基于比较基因组学的宁强马与济州马遗传多样性及矮小体型的遗传基础研究

doi:10.11843/j.issn.0366-6964.2025.12.020

Abstract

Abstract: This study aimed to comparatively analyze the genetic diversity and the genetic basis of small stature between Ningqiang ponies and Jeju ponies. This study compared and analyzed the genetic structure, genetic diversity, and genetic differentiation of Ningqiang ponies and Jeju ponies based on the whole-genome resequencing data from 199 modern domestic horses, focusing on comparing the genetic basis of small stature. Population structure analysis indicated that Ningqiang ponies belong to pony breeds of Southwestern China, while Jeju ponies had ancestral components that are distinct from those of the Southwestern ponies. Nucleotide diversity, inbreeding coefficient, and ROH analysis indicated that Jeju ponies had undergone strong artificial selection and breeding recently, with low genetic diversity, while Ningqiang ponies had high genetic diversity. Furthermore, the genetic distance between Ningqiang ponies and Debao ponies is the closest (F_ST=0.02), while Jeju ponies had a moderate degree of genetic differentiation from 11 domestic horse breeds (F_ST>0.05). Whole-genome selection scanning detected multiple differential candidate regions in the genomes of Ningqiang ponies and Jeju ponies, and identified genes related to growth and development (TBX5, TBX3, MEIS1, CECR2) and immunity (ADA2, AP3B1). In conclusion, Ningqiang ponies and Jeju ponies have different ancestral components and degrees of selection and breeding, with obvious genetic differentiation, and the genetic basis for small stature is also different. These results are of great significance for an in-depth understanding of the genetic basis of small stature traits in ponies and for the protection and utilization of horse breeds in China.

Key words: Ningqiang pony, Jeju pony, genetic diversity, genetic differentiation, small stature

CLC Number:

S821.2

HAN Jiale, GAO Feng, SUN Minhao, HU Qiaoyan, DING Fengyi, DANG Ruihua. Genetic Diversity and Genetic Basis of Small Stature in Ningqiang and Jeju Ponies Based on Comparative Genomics[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(12): 6167-6179.

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Genetic Diversity and Genetic Basis of Small Stature in Ningqiang and Jeju Ponies Based on Comparative Genomics

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