滇南小耳猪群体遗传结构和遗传多样性分析

doi:10.16288/j.yczz.26-112

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

• Research Article • Previous Articles Next Articles

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 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 Online:2026-07-14 Published:2026-07-14
Contact: Mei Liu E-mail:15993148878@163.com;Mei.Liu@hunau.edu.cn
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)

Abstract

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 (H_e) 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

Zhang Li, Qun Lan, Ming Li, Shengju Lian, Jiawen Liu, Heng Zhao, Haiming Ma, Hongjiang Wei, Yulong Yin, Mei Liu. Analysis of genetic structure and genetic diversity in Diannan small-ear pig[J]. Hereditas(Beijing), 2026, 48(8): 807-816.

Figures/Tables 4

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质量控制标准	SNP标记数目
SNP标记总数	30,648
最小等位基因频率<0.01的SNP标记	235
哈代-温伯格平衡检验P<10^-6的SNP标记	68
SNP检出率<0.90	211
X染色体上的SNP标记	588
通过质量控制的SNP总数	29,468

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

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