Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing

文献类型： 外文期刊

第一作者： Li, Lanlan

作者： Li, Lanlan;Quan, Jinqiang;Zhao, Shengguo;Liu, Hongyi;Yu, Haibo;Chen, Hongyan;Xia, Changyou;Gao, Caixia;Li, Lanlan

作者机构：

关键词： Laboratory ducks; Whole-genome resequencing; Genetic characteristics; Selection signature; Copy number variation

期刊名称：BMC GENOMICS （ 影响因子：4.4； 五年影响因子：4.7 ）

ISSN： 1471-2164

年卷期： 2024 年 25 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundSpecific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures.ResultsWe obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively.ConclusionsIn conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.

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