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
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湖南省科技人才托举工程项目(2022TJ-Q15);湖南省现代农业产业技术体系项目(HARS-05);湖南省研究生科研创新项目(CX20230711、CX20240645)


Assessment of genetic diversity and structure of local pig populations in Hunan using a 50K SNP array
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    摘要:

    采用2023—2024年种业监测中采集的湖南省4类地方猪品种共2 676头猪(湘西黑猪452头、宁乡猪1 427头、黔邵花猪451头、大围子猪346头)的血样,使用GGP 50K SNP芯片对其进行基因分型,并通过动物基因组品种构成方法筛选出纯种个体,再基于筛选的纯种个体对此4类地方猪品种的遗传多样性、血缘纯度、亲缘关系以及家系结构进行分析。结果显示:宁乡猪群体的多态信息含量(PIC)为0.251,平均观察杂合度(Ho)为0.245,平均期望杂合度(He)为0.251,平均连续纯合片段(ROH)长度(LROH)为5 166.733 kb,基于ROH片段计算的近交系数(FROH)为0.002 2,最小等位基因频率(MAF)为0.185;黔邵花猪群体的PIC为0.281,Ho为0.285,He为0.281,LROH为5 706.452 kb,FROH为0.002 5,MAF为0.207;大围子猪群体的PIC、Ho、He均为0.239,LROH为4 769.535 kb,FROH为0.002 1,MAF为0.177;湘西黑猪群体的PIC为0.390,Ho为0.343,He为0.390,LROH为5 201.896 kb,FROH为0.002 3,MAF为0.299。综合各项遗传多样性指标可知,湘西黑猪的遗传资源丰度最高,大围子猪的则相对较低。除黔邵花猪外,其他3类品种血缘纯度均保持较好,杂合个体较少,保种情况较好。主成分分析结果显示,4类品种在遗传空间内呈现明显的分离态势,其中湘西黑猪形成2个相对独立的簇,暗示其内部可能存在亚群分化,且整体上与其他品种距离最远,遗传背景最为独特;大围子猪则形成独立而紧凑的聚类,表现出的遗传独特性次之;宁乡猪与黔邵花猪的分布区域存在部分重叠,表明二者之间遗传关系较近,但仍保有各自独立的聚类核心,这说明其在共享一定遗传背景的同时,也积累了品种特有的变异。系统发育分析(NJ树)结果显示,同一品种的个体优先聚类,湘西黑猪和大围子猪分别位于较独立的分支,而宁乡猪与黔邵花猪则展现出更近的遗传距离。当假定祖先成分数(K)为2时,大围子猪即显现其独特性;当K=3时,湘西黑猪被区分为一个独立成分;而宁乡猪与黔邵花猪直至K=4时才被完全区分开来,这表明两者间较近的亲缘关系和相对复杂的遗传混合历史。此外,品种内NJ树揭示,各品种内部均可进一步划分为多个家系(宁乡猪10个、湘西黑猪8个、大围子猪9个、黔邵花猪7个),这表明即使在品种层面上,各群体内部仍保持着由不同家系贡献的遗传多样性基础。

    Abstract:

    A total of 2 676 blood samples from four local pig breeds in Hunan Province(452 Xiangxi Black Pigs, 1 427 Ningxiang Pigs, 451 Qianshao Spotted Pigs, and 346 Daweizi Pigs) were collected during seed industry monitoring from 2023 to 2024. Genotyping was performed using the GGP 50K SNP array. Purebred individuals were screened out through the animal genome breed composition method, and then the genetic diversity, bloodline purity, kinship and family structure of the fourlocal pig breeds in Hunan were analyzed based on the screened purebred individuals. The results showed that the polymorphic information content(PIC) of the Ningxiang Pig population was 0.251, the average observed heterozygosity(Ho) was 0.245, the average expected heterozygosity(He) was 0.251, and the average continuous homozygous fragment(ROH) length(LROH) was 5 166.733 kb. The inbreeding number(FROH) calculated based on the ROH fragment was 0.002 2, and the minimum allele frequency(MAF) was 0.185. The PIC of the Qianshao Spotted Pig population was 0.281, Ho was 0.285, He was 0.281, LROH was 5 706.452 kb, FROH was 0.002 5, and MAF was 0.207. The PIC, Ho and He of the Daweizi Pig population were all 0.239, the LROH was 4 769.535 kb, the FROH was 0.002 1, and the MAF was 0.177. The PIC of the Xiangxi Black Pig population was 0.390, Ho was 0.343, He was 0.390, LROH was 5 201.896 kb, FROH was 0.002 3, and MAF was 0.299. Considering all genetic diversity metrics, the Xiangxi Black Pig showed the highest genetic diversity, whereas the Daweizi Pig exhibited relatively lower diversity. Except for the Qianshao Spotted Pig, the other three breeds showed well-maintained lineage purity with few admixed individuals and a good conservation situation. Principal component analysis revealed clear genetic separation among the four breeds. Among them, the Xiangxi Black Pig formed two relatively independent subclusters, suggesting internal subpopulation differentiation and the farthest from other breeds, and the most unique genetic background. The Daweizi Pig clustered independently and compactly, indicating a secondary genetic uniqueness. The Ningxiang Pig and Qianshao Spotted Pig partially overlapped, reflecting a close genetic relationship while retaining distinct core clusters, which suggested that while sharing a certain genetic background, they had also accumulated specific variations of the breeds. Phylogenetic analysis(NJ tree) showed preferential clustering by breed, with the Xiangxi Black Pig and Daweizi Pig forming independent branches, whereas the Ningxiang Pig and Qianshao Spotted Pig were genetically closer. When the ancestral component number(K) was assumed to be 2, the uniqueness of the Daweizi Pig was revealed. When K=3, Xiangxi Black pig was classified as an independent component. The Ningxiang Pig and the Qianshao Spotted Pig were not completely distinguished until K=4, which indicated a relatively close genetic relationship and a relatively complex history of genetic mixing between the two breeds. Furthermore, within-breed NJ tree analysis indicated multiple family lineages in each breed(10 for Ningxiang Pig, 8 for Xiangxi Black Pig, 9 for Daweizi Pig, and 7 for Qianshao Spotted Pig), demonstrating substantial genetic variation maintained at the family level.

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袁瀚豪,杨芳,刘晨曦,熊聃,曾婧,郝中禹,姚辰,李宇飞,何俊*.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.

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  • 在线发布日期: 2026-01-23
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