基于SNP芯片解析永胜红骨绵羊的群体遗传结构

doi:10.19543/j.cnki.1673-4556.20260602.006

中国畜禽种业 ›› 2026, Vol. 22 ›› Issue (7): 38-44.doi: 10.19543/j.cnki.1673-4556.20260602.006cstr: 32418.14.j.cnki.1673-4556.20260602.006

基于SNP芯片解析永胜红骨绵羊的群体遗传结构

李锦南¹(), 王金明²(), 王识之¹, 朱兰¹, 杨冬梅², 刘彩娟², 杨开梅², 陈浩林³, 邵庆勇¹()

^1. 云南省畜牧兽医科学院，云南昆明 650224
^2. 永胜县畜牧站，云南丽江 674200
^3. 贵州省畜牧兽医研究所，贵州贵阳 550050

收稿日期:2025-11-17 出版日期:2026-07-26 发布日期:2026-07-18
通讯作者: 邵庆勇 E-mail:jinnan_li@outlook.com;shaoqingyong@163.com
作者简介:
李锦南（1997—），男，云南昆明人，助理研究员，主要从事动物遗传育种与遗传资源评价鉴定工作，E-mail：jinnan_li@outlook.com。^#共同第一作者
李锦南（1997—），男，云南昆明人，助理研究员，主要从事动物遗传育种与遗传资源评价鉴定工作，E-mail：jinnan_li@outlook.com。^#共同第一作者
王金明（1975—），男，云南永胜人，高级兽医师，主要从事牛羊科学养殖及畜禽粪污资源化利用工作，E-mail：yshxmxx@163.com。
基金资助:
云南省科技人才与平台计划(202505AF350008); 永胜红骨绵羊资源鉴定、评价与利用(2023HT015); 国家肉羊产业技术体系建设项目(CARS-38-36)

Analysis of population genetic structure of Yongsheng Red-bone sheep based on SNP chip

Jinnan Li¹(), Jinming Wang²(), Shizhi Wang¹, Lan Zhu¹, Dongmei Yang², Caijuan Liu², Kaimei Yang², Haolin Chen³, Qingyong Shao¹()

^1. Yunnan Animal Science and Veterinary Institute, Kunming, 650224, Yunnan
^2. Yongsheng Animal Husbandry Station, Lijiang, 674200, Yunnan
^3. Guizhou Animal Science and Veteirnary Institute, Guiyang, 550050, Yunnan

Received:2025-11-17 Online:2026-07-26 Published:2026-07-18
Contact: Qingyong Shao E-mail:jinnan_li@outlook.com;shaoqingyong@163.com

摘要/Abstract

摘要：

目的为探究永胜红骨绵羊的遗传背景，揭示其与云南及周边绵羊资源的关联性与独特性，为云南地方绵羊资源的鉴定及保护提供科学依据。方法本试验使用OvineSNP50芯片对24只永胜红骨绵羊进行基因分型，并以6个云南地方绵羊品种、西藏羊和威宁绵羊作参照，通过系统发育树构建、主成分分析、血统分析、连续纯合片段（Runs of homozygosity， ROH）检测以及遗传分化指数计算等方法系统解析永胜红骨绵羊的群体遗传结构。结果使用Illumina OvineSNP50芯片进行基因分型，9个绵羊群体共216个个体经质控后保留46129个高质量SNP用于后续分析。系统发育树结果显示，永胜红骨绵羊在树形上独立于其他绵羊群体。主成分分析结果显示，永胜红骨绵羊能与迪庆绵羊、兰坪乌骨绵羊、宁蒗黑绵羊、威宁绵羊区分开，分化程度相对较高。ADMIXTURE软件分析结果显示，K=7是9个绵羊群体的最佳模拟祖先血统预测数量，永胜红骨绵羊有独特的祖先血统结构，其中部分个体血统存在混杂。ROH统计结果显示，该群体ROH长度主要集中在2～3 Mb，群体近交系数（F_ROH）为0.0953。永胜红骨绵羊与兰坪乌骨绵羊的遗传分化指数（F_st）最小（0.0459），与其他绵羊群体之间的F_ST均大于0.06。结论综上，永胜红骨绵羊具有独特的群体遗传结构，与兰坪乌骨绵羊可能存在历史基因交流。

关键词: 永胜红骨绵羊, 遗传资源, 群体遗传结构, 种质资源鉴定

Abstract:

