遗传 ›› 2026, Vol. 48 ›› Issue (8): 807-816.doi: 10.16288/j.yczz.26-112

• 研究报告 • 上一篇    下一篇

滇南小耳猪群体遗传结构和遗传多样性分析

李张1,2(), 蓝群1,2, 李铭1,2, 练胜举1,2, 刘佳雯1,2, 赵恒3, 马海明1,2, 魏红江3, 印遇龙2,4, 刘梅1,2()   

  1. 1 湖南农业大学动物科学技术学院长沙 410128
    2 岳麓山实验室畜禽品种创制中心长沙 410128
    3 云南农业大学动物医学院昆明 650201
    4 中国科学院亚热带生态农业研究所长沙 410125
  • 收稿日期:2026-04-27 修回日期:2026-06-20 出版日期:2026-07-14 发布日期:2026-07-14
  • 通讯作者: 刘梅,博士,教授,研究方向:猪遗传育种与繁殖。E-mail: Mei.Liu@hunau.edu.cn
  • 作者简介:李张,硕士研究生,专业方向:猪遗传育种与繁殖。E-mail: 15993148878@163.com
  • 基金资助:
    国家自然科学基金联合基金项目(U23A20229);云南省科技人才与平台计划(202505AT350004);湖南省重大科技攻关项目(2025QK2003);湖南省自然科学基金优秀青年项目(2025JJ40017)

Analysis of genetic structure and genetic diversity in Diannan small-ear pig

Zhang Li1,2(), Qun Lan1,2, Ming Li1,2, Shengju Lian1,2, Jiawen Liu1,2, Heng Zhao3, Haiming Ma1,2, Hongjiang Wei3, Yulong Yin2,4, Mei Liu1,2()   

  1. 1 College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
    2 Livestock and Poultry Breed Innovation Center, Yuelu Mountain Laboratory, Changsha 410128, China
    3 College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
    4 Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
  • Received:2026-04-27 Revised:2026-06-20 Published:2026-07-14 Online:2026-07-14
  • Supported by:
    National Natural Science Foundation of China(U23A20229);Yunnan Provincial Science and Technology Talent and Platform Program(202505AT350004);Hunan Provincial Major Scientific Research Project(2025QK2003);Hunan Provincial Natural Science Foundation Outstanding Young Researcher Project(2025JJ40017)

摘要:

滇南小耳猪是我国云南特有的地方猪品种,因其独特的经济性状而具有重要的保种和利用价值。为分析滇南小耳猪群体遗传结构和遗传多样性,本研究利用猪Illumina 50K SNP芯片检测了424头滇南小耳猪全基因组SNP,利用PLINK软件得到29,468个有效SNPs,平均多态信息含量(polymorphism information content,PIC)为0.21,最小等位基因频率(minor allele frequency,MAF)为0.18,平均期望杂合度(expected heterozygosity,He)为0.24,表明滇南小耳猪群体遗传多样性呈中等偏低水平。采用MEGA X软件构建群体进化树,结果显示滇南小耳猪可分为8个家系;利用PLINK软件计算状态同源(identity by state,IBS)比例并构建距离矩阵,结果显示所有个体间的平均IBS为0.23;采用GCTA软件分析群体的亲缘关系,发现大部分滇南小耳猪呈中等程度的亲缘关系;此外,通过分析连续性纯合片段(runs of homozygosity,ROH),发现ROH片段共有5,301个,其中有59.54%的长度在0~5 Mb之间,基于ROH的平均近交系数为0.006,表明滇南小耳猪近交程度低。本研究为滇南小耳猪的后续保护与开发利用奠定了坚实的遗传学基础,提示后续保种工作可以适度引入其他亚群的基因流,在保持其独特优良性状的基础上进一步提升其遗传多样性,并结合基因组选择等现代生物育种技术深度挖掘并利用其携带的优良基因,提升其选育能力,最终实现这一珍贵遗传资源的科学保护与可持续开发利用。

关键词: 滇南小耳猪, SNP芯片, 遗传多样性, 群体遗传结构

Abstract:

The Diannan small-ear pig, an indigenous breed in Yunnan of China, has significant conservation and utilization value due to its unique economic traits. To investigate the population genetic diversity and structure of this breed, this study applied Illumina Porcine 50K SNP chip to detect genome-wide SNPs in 424 Diannan small-ear pigs. Using PLINK software, a total of 29,468 SNPs were detected. The results showed that the average polymorphism information content (PIC) was 0.21, the minor allele frequency (MAF) was 0.18, and the average expected heterozygosity (He) was 0.24, indicating a moderately low level of genetic diversity in the Diannan small-ear pigs population. Subsequently, the phylogenetic tree was constructed using MEGA X software, showing that the Diannan small-ear pigs could be divided into eight linages. Computed with Plink software, the distance matrix was built from pairwise identity by state (IBS) proportions. The results revealed that the average IBS proportion across all individual pairs was 0.23. Analysis of genetic relationships within the population with GCTA software revealed that most Diannan small-ear pigs exhibited moderate genetic proximity. Additionally, a total of 5,301 runs of homozygosity (ROH) segments were identified. 59.54% of those ROHs ranged from 0 to 5 Mb in length. The average inbreeding coefficient based on ROH was 0.006, indicating a low level of inbreeding in the Diannan small-ear pigs population. This study provides a worthwhile genetic foundation for the future conservation and utilization of Diannan small-ear pigs. These findings indicated that the Diannan small-ear pig conservation farm could introduce other more gene flows from other subpopulations to promote population genetic diversity based on preserving their unique and desirable traits, and integrate modern biotechnology for breeding organisms like genomic selection to promote its potential for the discovery and utilization of the merit phenotype-related genes, contributing to the long-term scientific protection and sustainable development and utilization of this valuable genetic resource.

Key words: Diannan small-ear pig, SNP chip, genetic diversity, population genetic structure