Affiliation:
1. School of Agricultural and Veterinarian Sciences São Paulo State University (Unesp) Jaboticabal Brazil
2. Centro de Pesquisa em Bovinos de Corte Instituto de Zootecnia (IZ) Sertãozinho Brazil
3. Embrapa Dairy Cattle Juiz de Fora Brazil
4. Embrapa Beef Cattle Campo Grande Brazil
5. National Council for Scientific and Technological Development (CNPq) Lago Sul Brazil
Abstract
AbstractFurther 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.
Funder
Conselho Nacional de Desenvolvimento Científico e Tecnológico
Empresa Brasileira de Pesquisa Agropecuária
Fundação de Amparo à Pesquisa do Estado de Minas Gerais
Fundação de Amparo à Pesquisa do Estado de São Paulo
Subject
Genetics,Animal Science and Zoology,General Medicine
Cited by
4 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献