Objective This study aims to explore the genetic background of Yongsheng Red-bone sheep and to reveal their genetic relationship and specificality with respect to sheep resources in Yunnan and surrounding areas and provides a scientific basis for the identification and conservation of local sheep genetic resources in Yunnan. Method A total of 24 Yongsheng Red-bone sheep were genotyped using the OvineSNP50 BeadChip. Six local Yunnan sheep breeds, Tibetan sheep, and Weining sheep were used for references. The population genetic structure of Yongsheng Red-bone sheep was systematically analyzed through phylogenetic tree construction, principal component analysis, ancestry analysis, runs of homozygosity (ROH) detection, and calculation of genetic differentiation index. Result Genotyping was performed using the Illumina Ovine SNP50 chip. A total of 46,129 high-quality SNPs were retained for subsequent analysis after quality control of 216 individuals in 9 sheep populations. The phylogenetic tree showed that Yongsheng Red-bone sheep formed a distinct branch independent of other sheep populations. The results of principal component analysis showed that Yongsheng Rred-bone sheep could be distinguished from Diqing sheep, Lanping Black-bone sheep, Ninglang sheep and Weining sheep, and the degree of differentiation was relatively high. ADMIXTURE analysis revealed that K=7 was the optimal number of ancestral populations for the nine sheep populations, and Yongsheng Red-bone sheep exhibited a unique ancestral composition, with some individuals showing admixture. ROH analysis indicated that the ROH lengths in this population were mainly concentrated in the range of 2~3 Mb, with an inbreeding coefficient(F_ROH) of 0.0953. The smallest genetic differentiation index(F_st) occurred between Yongsheng Red-boned sheep and Lanping Black-bone sheep(0.0459), while those with other populations were all greater than 0.06. Conclusion In summary, Yongsheng Red-bone sheep possess a unique population genetic structure and may have experienced historical gene flow with Lanping Black-bone sheep.

Key words: Yongsheng Red-bone sheep, Genetic resource, Population genetic structure, Genetic resource identification

中图分类号:

S826

李锦南, 王金明, 王识之, 朱兰, 杨冬梅, 刘彩娟, 杨开梅, 陈浩林, 邵庆勇. 基于SNP芯片解析永胜红骨绵羊的群体遗传结构[J]. 中国畜禽种业, 2026, 22(7): 38-44.

Jinnan Li, Jinming Wang, Shizhi Wang, Lan Zhu, Dongmei Yang, Caijuan Liu, Kaimei Yang, Haolin Chen, Qingyong Shao. Analysis of population genetic structure of Yongsheng Red-bone sheep based on SNP chip[J]. Chinese Livestock and Poultry Breeding, 2026, 22(7): 38-44.

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参考文献 21

[1]	胡万龙. 红骨绵羊遗传资源评价[D]. 昆明: 云南农业大学, 2016.
	HU W L. Evaluation of germplasm in the red bone sheep[D]. Kunming: Yunnan Agricultural University, 2016.
[2]	杨明, 马琳, 王宣懿, 等. 云南红骨绵羊屠宰性能及相关性状分析[J]. 中国草食动物科学, 2021, 41(5): 31-36.
	YANG M, MA L, WANG X Y, et al. Analysis on slaughtering and relative trait of Yunnan red bone sheep[J]. China Herbivore Science, 2021, 41(5): 31-36.
[3]	HAN D P, ZHANG Y Y, DENG W D, et al. FRRS1L variants and ferriheme overload drive hyperpigmentation and systemic Iron overload in Lanping black bone sheep[J]. Cell & Bioscience, 2025, 15(1): 87.
[4]	DORSHORST B, OKIMOTO R, ASHWELL C. Genomic regions associated with dermal hyperpigmentation, polydactyly and other morphological traits in the Silkie chicken[J]. The Journal of Heredity, 2010, 101(3): 339-350.
[5]	樊月圆, 余淑青, 曹振辉, 等. 云南红骨圭山山羊微卫星 DNA位点遗传多样性分析[J]. 云南农业大学学报(自然科学版), 2013(3): 329-335.
	FAN Y Y, YU S Q, CAO Z H, et al. Microsatellite analysis of genetic diversity of red-bone Guishan goats and common Guishan goats[J]. Journal of Yunnan Agricultural University (Natural Science), 2013(3): 329-335.
[6]	VIJH R K, SHARMA U, ARORA R, et al. Development and validation of the Axiom-MaruPri SNP chip for genetic analyses of domesticated old world camelids[J]. Gene, 2024, 921: 148541.
[7]	LI C L, TONG X L, GAO R, et al. Silk_40K SNP array facilitates the genomic prediction of complex traits in silkworm (Bombyx mori)[J]. Journal of Advanced Research, 2025:S2090-1232(25)00916-6
[8]	MALLORIE T L, JULIEN P, WILLIAM P, et al. Validation of a 60K SNP chip for caribou (Rangifer tarandus) for use in wildlife forensics, conservation, and management[J]. Forensic Science International: Animals and Environments, 2024, 6: 100093.
[9]	KARABAŞ M, YıLMAZ O. Identification of selection signatures and genetic diversity in the sheep[J]. Tropical Animal Health and Production, 2025, 57(2): 68.
[10]	LI X P, ZHU L J, ZHANG C L, et al. Genetic structure and selective sweeps in Kirghiz sheep using SNP50K bead chip[J]. Frontiers in Genetics, 2024, 15: 1432105.
[11]	YANG R Z, HAN Z P, ZHOU W, et al. Population structure and selective signature of Kirghiz sheep by Illumina Ovine SNP50 BeadChip[J]. PeerJ, 2024, 12: e17980.
[12]	CHANG C C, CHOW C C, TELLIER L C, et al. Second-generation PLINK: rising to the challenge of larger and richer datasets[J]. GigaScience, 2015, 4: 7.
[13]	LEE T H, GUO H, WANG X Y, et al. SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data[J]. BMC Genomics, 2014, 15(1): 162.
[14]	LETUNIC I, BORK P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool[J]. Nucleic Acids Research, 2024, 52(W1): W78-W82.
[15]	ALEXANDER D H, NOVEMBRE J, LANGE K. Fast model-based estimation of ancestry in unrelated individuals[J]. Genome Research, 2009, 19(9): 1655-1664.
[16]	DANECEK P, AUTON A, ABECASIS G, et al. The variant call format and VCFtools[C]. //Bioinformatics. ACM, 2011: 2156-2158.
[17]	阿旺措吉, 仁青措姆, 黄舒泓, 等. 基于重测序数据的昌都黑山羊遗传多样性及群体结构分析[J]. 家畜生态学报, 2022, 43(10): 30-35.
	A W, RENQINGCUOMU, HUANG S H, et al. Genetic diversity and population structure analysis of Changdu black sheep based on resequencing data[J]. Journal of Domestic Animal Ecology, 2022, 43(10): 30-35.
[18]	周隽, 覃星文, 吴细波, 等. 基于SNP芯片对陆川猪进行遗传多样性与遗传结构分析的研究[J]. 中国畜牧杂志, 2023, 59(8): 257-263.
	ZHOU J, QIN X W, WU X B, et al. Study on genetic diversity and genetic structure analysis of Luchuan pig based on SNP chip[J]. Chinese Journal of Animal Science, 2023, 59(8): 257-263.
[19]	YANG H L, DONG L, WANG H, et al. A simple way to visualize detailed phylogenetic tree of huge genome-wide SNP data constructed by SNPhylo[J]. Journal of Integrative Agriculture, 2018, 17(9): 1972-1978.
[20]	梁家充, 朱兰, 孙利民, 等. 云南地方绵羊品种遗传多样性分子评价[J]. 四川农业大学学报, 2018, 36(6): 822-830.
	LIANG J C, ZHU L, SUN L M, et al. Molecular evaluation of genetic diversity of native sheep breeds in Yunnan Province[J]. Journal of Sichuan Agricultural University, 2018, 36(6): 822-830.
[21]	陈红艳, 马月辉, 叶绍辉. 云南5个地方绵羊品种遗传多样性研究[J]. 中国畜牧兽医, 2013, 40(12): 125-131.
	CHEN H Y, MA Y H, YE S H. Study on genetic diversity of five local sheep breeds in Yunnan[J]. China Animal Husbandry & Veterinary Medicine, 2013, 40(12): 125-131.

