Journal of Integrative Agriculture

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391份中国家驴全基因组重测序数据分析揭示其群体遗传结构与适应性性状遗传基础

  

  • 修回日期:2025-02-17

Whole-genome resequencing of 391 Chinese donkeys reveals a population structure and provides insights into their morphological and adaptive traits

Ge Yang1*, Yujiang Sun2*, Zhaofei Wang1, Cong Li1, Xiangqin Zhai1, Jiaqiang Zhang1, Halima Jafari1, Gang Ren1, Chuzhao Lei1, Ruihua Dang1#, Shuqin Liu2#   

  1. 1 Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China

    2 College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China

  • Revised:2025-02-17
  • Supported by:

    This work was supported by the Funding for the Third National Census of Livestock and Poultry Genetic Resources (K4050422227), the 2020 Scientist plus Engineer program of Shaanxi Province of China, the Central Guidance on Local Science and Technology Development Fund (K3030922098), and Shaanxi Province Innovation Capability Support Plan (2018XY-021). 

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摘要：

目的：了解中国家驴表型变异背后的遗传变异有助于家驴的遗传改良及繁育工作。然而，中国家驴群体遗传结构以及与形态（毛色和体型）和适应性（高海拔适应）性状相关的关键候选基因目前研究不多，需要进一步挖掘和深入分析。

方法：本研究基于391份中国家驴全基因组重测序数据和代表性品种的PacBio HiFi测序数据，全面挖掘其单核苷酸多态性（single nucleotide polymorphisms，SNP）和结构变异（Structural variation，SV）等不同类型遗传变异，研究其频率分布规律，并通过选择信号检测等方法挖掘与形态（毛色和体型）和适应性（高海拔适应）等性状有关的候选突变，最终通过PCR和细胞实验验证变异序列的功能作用。

结果：群体基因组分析显示，中国家驴分化为三个不同的类群，西南高原、北方平原和关中平原。本研究鉴定到127个与毛色相关、117个与体型相关以及169个与高海拔适应相关的选择信号基因，其中ARID3B基因可能影响中国家驴的毛色；EPAS1是一个高海拔适应基因，但是，研究发现FAM184B 基因在中国家驴应对高海拔环境时呈现出更强的信号。选择性信号分析和全基因组关联分析（GWAS）表明，LCORL和TMEM154基因可能与中国驴的体型相关。利用关中驴和川驴三代PacBio HiFi测序数据，鉴定了关中驴（大型驴）和川驴（小型驴）之间的结构变异。基于此结构变异数据，对来自24个品种的153个二代中国家驴数据进行SV分型，鉴定到了一个关中驴（大型驴）和川驴（小型驴）之间TMEM154基因上880bp的缺失，这一结果通过PCR得到了验证，推测其是与体型相关的候选SV。转录组测序数据显示，与川驴（小型驴）相比，TMEM154基因在关中驴（大型驴）的肌肉中表达量高；多物种序列比对分析表明，TMEM154基因区域中880bp序列在马、斑马、藏野驴以及两个大型驴品种（德州驴和关中驴）中存在，在小型驴川驴上缺失。此外，将880bp缺失序列转染到3T3-L1和HEK293T细胞后，结果显示该突变的相对荧光素酶活性相较于野生型显著降低；综合上述结果表明，TMEM154基因中880bp的缺失序列可能在驴的体型性状方面发挥着重要作用。

结论：研究结果确定了中国家驴的群体遗传结构，挖掘了中国家驴毛色、高海拔适应和体型性状相关的重要候选基因，并推测TMEM154基因上的SV可能在中国家驴体型形成中具有重要作用。这些结果将为开展中国家驴体型性状的标记辅助选择提供参考依据，为中国家驴遗传改良提供参考。

Abstract:

Understanding the genetic changes behind the phenotypic variation of Chinese donkeys is helpful to the genetic improvement and breeding of donkeys. However, the population structure and novel genes associated with morphological (coat color and body size) and adaptive (high-altitude adaptation) traits of Chinese donkeys remain largely unknown. Here, we analyzed 391 whole-genome sequencing (WGS) data of Chinese donkeys. Population genomic analyses showed that Chinese native donkey breeds mainly consist of three distinct populations (Southwest plateau, North plain, and Guanzhong plain), and a newly discovered population (Guanzhong plain) was identified. Moreover, we characterized a high-confidence list of 127, 117, and 169 selective signal genes for coat color, body size, and high-altitude adaptation, respectively. We discovered ARID3B gene with strong signals of selection, which may account for coat color in Chinese donkeys. Our study identified EPAS1 as a high-altitude adaptive gene. However, the FAM184B gene shows a stronger signal in response to high-altitude environments in Chinese donkeys. The selective sweep and GWAS analysis showed that LCORL and TMEM154 genes are potentially associated with body size in Chinese donkeys. Utilizing PacBio HiFi sequencing data, this study presents 15,954 highly reliable structural variations (SVs) between large-sized and small-sized donkeys. Utilizing SV data and a graph-based method, we identified an 880-bp deletion in the TMEM154 gene in Sichuan donkeys (small-sized) compared to Guanzhong donkeys (large-sized), which was verified by PCR and is a candidate SV related to body size. Transcriptome sequencing data showed that the TMEM154 gene is highly expressed in the muscle of Guanzhong donkeys (large-sized) compared to Sichuan donkeys (small-sized). Multi-species alignment analysis revealed that the region surrounding the 880-bp deletion in the TMEM154 gene region is conserved in horse, zebra, kiang, as well as two large-sized donkey breeds (Dezhou and Guanzhong), except in in the small-sized Sichuan donkey. Furthermore, after the 880 bp deletion was transfected into 3T3-L1 and HEK293T cells, it was demonstrated that the relative luciferase activity of the mutation was markedly decreased in comparison with that of the wild type. These results suggest that this 880-bp deletion in the TMEM154 gene may play an important role in body size trait of donkey. This study provides valuable genome resources for donkey breeding and sheds light on the domestication history of Chinese donkeys.

Key words: Donkey , selective signal, body size ,  structural variation ,  TMEM154 gene