Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole‐genome re‐sequencing data

• Published in: Animal genetics Vol. 54; no. 3; pp. 254 - 270
• Main Authors: Peripolli, Elisa, Stafuzza, Nedenia Bonvino, Machado, Marco Antonio, Carmo Panetto, João Cláudio, Egito, Andréa Alves, Baldi, Fernando, Silva, Marcos Vinícius Gualberto Barbosa
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01-06-2023
• Subjects: Amino acid sequence; Animals; Annotations; Bos primigenius taurus; Brazil; Cattle; CNV; Copy number; creole breeds; Defensins; DNA Copy Number Variations; Environmental conditions; Gene sequencing; Genes; Genetic diversity; Genome; Genomes; Harsh environments; Natural selection; next‐generation sequencing; Phenotype; Phenotypes; Phenotypic variations; Quantitative trait loci; Structural analysis; structural variants; Whole Genome Sequencing - veterinary; Brazil; structural variants; CNV; creole breeds; Bos primigenius taurus; next-generation sequencing
• ISSN: 0268-9146; 1365-2052
• DOI: 10.1111/age.13298

Further characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective pressures and phenotype variation. A comprehensive genome‐wide assessment of copy number variations (CNVs) based on whole‐genome re‐sequencing data was performed on three Brazilian locally adapted cattle breeds (Caracu Caldeano, Crioulo Lageano, and Pantaneiro) using the ARS‐UCD1.2 genome assembly. Data from 36 individuals with an average coverage depth of 14.07× per individual was used. A total of 24 945 CNVs were identified distributed among the breeds (Caracu Caldeano = 7285, Crioulo Lageano = 7297, and Pantaneiro = 10 363). Deletion events were 1.75–2.07‐fold higher than duplications, and the total length of CNVs is composed mostly of a high number of segments between 10 and 30 kb. CNV regions (CNVRs) are not uniformly scattered throughout the genomes (n = 463), and 105 CNVRs were found overlapping among the studied breeds. Functional annotation of the CNVRs revealed variants with high consequence on protein sequence harboring relevant genes, in which we highlighted the BOLA‐DQB, BOLA‐DQA5, CD1A, β‐defensins, PRG3, and ULBP21 genes. Enrichment analysis based on the gene list retrieved from the CNVRs disclosed over‐represented terms (p < 0.01) strongly associated with immunity and cattle resilience to harsh environments. Additionally, QTL associated with body conformation and dairy‐related traits were also unveiled within the CNVRs. These results provide better understanding of the selective forces shaping the genome of such cattle breeds and identify traces of natural selection pressures by which these populations have been exposed to challenging environmental conditions.