湖南5个地方猪品种线粒体全基因组序列特征与系统发育分析

doi:10.16174/j.issn.1673-4645.2026.05.007

Abstract

Abstract: To elucidate the maternal genetic differentiation pattern of indigenous pig breeds in Hunan, this study retrieved 11 complete mitochondrial genome sequences from the NCBI GenBank database, including five Hunan indigenous pig breeds, Rongchang pig, Meishan pig, wild boar and outgroup taxa. Composition was analyzed using MEGA 12.0, genetic distances were calculated based on the Kimura 2‑parameter (K2P) model, and a phylogenetic tree was reconstructed using the Neighbor‑Joining (NJ) method. Analyses based on the single‑sample dataset revealed the following findings: ⑴The K2P genetic distances between the five Hunan indigenous pig breeds and Rongchang pig, Meishan pig ranged from 0.000 3 to 0.001 4, markedly lower than the divergence levels between these breeds and wild boar (0.011 3～0.022 4) and outgroup taxa (0.097 9～0.111 3). ⑵Shaziling pig occupied a basal position within the monophyletic clade formed by all seven domestic pig breeds, representing an early‑differentiated maternal lineage among the five Hunan breeds with relatively high genetic distinctiveness. Daweizi pig showed moderate genetic relatedness to the other Hunan pig breeds and Meishan pig, forming an independent sub‑clade. Ningxiang pig, Qianshao spotted pig and Xiangxi black pig were closely related and jointly formed the core genetic cluster. ⑶Genetic relationships among Hunan indigenous pig breeds were not fully consistent with their geographical distribution, suggesting that anthropogenic factors such as breed introduction and gene flow may have been involved in the formation of indigenous pig breeds, rather than being merely shaped by geographical isolation‑mediated divergence. Collectively, these results revealed the maternal genetic differentiation pattern of the five major indigenous pig breeds in Hunan, provided maternal-lineage genetic information for the conservation and utilization of indigenous pig germplasm resources.

Key words: indigenous pig, mitochondrial, whole genome, phylogeny, genetic distance, maternal origin

CLC Number:

S828

WU Qunqing, ZHANG Yuebo, TANG Xiangwei. Sequence characteristics and phylogenetic analysis of the complete mitochondrial genomes of five indigenous pig breeds in Hunan province[J].China Swine Industry, 2026, 21(5): 33-40.

