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Prune homolog 2 with BCH domain (PRUNE2) gene expression is associated with feed efficiency-related traits in Nelore steers

Abstract

Animal feeding is a critical factor in increasing producer profitability. Improving feed efficiency can help reduce feeding costs and reduce the environmental impact of beef production. Candidate genes previously identified for this trait in differential gene expression studies (e.g., case–control studies) have not examined continuous gene-phenotype variation, which is a limitation. The aim of this study was to investigate the association between the expression of five candidate genes in the liver, measured by quantitative real-time PCR and feed-related traits. We adopted a linear mixed model to associate liver gene expression from 52 Nelore steers with the following production traits: average daily gain (ADG), body weight (BW), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), Kleiber index (KI), metabolic body weight (MBW), residual feed intake (RFI), and relative growth ratio (RGR). The total expression of the prune homolog 2 (PRUNE2) gene was significantly associated with DMI, FCR, FE, and RFI (P < 0.05). Furthermore, we have identified a new transcript of PRUNE2 (TCONS_00027692, GenBank MZ041267) that was inversely correlated with FCR and FE (P < 0.05), in contrast to the originally identified PRUNE2 transcript. The cytochrome P450 subfamily 2B (CYP2B6), early growth response protein 1 (EGR1), collagen type I alpha 1 chain (COL1A1), and connective tissue growth factor (CTGF) genes were not associated with any feed efficiency-related traits (P > 0.05). The findings reported herein suggest that PRUNE2 expression levels affects feed efficiency-related traits variation in Nelore steers.

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Data availability

The new transcript of PRUNE2 here identified, called TCONS_00027692, is available in the GenBank repository by the access number MZ041267. The RNA-Seq data from which this new transcript was identified were previously published (Tizioto et al. 2015) and are available in the ENA repository (EMBL-EBI), under accession PRJEB7669.

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Acknowledgements

We thank CNPq (Grant No: 473091/2012-7 and 4491792/2014-7) and FAPESP (Processes 2012/23638-8 and 2019/04089-2) for financial support in this study. We thank Capes and CNPq (Grant No: 204970/2017-2) for the scholarship for the first author. We thank the Embrapa Pecuária Sudeste responsible for taking care of the animals.

Funding

This project was funded by CNPq (Grant No: 473091/2012-7 and 4491792/2014-7) and FAPESP (Processes 2012/23638-8 and 2019/04089-2).

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Contributions

AOL, JMM, LLC, PCT, AZN, GBM, and LCAR conceptualized the idea. AOL, WJSD, FAB, PCT, PSNO, JASR, and MIPR performed the experiments. AOL, JMM, JA, WJSD, PCT, KSO, BGNA, HB, and JMR performed the bioinformatic analysis. AOL, JP, and GBM performed the statistical analysis. AOL, JMM, JA, LLC, WJSD, FAB, PSNO, MIPR, HF, HB, JMR, AZN, GBM, and LCAR collaborated in the interpretation of results, discussion, and review of this manuscript. AOL, JMM, JA, and LCAR drafted the manuscript. All authors revised and approved the final manuscript.

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Correspondence to Luciana Correia de Almeida Regitano.

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The experimental procedures were conducted under the Institutional Animal Care and Use Committee Guidelines of the Brazilian Agricultural Research Corporation—EMBRAPA. Protocol CEUA 01/2013).

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The experimental procedures were conducted under the Institutional Animal Care and Use Committee Guidelines of the Brazilian Agricultural Research Corporation—EMBRAPA. Protocol CEUA 01/2013).

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Lima, A.O., Malheiros, J.M., Afonso, J. et al. Prune homolog 2 with BCH domain (PRUNE2) gene expression is associated with feed efficiency-related traits in Nelore steers. Mamm Genome (2022). https://doi.org/10.1007/s00335-022-09960-1

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