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马的微型特征相关的全基因组拷贝数变异的检测。

Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses.

机构信息

Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China.

Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.

出版信息

Genes (Basel). 2023 Oct 13;14(10):1934. doi: 10.3390/genes14101934.

DOI:10.3390/genes14101934
PMID:37895283
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10606273/
Abstract

Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a specific focus on identifying genomic regions associated with miniature features in horses. Using whole-genome next-generation resequencing data, we identified 18,974 CNVs across 31 autosomes. Among the breeds, we found 4279 breed-specific CNV regions (CNVRs). Baise, Debao, and Warmblood displayed 2978, 986, and 895 distinct CNVRs, respectively, with 202 CNVRs shared across all three breeds. After removing duplicates, we obtained 1545 CNVRs from 26 horse genomes. Functional annotation reveals enrichment in biological functions, including antigen processing, cell metabolism, olfactory conduction, and nervous system development. Debao horses have 970 genes overlapping with CNVRs, possibly causing their small size and mountainous adaptations. We also found that the genes GHR, , and may be responsible for the miniature features of the Debao horse by analyzing their overlapping CNVRs. Overall, this study offers valuable insights into the widespread presence of CNVs in the horse genome. The findings contribute to mapping horse CNVs and advance research on unique miniature traits observed in the Debao horse.

摘要

拷贝数变异（CNVs）是影响人类和家畜复杂特征的关键结构基因组变异。本研究旨在对三个品种（德保、百色和温血马）进行全面的比较拷贝数变异分析，重点是鉴定与马的小型特征相关的基因组区域。使用全基因组新一代重测序数据，我们在 31 条常染色体上鉴定出 18974 个 CNVs。在这些品种中，我们发现了 4279 个品种特异性 CNV 区域（CNVRs）。百色、德保和温血马分别显示 2978、986 和 895 个独特的 CNVR，所有三个品种共有 202 个 CNVR。去除重复后，我们从 26 个马基因组中获得了 1545 个 CNVR。功能注释显示，生物功能富集，包括抗原加工、细胞代谢、嗅觉传导和神经系统发育。德保马有 970 个基因与 CNVRs 重叠，可能导致其体型小和适应山区。通过分析其重叠的 CNVR，我们还发现 GHR、和 基因可能是导致德保马小型特征的原因。总体而言，这项研究为马基因组中广泛存在的 CNVs 提供了有价值的见解。研究结果有助于绘制马的 CNVs 图谱，并推进对德保马独特小型特征的研究。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/9588507b7734/genes-14-01934-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/ff38e4997b9e/genes-14-01934-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/fd86a5768e9b/genes-14-01934-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/17bb2c80bc12/genes-14-01934-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/cc56ae29c0a5/genes-14-01934-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/7f555a936dac/genes-14-01934-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/8fb456e16189/genes-14-01934-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/9588507b7734/genes-14-01934-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/ff38e4997b9e/genes-14-01934-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/fd86a5768e9b/genes-14-01934-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/17bb2c80bc12/genes-14-01934-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/cc56ae29c0a5/genes-14-01934-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/7f555a936dac/genes-14-01934-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/8fb456e16189/genes-14-01934-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6fcd/10606273/9588507b7734/genes-14-01934-g007.jpg

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Discovering Copy Number Variation in Dual-Purpose XinJiang Brown Cattle.
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Front Genet. 2022 Feb 11;12:747431. doi: 10.3389/fgene.2021.747431. eCollection 2021.
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Two Different Copy Number Variations of the Gene in Chinese Cattle and Their Association with Growth Traits.中国黄牛中该基因的两种不同拷贝数变异及其与生长性状的关联。
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A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses.TBX3 增强子内的单核苷酸突变增加了中国马的体尺。
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