Resequencing of Brazilian locally adapted cattle breeds revealed variants in candidate genes and transcription factors for meat fatty acid profile.

Autor: Vieira JIG; Universidade Federal dos Vales Do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil., Braga LG; Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, São Paulo, Brazil., Chud TCS; PEAK, URUS Group, Madison, Wisconsin, USA., Ferreira PH; Universidade Federal dos Vales Do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil., Guimarães SEF; Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil., Martins MF; Embrapa Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil., do Carmo Panetto JC; Embrapa Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil., Machado MA; Embrapa Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil., Silva DBDS; Universidade Prof. Edson Antônio Velano (Unifenas), Alfenas, Minas Gerais, Brazil., Bonafé CM; Universidade Federal dos Vales Do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil., Magalhães AFB; Universidade Federal dos Vales Do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil., da Silva MVGB; Embrapa Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil., Verardo LL; Universidade Federal dos Vales Do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil.
Jazyk: angličtina
Zdroj: Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie [J Anim Breed Genet] 2024 Nov; Vol. 141 (6), pp. 628-642. Date of Electronic Publication: 2024 Apr 30.
DOI: 10.1111/jbg.12869
Abstrakt: The beef cattle industry has experienced a shift driven by a market demand for healthier meat, cost efficiency and environmental sustainability in recent years. Consequently, there has been a growing focus on the fatty acids content and functions of meat in cattle breeding programmes. Besides, a deeper understanding of the biological mechanisms influencing the expression of different phenotypes related to fatty acid profiles is crucial. In this study, we aimed to identify Single-Nucleotide Variants (SNV) and Insertion/Deletion (InDels) DNA variants in candidate genes related to fatty acid profiles described in genomic, transcriptomic and proteomic studies conducted in beef cattle breeds. Utilizing whole-genome re-sequencing data from Brazilian locally adapted bovine breeds, namely Caracu and Pantaneiro, we identified SNVs and InDels associated with 23,947 genes. From these, we identified 318 candidate genes related to fatty acid profiles that contain variants. Subsequently, we select only genes with SNVs and InDels in their promoter, 5' UTR and coding region. Through the gene-biological process network, approximately 19 genes were highlighted. Furthermore, considering the studied trait and a literature review, we selected the main transcription factors (TF). Functional analysis via gene-TF network allowed us to identify the 30 most likely candidate genes for meat fatty acid profile in cattle. LIPE, MFSD2A and SREBF1 genes were highlighted in networks due to their biological importance. Further dissection of these genes revealed 15 new variants found in promoter regions of Caracu and Pantaneiro sequences. The gene networks facilitated a better functional understanding of genes and TF, enabling the identification of variants potentially related to the expression of candidate genes for meat fatty acid profiles in cattle.
(© 2024 Wiley‐VCH GmbH. Published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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