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Article

Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

1
Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil
2
Commonwealth Scientific and Industrial Research Organization, Agriculture & Food, St. Lucia, Brisbane, QLD 4067, Australia
3
Department of Animal Science, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil
*
Author to whom correspondence should be addressed.
Genes 2020, 11(9), 997; https://doi.org/10.3390/genes11090997
Received: 29 July 2020 / Revised: 19 August 2020 / Accepted: 21 August 2020 / Published: 25 August 2020
(This article belongs to the Special Issue Genetics and Genomics Applied to Livestock Production)
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. View Full-Text
Keywords: Bos indicus; co-expression network; residual feed intake; RNA-Seq Bos indicus; co-expression network; residual feed intake; RNA-Seq
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MDPI and ACS Style

Alexandre, P.A.; Reverter, A.; Berezin, R.B.; Porto-Neto, L.R.; Ribeiro, G.; Santana, M.H.A.; Ferraz, J.B.S.; Fukumasu, H. Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle. Genes 2020, 11, 997. https://doi.org/10.3390/genes11090997

AMA Style

Alexandre PA, Reverter A, Berezin RB, Porto-Neto LR, Ribeiro G, Santana MHA, Ferraz JBS, Fukumasu H. Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle. Genes. 2020; 11(9):997. https://doi.org/10.3390/genes11090997

Chicago/Turabian Style

Alexandre, Pâmela A., Antonio Reverter, Roberta B. Berezin, Laercio R. Porto-Neto, Gabriela Ribeiro, Miguel H. A. Santana, José Bento S. Ferraz, and Heidge Fukumasu. 2020. "Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle" Genes 11, no. 9: 997. https://doi.org/10.3390/genes11090997

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