Genomic insights into the genetic diversity and genetic basis of body height in endangered Chinese Ningqiang ponies.

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Jiale Han, Hanrui Shao, Minhao Sun, Feng Gao, Qiaoyan Hu, Ge Yang, Halima Jafari, Na Li, Ruihua Dang
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引用次数: 0

Abstract

Background: Genetic diversity in livestock and poultry is critical for adapting production systems to future challenges. However, inadequate management practices, particularly in developing countries, have led to the extinction or near extinction of several species. Understanding the genetic composition and historical background of local breeds is essential for their effective conservation and sustainable use. This study compared the genomes of 30 newly sequenced Ningqiang ponies with those of 56 other ponies and 104 horses to investigate genetic diversity, genetic differentiation, and the genetic basis of body height differences.

Result: Population structure and genetic diversity analyses revealed that Ningqiang ponies belong to southwestern Chinese ponies. They exhibit a moderate level of inbreeding compared to other pony and horse breeds. Mitochondrial DNA analysis indicated that Ningqiang and Debao ponies share the dominant haplogroups A and C, suggesting a likely common maternal origin. Our study identified low genetic differentiation and detectable gene flow between Ningqiang ponies and Datong horses. The study also indicated the effective population size of Ningqiang ponies showed a downward trend. These findings potentially reflect the historical formation of Ningqiang ponies and population size changes. A selection signal scan (CLR and θπ) within Ningqiang ponies detected several key genes associated with bone development (ANKRD11, OSGIN2, JUNB, and RPL13) and immune response (RIPK2). The combination of genome-wide association analysis and selective signature analysis (FST) revealed significant single nucleotide polymorphisms and selective genes associated with body height, with the most prominent finding being the TBX3 gene on equine chromosome (ECA) 8. Additionally, TBX5, ASAP1, CDK12, CA10, and CSMD1 were identified as important candidate genes for body height differences between ponies and horses.

Conclusion: The results of this study elucidate the genetic diversity, genetic differentiation, and effective population size of Ningqiang ponies compared to other ponies and horses, further deepen the understanding of their small stature, and provide valuable insights into the conservation and breeding of local horse breeds in China.

濒危宁强矮种马体高遗传多样性及遗传基础的基因组学研究。
背景:畜禽遗传多样性对于使生产系统适应未来挑战至关重要。然而,特别是在发展中国家,不适当的管理做法已导致若干物种灭绝或接近灭绝。了解地方品种的遗传组成和历史背景对其有效保护和可持续利用至关重要。本研究将30匹新测序的宁强矮种马与56匹其他矮种马和104匹马的基因组进行比较,探讨遗传多样性、遗传分化及身高差异的遗传基础。结果:种群结构和遗传多样性分析表明,宁强矮种马属于中国西南矮种马。与其他小马和马品种相比,它们表现出适度的近交。线粒体DNA分析表明,宁强马和德宝马具有相同的优势单倍群A和C,可能有共同的母系起源。本研究发现宁强马与大同马的遗传分化程度低,基因流可检测。研究还表明,宁强矮种马的有效种群规模呈下降趋势。这些发现可能反映了宁强矮种马的历史形成和种群规模的变化。通过选择信号扫描(CLR和θπ)检测到与骨发育(ANKRD11、OSGIN2、JUNB和RPL13)和免疫反应(RIPK2)相关的几个关键基因。结合全基因组关联分析和选择性特征分析(FST),发现了显著的单核苷酸多态性和与身高相关的选择性基因,其中最突出的是马染色体(ECA) 8上的TBX3基因。此外,TBX5、ASAP1、CDK12、CA10和CSMD1被确定为小马和马之间身高差异的重要候选基因。结论:本研究结果阐明了宁强矮种马与其他矮种马的遗传多样性、遗传分化和有效种群规模,进一步加深了对宁强矮种马的认识,为中国地方马品种的保护和育种提供了有价值的见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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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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