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群体Population name	缩写Abbreviation	采样地点Sampling location	采样时间Sampling time	样本量Sample size/个
永胜红骨绵羊Yongsheng Red-bone sheep	YS	云南省丽江市永胜县	2023.10	24
迪庆绵羊Diqing sheep	DQ	云南省迪庆州香格里拉市	2023.10	24
兰坪乌骨绵羊Lanping Black-bone sheep	LP	云南省怒江州兰坪县	2023.08	24
宁蒗黑绵羊Ninglang Black sheep	NL	云南省丽江市宁蒗县	2023.08	24
石屏青绵羊Shiping Cyan sheep	SP	云南省红河州石屏县	2023.09	24
腾冲绵羊Tengchong sheep	TC	云南省保山市腾冲市	2023.06	15
西藏羊Tibetan sheep	TIB	西藏自治区昌都市	-	37
威宁绵羊Weining sheep	WN	贵州省毕节市威宁县	2024.8	24
昭通绵羊Zhaotong sheep	ZT	云南省昭通市昭阳区	2023.10	20

群体 Populations	石屏青绵羊 SP	腾冲绵羊 TC	永胜红骨绵羊 YS	迪庆绵羊 DQ	兰坪乌骨绵羊 LP	昭通绵羊 ZT	宁蒗黑绵羊 NL	威宁绵羊 WN	西藏绵羊 TIB
石屏青绵羊SP	—
腾冲绵羊TC	0.1578	—
永胜红骨绵羊YS	0.1203	0.1089	—
迪庆绵羊DQ	0.1102	0.1041	0.0601	—
兰坪乌骨绵羊LP	0.0940	0.0889	0.0459	0.0327	—
昭通绵羊ZT	0.1046	0.0981	0.0627	0.0475	0.0345	—
宁蒗黑绵羊NL	0.1188	0.1040	0.0642	0.0554	0.0426	0.0546	—
威宁绵羊WN	0.1132	0.0900	0.0611	0.0555	0.0431	0.0490	0.0542	—
西藏绵羊TIB	0.1399	0.1181	0.0869	0.0815	0.0689	0.0829	0.0814	0.0673	—

基于SNP芯片解析永胜红骨绵羊的群体遗传结构

Analysis of population genetic structure of Yongsheng Red-bone sheep based on SNP chip

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