References

[1] 魏大鹏. 地方猪种资源在现代养猪业中的利用[J]. 养猪, 2025(2): 24-25. WEI D P. Utilization of local pig breed resources in modern pig farming[J]. Swine Production, 2025(2): 24-25. [2] 中华人民共和国农业农村部. 国家级畜禽遗传资源保护名录(中华人民共和国农业农村部公告第940)[EB/OL]. (2025-10-27). https://www.moa.gov.cn/govpublic/nybzj1/202510/t20251029_ 6478525.htm. Ministry of Agriculture and Rural Affairs of the People's Republic of China. National protection list of livestock and poultry genetic resources (Announcement No. 940 of the Ministry of Agriculture and Rural Affairs of the People's Republic of China)[EB/OL]. (2025-10-27). https://www.moa.gov.cn/govpublic/nybzj1/202510/t20251029_ 6478525.htm. [3] 杨攀, 许栋, 马海明. 不同猪种肉质相关基因FTO多态性研究[J]. 国外畜牧学(猪与禽), 2016, 36(2): 45-46. YANG P, XU D, MA H M. Study on FTO polymorphism of meat quality-related genes in different pig breeds[J]. Animal Science Abroad(Pigs and Poultry), 2016, 36(2): 45-46. [4] 丁能水. 主效基因及其育种应用[J]. 国外畜牧学(猪与禽), 2015, 35(4):31-34. DING N S. Major gene and its application in breeding[J]. Animal Science Abroad(Pigs and Poultry), 2015, 35(4):31-34. [5] 涂尾龙, 蒋玮, 何川, 等. 四个上海地方猪肉品质比较分析[J]. 上海畜牧兽医通讯, 2024(2):1-4. TU W L, JIANG W, HE C, et al. Comparative analysis of the quality of four local pork products from Shanghai[J]. Shanghai Journal of Animal Husbandry and Veterinary Medicine, 2024(2):1-4. [6] 朱吉, 孙建帮, 彭英林, 等. 部分湖南地方猪种的聚类分析[J]. 湖南畜牧兽医, 2011(5): 8-12. ZHU J, SUN J B, PENG Y L, et al. Cluster analysis of some Hunan local pig breeds[J]. Hunan Animal Science & Veterinary Medicine, 2011(5): 8-12. [7] 周鑫, 林茂, 管永晶, 等. 线粒体基因组在物种进化、生态适应与多样性研究中的应用与挑战[J]. 应用海洋学学报, 2026, 45(3): 489-501. ZHOU X, LIN M, GUAN Y J, et al. Applications and challenges of mitochondrial genomes in species evolution, ecological adaptation, and biodiversity research[J]. Journal of Applied Oceanography, 2026, 45(3): 489-501. [8] 陶勇, 任善茂, 董晓君, 等. 苏姜猪线粒体DNA D-Loop区遗传多样性及系统进化研究[J]. 黑龙江畜牧兽医, 2023(22): 51-56. TAO Y, REN S M, DONG X J, et al. Genetic diversity and phylogenetic evolution in mitochondrial DNA D-Loop region of Sujiang pigs[J]. Heilongjiang Animal Science and Veterinary Medicine, 2023(22): 51-56. [9] 周传江, 马爱喆, 汪曦, 等. 鱼类线粒体基因组研究进展[J]. 河南师范大学学报(自然科学版), 2019, 47(2): 74-82. ZHOU C J, MA A Z, WANG X, et al. Progress on fish mitochondrial genome[J]. Journal of Henan Normal University (Natural Science Edition), 2019, 47(2): 74-82. [10] NAGARAJAN M, NIMISHA K, KUMAR S. Mitochondrial DNA variability of domestic river buffalo (Bubalus bubalis) populations: genetic evidence for domestication of river buffalo in Indian subcontinent[J]. Genome Biology and Evolution, 2015, 7(5): 1252-1259. [11] DEMIR E, MORAV?íKOVá N, ARGUN K B, et al. Mitochondrial DNA diversity of D-loop region in three native Turkish cattle breeds[J]. Archives Animal Breeding, 2023, 66(1): 31-40. [12] 黄振, 郭琼霞. 瘤胫果实蝇线粒体全基因组分析与系统发育[J]. 福建农业学报, 2024, 39(4): 482-491. HUANG Z, GUO Q X. Mitochondrial genome and phylogeny of Bactrocera(B.)tuberculata[J]. Fujian Journal of Agricultural Sciences, 2024, 39(4): 482-491. [13] ARIF I A, BAKIR M A, KHAN H A. Inferring the phylogeny of Bovidae using mitochondrial DNA sequences: resolving power of individual genes relative to complete genomes[J]. Evolutionary Bioinformatics Online, 2012, 8: 139-150. [14] BIRAY B, AKIN PEKSEN C, BILGIN C C. Heteroplasmy in the mitochondrial D-loop region in Turkish domestic pigeon breeds (Columba livia Domestica) obfuscates their phylogeny[J]. European Poultry Science, 2025, 89(1/2): 100006. [15] AGBANI A, AMINOU O, MACHMOUM M, et al. A systematic literature review of mitochondrial DNA analysis for horse genetic diversity[J]. Animals, 2025, 15(6): 885. [16] YU G H, XIANG H, WANG J K, et al. The phylogenetic status of typical Chinese native pigs: analyzed by Asian and European pig mitochondrial genome sequences[J]. Journal of Animal Science and Biotechnology, 2013, 4(1): 9. [17] 吴买生. 