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. 2024 Jan 11;25(1):54.
doi: 10.1186/s12864-024-09976-8.

Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle

Lorena F Benfica  1   2 , Luiz F Brito  3 , Ricardo D do Bem  4 , Henrique A Mulim  3 , Joseph Glessner  5   6 , Larissa G Braga  4 , Leonardo S Gloria  3 , Joslaine N S G Cyrillo  7 , Sarah F M Bonilha  7 , Maria E Z Mercadante  8
Affiliations

Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle

Lorena F Benfica et al. BMC Genomics. .

Abstract

Background: Feeding costs represent the largest expenditures in beef production. Therefore, the animal efficiency in converting feed in high-quality protein for human consumption plays a major role in the environmental impact of the beef industry and in the beef producers' profitability. In this context, breeding animals for improved feed efficiency through genomic selection has been considered as a strategic practice in modern breeding programs around the world. Copy number variation (CNV) is a less-studied source of genetic variation that can contribute to phenotypic variability in complex traits. In this context, this study aimed to: (1) identify CNV and CNV regions (CNVRs) in the genome of Nellore cattle (Bos taurus indicus); (2) assess potential associations between the identified CNVR and weaning weight (W210), body weight measured at the time of selection (WSel), average daily gain (ADG), dry matter intake (DMI), residual feed intake (RFI), time spent at the feed bunk (TF), and frequency of visits to the feed bunk (FF); and, (3) perform functional enrichment analyses of the significant CNVR identified for each of the traits evaluated.

Results: A total of 3,161 CNVs and 561 CNVRs ranging from 4,973 bp to 3,215,394 bp were identified. The CNVRs covered up to 99,221,894 bp (3.99%) of the Nellore autosomal genome. Seventeen CNVR were significantly associated with dry matter intake and feeding frequency (number of daily visits to the feed bunk). The functional annotation of the associated CNVRs revealed important candidate genes related to metabolism that may be associated with the phenotypic expression of the evaluated traits. Furthermore, Gene Ontology (GO) analyses revealed 19 enrichment processes associated with FF.

Conclusions: A total of 3,161 CNVs and 561 CNVRs were identified and characterized in a Nellore cattle population. Various CNVRs were significantly associated with DMI and FF, indicating that CNVs play an important role in key biological pathways and in the phenotypic expression of feeding behavior and growth traits in Nellore cattle.

Keywords: Bos indicus; Bovine genome; SNP panel; Structural variants.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Distribution of copy number variation regions (deletions, duplications, and mixed type) by chromosome
See this image and copyright information in PMC

References

    1. Goulart RS, Tedeschi LO, Silva SL, Leme PR, De Alencar MM, Lanna DPD. The energy requirement for maintenance of Nellore crossbreds in tropical conditions during the finishing period. J Anim Sci. 2022;100:1–12. doi: 10.1093/jas/skac125. - DOI - PMC - PubMed
    1. Cooke RF, Daigle CL, Moriel P, Smith SB, Tedeschi LO, Vendramini JMB. Cattle adapted to tropical and subtropical environments: Social, nutritional, and carcass quality considerations. J Anim Sci J Anim Sci. 2020;98:1–20. - PMC - PubMed
    1. Kelly AK, McGee M, Crews DH, Fahey AG, Wylie AR, Kenny DA. Effect of divergence in residual feed intake on feeding behavior, blood metabolic variables, and body composition traits in growing beef heifers. J Anim Sci. 2010;88:109–23. doi: 10.2527/jas.2009-2196. - DOI - PubMed
    1. Basarab JA, Price MA, Aalhus JL, Okine EK, Snelling WM, Lyle KL. Residual feed intake and body composition in young growing cattle. Can J Anim Sci. 2003;189–204.
    1. Nkrumah JD, Crews DH, Basarab JA, Price MA, Okine EK, Wang Z, et al. Genetic and phenotypic relationships of feeding behavior and temperament with performance, feed efficiency, ultrasound, and carcass merit of beef cattle. J Anim Sci. 2007;85:2382–90. doi: 10.2527/jas.2006-657. - DOI - PubMed

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