle with different growth potentials and residual feed intakes","volume":"85","author":"Paulino","year":"2007","journal-title":"J. Anim. Sci."},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Widmann, P., Reverter, A., Weikard, R., Suhre, K., Hammon, H.M., Albrecht, E., and Kuehn, C. (2015). Systems biology analysis merging phenotype, metabolomic and genomic data identifies Non-SMC Condensin I Complex, Subunit G (NCAPG) and cellular maintenance processes as major contributors to genetic variability in Bovine feed efficiency. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0124574"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"14016","DOI":"10.1038\/ncomms14016","article-title":"Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD","volume":"8","author":"Yu","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"14718","DOI":"10.1038\/ncomms14718","article-title":"Lnc-mg is a long non-coding RNA that promotes myogenesis","volume":"8","author":"Zhu","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.gene.2018.05.114","article-title":"Identification of a novel antisense long non-coding RNA PLA2G16-AS that regulates the expression of PLA2G16 in pigs","volume":"671","author":"Liu","year":"2018","journal-title":"Gene"},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Zhan, S., Dong, Y., Zhao, W., Guo, J., Zhong, T., Wang, L., Li, L., and Zhang, H. (2016). Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. BMC Genom., 17.","DOI":"10.1186\/s12864-016-3009-3"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41419-019-1399-2","article-title":"Long non-coding RNA Irm enhances myogenic differentiation by interacting with MEF2D","volume":"10","author":"Sui","year":"2019","journal-title":"Cell Death Dis."},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"C\u00f4nsolo, N.R.B., Da Silva, J., Buarque, V.L.M., Higuera-Padilla, A., Barbosa, L.C.G.S., Zawadzki, A., Colnago, L.A., Saran Netto, A., Gerrard, D.E., and Silva, S.L. (2020). Selection for growth and precocity alters muscle metabolism in nellore cattle. Metabolites, 10.","DOI":"10.3390\/metabo10020058"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"2147","DOI":"10.2527\/jas.2006-764","article-title":"Genetic and phenotypic relationships of serum leptin concentration with performance, efficiency of gain, and carcass merit of feedlot cattle","volume":"85","author":"Nkrumah","year":"2007","journal-title":"J. Anim. Sci."},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Widmann, P., Reverter, A., Fortes, M.R.S., Weikard, R., Suhre, K., Hammon, H., Albrecht, E., and Kuehn, C. (2013). A systems biology approach using metabolomic data reveals genes and pathways interacting to modulate divergent growth in cattle. BMC Genom., 14.","DOI":"10.1186\/1471-2164-14-798"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1152\/physiolgenomics.00021.2018","article-title":"Feed-efficient pigs exhibit molecular patterns allowing a timely circulation of hormones and nutrients","volume":"50","author":"Reyer","year":"2018","journal-title":"Physiol. Genom."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s12711-019-0490-6","article-title":"Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs","volume":"51","author":"Ballester","year":"2019","journal-title":"Genet. Sel. Evol."},{"key":"ref_83","first-page":"1","article-title":"Neuronal signal transduction-involved genes in pig hypothalamus affect feed efficiency as revealed by transcriptome analysis","volume":"2018","author":"Hou","year":"2018","journal-title":"Biomed Res. Int."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1016\/j.domaniend.2011.01.005","article-title":"Temperament and hypothalamic-pituitary-adrenal axis function are related and combine to affect growth, efficiency, carcass, and meat quality traits in Brahman steers","volume":"40","author":"Cafe","year":"2011","journal-title":"Domest. Anim. Endocrinol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"109","DOI":"10.2527\/jas.2009-2196","article-title":"Effect of divergence in residual feed intake on feeding behavior, blood metabolic variables, and body composition traits in growing beef heifers","volume":"88","author":"Kelly","year":"2010","journal-title":"J. Anim. Sci."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1071\/EA02219","article-title":"Metabolic differences in Angus steers divergently selected for residual feed intake","volume":"44","author":"Richardson","year":"2004","journal-title":"Aust. J. Exp. Agric."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.domaniend.2015.12.007","article-title":"Leptin concentrations in finishing beef steers and heifers and their association with dry matter intake, average daily gain, feed efficiency, and body composition","volume":"55","author":"Foote","year":"2016","journal-title":"Domest. Anim. Endocrinol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"3069","DOI":"10.2527\/jas.2008-1268","article-title":"Genetic associations of residual feed intake with serum insulin-like growth factor-I and leptin concentrations, meat quality, and carcass cross sectional fat area ratios in Duroc pigs","volume":"87","author":"Hoque","year":"2009","journal-title":"J. Anim. Sci."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.2527\/jas.2013-7020","article-title":"Effect of residual feed intake on hypothalamic gene expression and meat quality in Angus-sired cattle grown during the hot season1,2","volume":"92","author":"Perkins","year":"2014","journal-title":"J. Anim. Sci."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"549","DOI":"10.2527\/jas.2013-7019","article-title":"Residual feed intake studies in Angus-sired cattle reveal a potential role for hypothalamic gene expression in regulating feed efficiency1,2","volume":"92","author":"Perkins","year":"2014","journal-title":"J. Anim. Sci."},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Barrett, J., Canning, B., Dombrowsky, E., Douglas, S., Fong, T., Heyward, C., Leeman, S., and Remeshwar, P. (2019). Tachykinin receptors (version 2019.4) in the IUPHAR\/BPS Guide to pharmacology database. IUPHAR\/BPS Guid. Pharm., 2019.","DOI":"10.2218\/gtopdb\/F62\/2019.4"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.tics.2010.11.001","article-title":"Reward, dopamine and the control of food intake: Implications for obesity","volume":"15","author":"Volkow","year":"2011","journal-title":"Trends Cogn. Sci."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.pbb.2013.06.011","article-title":"Oxytocin, motivation and the role of dopamine","volume":"119","author":"Love","year":"2014","journal-title":"Pharm. Biochem. Behav."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1016\/j.biopsych.2012.09.001","article-title":"Dual Roles of Dopamine in food and drug seeking","volume":"73","author":"Wise","year":"2013","journal-title":"Biol. Psychiatry"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"14666","DOI":"10.1074\/jbc.M113.537258","article-title":"Hepatic scavenger receptor bi protects against polymicrobial-induced sepsis through promoting LPS clearance in mice","volume":"289","author":"Guo","year":"2014","journal-title":"J. Biol. Chem."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"3117","DOI":"10.3390\/ijms12053117","article-title":"Inflammation, oxidative stress, and obesity","volume":"12","author":"Bautista","year":"2011","journal-title":"Int. J. Mol. Sci."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/nrendo.2015.48","article-title":"Hypothalamic innate immune reaction in obesity","volume":"11","author":"Heppner","year":"2015","journal-title":"Nat. Rev. Endocrinol."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/11\/9\/997\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:06:34Z","timestamp":1760177194000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/11\/9\/997"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,8,25]]},"references-count":97,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2020,9]]}},"alternative-id":["genes11090997"],"URL":"https:\/\/doi.org\/10.3390\/genes11090997","relation":{"has-preprint":[{"id-type":"doi","id":"10.20944\/preprints202007.0711.v1","asserted-by":"object"}]},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,8,25]]}}}