Introduction: Nellore cattle (Bos taurus indicus) is the main beef cattle breed raised in Brazil. This breed is well adapted to tropical conditions and, more recently, has experienced intensive genetic selection for multiple performance traits. Over the past 43 years, an experimental breeding program has been developed in the Institute of Animal Science (IZ, Sertaozinho, SP, Brazil), which resulted in three differentially-selected lines known as Nellore Control (NeC), Nellore Selection (NeS), and Nellore Traditional (NeT). The primary goal of this selection experiment was to determine the response to selection for yearling weight (YW) and residual feed intake (RFI) on Nellore cattle. The main objectives of this study were to: 1) identify copy number variation (CNVs) in Nellore cattle from three selection lines; 2) identify and characterize CNV regions (CNVR) on these three lines; and 3) perform functional enrichment analyses of the CNVR identified.Results: A total of 14,914 unique CNVs and 1,884 CNVRs were identified when considering all lines as a single population. The CNVRs were non-uniformly distributed across the chromosomes of the three selection lines included in the study. The NeT line had the highest number of CNVRs (n = 1,493), followed by the NeS (n = 823) and NeC (n = 482) lines. The CNVRs covered 23,449,890 bp (0.94%), 40,175,556 bp (1.61%), and 63,212,273 bp (2.54%) of the genome of the NeC, NeS, and NeT lines, respectively. Two CNVRs were commonly identified between the three lines, and six, two, and four exclusive regions were identified for NeC, NeS, and NeT, respectively. All the exclusive regions overlap with important genes, such as SMARCD3, SLC15A1, and MAPK1. Key biological processes associated with the candidate genes were identified, including pathways related to growth and metabolism.Conclusion: This study revealed large variability in CNVs and CNVRs across three Nellore lines differentially selected for YW and RFI. Gene annotation and gene ontology analyses of the exclusive CNVRs to each line revealed specific genes and biological processes involved in the expression of growth and feed efficiency traits. These findings contribute to the understanding of the genetic mechanisms underlying the phenotypic differences among the three Nellore selection lines.

中文翻译：

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三个差异选择的内洛尔牛群体拷贝数变异的检测和表征

简介： 内洛尔牛（印度牛）是巴西饲养的主要肉牛品种。该品种很好地适应了热带条件，并且最近经历了针对多种性能特征的密集遗传选择。在过去的 43 年里，动物科学研究所（IZ，Sertaozinho，SP，巴西）开发了一项实验育种计划，产生了三个差异选择品系，称为 Nellore Control (NeC)、Nellore Selection (NeS)和内洛尔传统 (NeT)。该选择实验的主要目标是确定 Nellore 牛对一岁体重 (YW) 和剩余采食量 (RFI) 选择的反应。本研究的主要目的是：1）从三个选择品系中鉴定内洛尔牛的拷贝数变异（CNV）； 2) 识别并表征这三条线上的 CNV 区域 (CNVR)； 3) 对识别出的 CNVR 进行功能富集分析。 结果：将所有品系视为一个群体时，总共识别出 14,914 个独特的 CNV 和 1,884 个 CNVR。 CNVR 在研究中包括的三个选择系的染色体上分布不均匀。 NeT 系列的 CNVR 数量最多（n= 1,493)，然后是 NeS (n= 823) 和 NeC (n= 482）行。 CNVR分别覆盖了NeC、NeS和NeT系基因组的23,449,890 bp (0.94%)、40,175,556 bp (1.61%)和63,212,273 bp (2.54%)。三个品系之间通常鉴定出两个 CNVR，并且分别鉴定出 NeC、NeS 和 NeT 的 6 个、2 个和 4 个专属区域。所有专属区域都与重要基因重叠，例如SMARCD3,SLC15A1， 和MAPK1。确定了与候选基因相关的关键生物过程，包括与生长和代谢相关的途径。结论：这项研究揭示了针对 YW 和 RFI 差异选择的三个 Nellore 品系中 CNV 和 CNVR 的巨大变异性。每个品系独有的 CNVR 的基因注释和基因本体分析揭示了涉及生长和饲料效率性状表达的特定基因和生物过程。这些发现有助于理解三个内洛尔选择系之间表型差异背后的遗传机制。