Peripolli Elisa, Stafuzza Nedenia Bonvino, Machado Marco Antonio, do Carmo Panetto João Cláudio, do Egito Andréa Alves, Baldi Fernando, da Silva Marcos Vinícius Gualberto Barbosa
School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil.
Centro de Pesquisa em Bovinos de Corte, Instituto de Zootecnia (IZ), Sertãozinho, Brazil.
Anim Genet. 2023 Jun;54(3):254-270. doi: 10.1111/age.13298. Epub 2023 Feb 6.
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.
鉴于小型和濒危本地品种在揭示选择性压力和表型变异背后的基因及结构变异方面的作用，对遗传结构变异的进一步特征分析应重点关注这些品种。利用ARS-UCD1.2基因组组装，基于全基因组重测序数据，对三个巴西本地适应牛品种（卡拉库卡尔代亚诺牛、拉热亚诺克里奥洛牛和潘塔内罗牛）进行了全基因组范围内拷贝数变异（CNV）的综合评估。使用了来自36个个体的数据，每个个体的平均覆盖深度为14.07倍。共鉴定出24945个CNV，分布在各品种中（卡拉库卡尔代亚诺牛=7285个，拉热亚诺克里奥洛牛=7297个，潘塔内罗牛=10363个）。缺失事件比重复事件高1.75 - 2.07倍，CNV的总长度主要由大量10至30 kb的片段组成。CNV区域（CNVR）并非均匀地散布在整个基因组中（n = 463），在研究的品种中发现105个CNVR重叠。对CNVR的功能注释揭示了对携带相关基因的蛋白质序列有高度影响的变异，其中我们突出了BOLA-DQB、BOLA-DQA5、CD1A、β-防御素、PRG3和ULBP21基因。基于从CNVR中检索到的基因列表进行的富集分析揭示了与免疫和牛对恶劣环境的适应能力密切相关的过度代表术语（p < 0.01）。此外，在CNVR内还发现了与体型和乳制品相关性状相关的数量性状位点（QTL）。这些结果有助于更好地理解塑造这些牛品种基因组的选择力量，并识别这些种群在面临具有挑战性的环境条件时所受到的自然选择压力的痕迹。