湖南地方猪种聚类分析[J]. 当代畜牧, 1993(1): 28-29. WU M S. Cluster analysis of Hunan local pig breeds[J]. Contemporary Animal Husbandry, 1993(1): 28-29. [18] 袁瀚豪, 杨芳, 刘晨曦, 等. 基于50K SNP芯片评估湖南地方猪群体遗传结构及遗传多样性[J]. 湖南农业大学学报(自然科学版), 2025, 51(6): 103-108. YUAN H H, YANG F, LIU C X, et al. Assessment of genetic diversity and structure of local pig populations in Hunan using a 50K SNP array[J]. Journal of Hunan Agricultural University (Natural Sciences), 2025, 51(6): 103-108. [19] KUMAR S, STECHER G, SULESKI M, et al. MEGA12: molecular evolutionary genetic analysis version 12 for adaptive and green computing[J]. Molecular Biology and Evolution, 2024, 41(12): msae263. [20] KIMURA M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences[J]. Journal of Molecular Evolution, 1980, 16(2): 111-120. [21] SAITOU N, NEI M. The neighbor-joining method: a new method for reconstructing phylogenetic trees[J]. Molecular Biology and Evolution, 1987, 4(4): 406-425. [22] ZHANG Y Z, ZHANG T, DUAN J Y, et al. The complete mitochondrial DNA sequence of Yimeng black pig (Sus Scrofa)[J]. Mitochondrial DNA Part B, 2020, 5(2): 1165-1166. [23] SHEN L Y, ZHANG S H, ZHU L. Complete mitochondrial genome sequence of Chenghua pig (Sus Scrofa) and its phylogenetic analysis[J]. Mitochondrial DNA Part B, 2016, 1(1): 530-531. [24] DAS P J, KUMAR S, CHOUDHURY M, et al. Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs[J]. Scientific Reports, 2025, 15: 2219. [25] 杨岸奇. 沙子岭猪不同时期睾丸组织全基因组甲基化分析[D]. 长沙: 湖南农业大学, 2023. YANG A Q. Analysis of dynamic genomic methylation patterns during testicular development of Shaziling pigs[D]. Changsha: Hunan Agricultural University, 2023. [26] 胡雄贵, 朱吉, 任慧波, 等. 湖南地方猪—湘西黑猪种质资源特性调查与研究[J]. 养猪, 2011(5): 45-48. HU X G, ZHU J, REN H B, et al. Investigation and study on the characteristics of Hunan local pig-Xiangxi black pig germplasm resources[J]. Swine Production, 2011(5): 45-48. [27] 张冬杰, 刘娣, 何鑫淼, 等. 中国地方猪品种的遗传多样性与聚类分析[J]. 畜牧与兽医, 2015, 47(10): 1-4. ZHANG D J, LIU D, HE X M, et al. Diversity and cluster analysis of China local pig breeds[J]. Animal Husbandry & Veterinary Medicine, 2015, 47(10): 1-4. [28] 胡慧艳, 贾青, 刘津, 等. 中国地方猪种线粒体基因组遗传多样性及其系统发育分析[J]. 中国畜牧兽医, 2017, 44(8): 2360-2368. HU H Y, JIA Q, LIU J, et al. Genetic diversity and phylogenetic relationships of the complete mitochondrial genome in Chinese indigenous pig breeds[J]. China Animal Husbandry & Veterinary Medicine, 2017, 44(8): 2360-2368. [29] 罗创国, 陈永刚, 李珊倩, 等. 现代猪育种新技术[J]. 畜牧兽医杂志, 2016, 35(5): 38-41. LUO C G, CHEN Y G, LI S Q, et al. New technologies in modern pig breeding[J]. Journal of Animal Science and Veterinary Medicine, 2016, 35(5): 38-41. [30] 高祥, 王拓原, 孙雅妮, 等. 地方猪育种研究进展[J]. 中国猪业, 2025, 20(2): 63-74. GAO X, WANG T Y, SUN Y N, et al. Progress in local pig breeding research [J]. China Swine Industry, 2025, 20(2): 63-74.

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

Comments

Recommended 0

No Suggested Reading articles found!

Sequence characteristics and phylogenetic analysis of the complete mitochondrial genomes of five indigenous pig breeds in Hunan province

PDF (PC)

Abstract

Cite this article

share this article

References

Related Articles 6

Metrics

Comments

Recommended 0

[1]	. [J]. China Swine Industry, 2026, 21(3): 60-67.
[2]	. [J]. China Swine Industry, 2026, 21(3): 52-59.
[3]	. [J]. China Swine Industry, 2026, 21(3): 23-35.
[4]	. [J]. China Swine Industry, 2026, 21(1): 12-19.
[5]	. [J]. China Swine Industry, 2025, 20(4): 73-83.
[6]	. [J]. China Swine Industry, 2025, 20(2): 63-74.