Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions.

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Jan Berghöfer, Nadia Khaveh, Stefan Mundlos, Julia Metzger
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引用次数: 0

Abstract

Background: Copy number variations (CNVs) represent a common and highly specific type of variation in the genome, potentially influencing genetic diversity and mammalian phenotypic development. Structural variants, such as deletions, duplications, and insertions, have frequently been highlighted as key factors influencing traits in high-production pigs. However, comprehensive CNV analyses in miniature pig breeds are limited despite their value in biomedical research.

Results: This study performed whole-genome sequencing in 36 miniature pigs from nine breeds from America, Asia and Oceania, and Europe. By employing a multi-tool approach (CNVpytor, Delly, GATK gCNV, Smoove), the accuracy of CNV identification was improved. In total, 34 homozygous CNVs overlapped with exonic regions in all samples, suggesting a role in expressing specific phenotypes such as uniform growth patterns, fertility, or metabolic function. In addition, 386 copy number variation regions (CNVRs) shared by all breeds were detected, covering 33.6 Mb (1.48% of the autosomal genome). Further, 132 exclusive CNVRs were identified for American breeds, 47 for Asian and Oceanian breeds, and 114 for European breeds. Functional enrichment analysis revealed genes within the common CNVRs involved in body height determination and other growth-related parameters. Exclusive CNVRs were located in the region of genes enriched for lipid metabolism in American minipigs, reproductive traits in Asian and Oceanian breeds, and cardiovascular features and body height in European breeds. In the selected groups, quantitative trait loci associated with body size, meat quality, reproduction, and disease susceptibility were highlighted.

Conclusion: This investigation of the CNV landscape of minipigs underlines the impact of selective breeding on structural variants and its role in the development of specific breed phenotypes across geographical areas. The multi-tool approach provides a valuable resource for future studies on the effects of artificial selection on livestock genomes.

背景:拷贝数变异(CNV)是基因组中一种常见且高度特异的变异类型,可能会影响遗传多样性和哺乳动物的表型发育。结构变异,如缺失、重复和插入,经常被强调为影响高产猪性状的关键因素。然而,尽管微型猪在生物医学研究中很有价值,但对其进行全面的 CNV 分析却很有限:本研究对来自美洲、亚洲、大洋洲和欧洲 9 个品种的 36 头小型猪进行了全基因组测序。通过采用多工具方法(CNVpytor、Delly、GATK gCNV、Smoove),提高了 CNV 鉴定的准确性。在所有样本中,共有 34 个同源 CNV 与外显子区域重叠,表明它们在表达特定表型(如均匀生长模式、生育能力或代谢功能)方面发挥作用。此外,还检测到所有品种共有的 386 个拷贝数变异区(CNVR),覆盖 33.6 Mb(常染色体基因组的 1.48%)。此外,还发现了 132 个美国品种独有的 CNVR,47 个亚洲和大洋洲品种独有的 CNVR,以及 114 个欧洲品种独有的 CNVR。功能富集分析表明,常见 CNVRs 中的基因涉及体高决定和其他生长相关参数。专属 CNVR 位于美洲小型猪脂质代谢、亚洲和大洋洲品种生殖特征以及欧洲品种心血管特征和体高的富集基因区域。在选定的群体中,与体型、肉质、繁殖和疾病易感性相关的数量性状位点得到了强调:对小型猪 CNV 景观的调查强调了选择性育种对结构变异的影响及其在不同地理区域特定品种表型发展中的作用。多工具方法为今后研究人工选择对家畜基因组的影响提供了宝贵的资源。
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来源期刊
BMC Genomics
BMC Genomics 生物-生物工程与应用微生物
CiteScore
7.40
自引率
4.50%
发文量
769
审稿时长
6.4 months
期刊介绍: BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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