利用全基因组重测序数据检测8个鸭品种基因组拷贝数变异

doi:10.11843/j.issn.0366-6964.2023.09.011

摘要/Abstract

摘要： 旨在鉴别与鸭重要经济性状潜在相关的拷贝数变异(copy number variations, CNVs),为解析CNVs对鸭经济性状的影响提供前期研究基础。本研究利用从美国国家生物技术信息中心(National Center for Biotechnology Information, NCBI)公共数据库中下载的8个鸭品种共78个个体的全基因组重测序数据,采用CNVnator和CNVcaller软件进行全基因组CNVs检测,同时只保留两个软件检测结果中存在至少1 bp重叠的同类型CNVRs,以消除假阳性对试验结果的影响。结果显示,8个鸭品种的CNVs合并后共检测出7 550个CNV regions (CNVRs),其中包括7 098个duplications和452个deletions。这些CNVRs在鸭29条常染色体上呈不均匀分布,总长度为16 111.2 kb,平均长度为2 134 bp,约占鸭基因组的1.51%。此外,本研究在8个鸭品种共筛选到4 304个潜在的品种特异性CNVRs,覆盖1 230个注释基因。通过基因功能Gene Ontology(GO)富集分析,鉴别到38个可能与生长和繁殖相关的CNVRs。本研究共发现7 550个CNVRs,筛选出4 304个潜在的品种特异性CNVRs,并鉴别到38个与鸭生长和繁殖潜在相关的CNVRs,为深入探究CNVs对鸭重要经济性状的影响提供了必要的研究基础。

关键词: 鸭, 全基因组重测序数据, 基因组, 拷贝数变异, CNVs

Abstract: The main purpose of this study was to identify the potentially copy number variations (CNVs) related to economically important traits of ducks, and provide a basis for the analysis of the effects of CNVs on economic traits of ducks. In this study, the whole genome resequencing data of 8 duck breeds was used, including 78 individuals downloaded from the National Center for Biotechnology Information (NCBI) public database to detect CNVs in the duck genome via CNVnator and CNVcaller software. Only the same type of CNVRs with at least 1 bp overlap in the two softwares was retained to eliminate the influence of false positive results. A total of 7 550 CNVRs including 7 098 duplications and 452 deletions were identified by merging CNVs in 8 duck breeds. These CNVRs were unevenly distributed on 29 autosomes, which occupied about 1.51% of the duck whole genome sequence, their total length was 16 111.2 kb and the average length was 2 134 bp. Furthermore, 4 304 potential breed-specific CNVRs were screened from 8 duck breeds, covering 1 230 annotated genes. Moreover, 38 CNVRs possibly related to the growth and reproduction of ducks were identified by Gene Ontology (GO) enrichment analysis. In this study, a total of 7 550 CNVRs were detected, in which 4 304 potential breed-specific CNVRs were screened and 38 CNVRs potentially related to the growth and reproduction were identified. The results provides a necessary basis for further research on the effects of CNVs on economically important traits of ducks.

Key words: duck, whole genome resequencing data, genome, copy number variations, CNVs

中图分类号:

S834.2

林燕, 黄敏, 李秀金, 张续勐, 黄运茂, 田允波, 伍仲平. 利用全基因组重测序数据检测8个鸭品种基因组拷贝数变异[J]. 畜牧兽医学报, 2023, 54(9): 3700-3709.

LIN Yan, HUANG Min, LI Xiujin, ZHANG Xumeng, HUANG Yunmao, TIAN Yunbo, WU Zhongping. Uncovering Genome-wide Copy Number Variations in 8 Duck Breeds Using Whole Genome Resequencing Data[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3700-3709.

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