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中国山东省本地家鸭的全基因组结构变异分析与品种比较

Genome-Wide Structural Variation Analysis and Breed Comparison of Local Domestic Ducks in Shandong Province, China.

作者信息

Ren Pengwei, Zhang Meixia, Khan Muhammad Zahoor, Yang Liu, Jing Yadi, Liu Xiang, Yang Xiaohui, Zhang Chaoran, Zhang Min, Zhu Zhiming, Zheng Nenzhu, Zhang Lujiao, Zhang Shuer, Zhu Mingxia

机构信息

College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.

Shandong Animal Husbandry Station, Jinan 250010, China.

出版信息

Animals (Basel). 2024 Dec 18;14(24):3657. doi: 10.3390/ani14243657.

DOI:10.3390/ani14243657
PMID:39765561
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11672513/
Abstract

Structural variations in the duck genome significantly impact the environmental adaptability and phenotypic diversity of duck populations. Characterizing these SVs in local domestic duck breeds from Shandong province offers valuable insights for breed selection and the development of new breeds. This study aimed to profile the genomic SVs in three local duck breeds (Matahu duck, Weishan partridge duck, and Wendeng black duck) and explore their differential distributions. A total of 21,673 SVs were detected using LUMPY (v0.2.13) and DELLY (v1.0.3) software, with 46% located in intergenic regions, 33% in intronic regions, and frameshift deletions being the most prevalent in exonic regions (3%). SVs distribution showed a decreasing trend with shorter chromosome lengths. Population structure analysis revealed distinct genetic profiles, with Matahu and Weishan partridge ducks showing closer affinities and the Wendeng black duck having a more homogeneous genetic background, likely due to geographic isolation. Functional annotation identified genes related to nervous system development, mitosis, spindle assembly, and energy metabolism. Notable genes included , , , , , , and . Additionally, genes such as , , and were linked to energy metabolism and reproductive activity. The study provides a comprehensive analysis of SVs, revealing significant genetic differentiation and identifying genes associated with economically important traits, offering valuable resources for the genetic improvement and breeding of local duck breeds.

摘要

鸭基因组中的结构变异对鸭群体的环境适应性和表型多样性有显著影响。对山东省当地家鸭品种中的这些结构变异进行表征，为品种选育和新品种开发提供了有价值的见解。本研究旨在剖析三个当地鸭品种（麻鸭、微山麻鸭和文登黑鸭）的基因组结构变异，并探究它们的差异分布。使用LUMPY（v0.2.13）和DELLY（v1.0.3）软件共检测到21,673个结构变异，其中46%位于基因间区域，33%位于内含子区域，移码缺失在外显子区域最为常见（3%）。结构变异的分布随染色体长度缩短呈下降趋势。群体结构分析揭示了不同的遗传特征，麻鸭和微山麻鸭表现出更密切的亲缘关系，而文登黑鸭具有更均匀的遗传背景，这可能是由于地理隔离所致。功能注释鉴定出与神经系统发育、有丝分裂、纺锤体组装和能量代谢相关的基因。显著的基因包括 、 、 、 、 、 和 。此外， 、 和 等基因与能量代谢和生殖活动有关。该研究对结构变异进行了全面分析，揭示了显著的遗传分化，并鉴定出与经济重要性状相关的基因，为当地鸭品种的遗传改良和育种提供了有价值的资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/862b2e8ea589/animals-14-03657-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/73b3ea2dd89a/animals-14-03657-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/2e94a35bd48f/animals-14-03657-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/3748c64ae6b1/animals-14-03657-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/d284faf5d9be/animals-14-03657-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/211b9fc4c180/animals-14-03657-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/862b2e8ea589/animals-14-03657-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/73b3ea2dd89a/animals-14-03657-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/2e94a35bd48f/animals-14-03657-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/3748c64ae6b1/animals-14-03657-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/d284faf5d9be/animals-14-03657-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/211b9fc4c180/animals-14-03657-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a970/11672513/862b2e8ea589/animals-14-03657-g006.jpg

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