基于全基因组SNPs分析陆丰黄牛和雷琼牛的群体结构与遗传多样性特征

doi:10.3864/j.issn.0578-1752.2023.14.014

中国农业科学 ›› 2023, Vol. 56 ›› Issue (14): 2798-2811.doi: 10.3864/j.issn.0578-1752.2023.14.014

基于全基因组SNPs分析陆丰黄牛和雷琼牛的群体结构与遗传多样性特征

童雄(), 罗威(), 闵力, 张志飞, 马新燕, 罗成龙, 陈卫东, 徐斌(), 李大刚()

广东省农业科学院动物科学研究所/畜禽育种国家重点实验室/岭南现代农业科学与技术广东省实验室河源分中心/广东省畜禽育种与营养研究重点实验室，广州 510640

收稿日期:2023-01-04 接受日期:2023-04-23 出版日期:2023-07-16 发布日期:2023-07-21
通信作者:
徐斌，E-mail：xubin@gdaas.cn。
李大刚，E-mail：lidagang@gdaas.cn
联系方式: 童雄，E-mail：tongxiong@gdaas.cn。罗威，E-mail：luowei@gdaas.cn。童雄和罗威为同等贡献作者。
基金资助:
广东省现代农业产业技术体系创新团队项目(2022KJ114); 岭南现代农业科学与技术广东省实验室河源分中心自主科研项目(DT20220023); 2022年省级乡村振兴战略专项资金种业振兴项目(2022-XBH-00-008)

Population Structure and Genetic Diversity of Lufeng Cattle and Leiqiong Cattle Based on Genome-Wide SNPs

TONG Xiong(), LUO Wei(), MIN Li, ZHANG ZhiFei, MA XinYan, LUO ChengLong, CHEN WeiDong, XU Bin(), LI DaGang()

Institute of Animal Science, Guangdong Academy of Agricultural Sciences/State Key Laboratory of Livestock and Poultry Breeding/ Heyuan Branch of Guangdong Laboratory for Lingnan Modern Agriculture/Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640

Received:2023-01-04 Accepted:2023-04-23 Published:2023-07-16 Online:2023-07-21

摘要/Abstract

摘要：

【目的】研究陆丰黄牛和雷琼牛与世界不同地域家牛中的系统发育关系，解析不同家牛群体的遗传多样性，为地方家牛资源的鉴定与保护奠定理论基础。【方法】采集12头陆丰黄牛和17头雷琼牛的组织样品进行全基因组重测序，整合世界范围内分布的24个品种92个体的NCBI公共基因组数据，共计25个品种121个个体的信息开展群体遗传学研究。选用Bos taurus ARS-UCD1.2作为参考基因组，经基因组序列比对与质量控制获取高质量Reads，应用GATK软件检测基因组SNPs。进一步基于群体SNPs，利用系统进化树构建、PCA聚类和Admixture评估进行群体结构分析，通过核苷酸多样性（Pi）、杂合度（Hp）和连锁不平衡（LD）水平研究群体的遗传多样性。【结果】29头广东地方牛经基因组测序获取6 905 944 306个Clean Reads，每个样本平均基因组覆盖率为97.99%，平均测序深度分别为12.78×。整合NCBI公共基因组数据，经质控后共检测出14 664 391个群体SNPs。整合系统进化树、PCA、Admixture的结果发现普通牛与瘤牛分化，瘤牛群体存在中国瘤牛与印度瘤牛分化，普通牛群体中东北亚普通牛（韩牛、延边牛）和西藏牛与欧洲普通牛分化，温岭高峰牛和舟山牛从中国瘤牛群体中分化。陆丰黄牛和雷琼牛均属于纯正的中国瘤牛，但陆丰黄牛与皖南牛之间、雷琼牛与吉安牛之间呈现最近的亲缘关系，说明陆丰黄牛与地域临近的雷琼牛属于两个独立的品种。部分陆丰黄牛与雷琼牛均存在欧洲普通牛和东北亚普通牛的血统混杂，且混杂比例较高，说明这两个品种牛急需加强群体内的提纯复壮。相较于欧洲普通牛和韩牛，中国家牛群体的LD衰减速率更快，核苷酸多样性Pi和杂合度Hp更高，说明其遗传多样性更丰富。相较于其他中国家牛，陆丰黄牛和雷琼牛的LD水平更低，杂合度Hp更高，且核苷酸多样性Pi和杂合度Hp的密度分布更为集中，说明两者受人工选择强度较低，且维持较高的群体遗传多样性。【结论】通过全基因组SNPs标记，系统解析了陆丰黄牛与雷琼牛的群体遗传结构和多样性特征，为这两个品种独立分类及其保护利用提供数据支撑。

关键词: 陆丰黄牛, 雷琼牛, 全基因组SNPs, 群体结构

Abstract:

【Objective】Phylogenetic relationship among Lufeng cattle, Leiqiong cattle and domestic cattle in different regions worldwide, and genetic diversity of different domestic cattle populations were studied, so as to lay a theoretical foundation for the identification and protection of domestic cattle resources. 【Method】Tissue samples of 12 individuals of Lufeng cattle and 17 ones of Leiqiong cattle were collected for whole genome resequencing. Combined with another 92 cattle genomes from 24 breeds worldwide available in the NCBI database, a panel of cattle genomes comprising 121 individuals were generated from 25 breeds to carry out population genetics study. Bos taurus ARS-UCD1.2 assembly was selected as the reference genome. High-quality reads were obtained by genome alignment and quality control. Genomic SNPs were detected by GATK software. Population structure was analyzed by phylogenetic tree construction, PCA clustering, and Admixture evaluation. Genetic diversity of the populations was studied by estimating nucleotide diversity (Pi), heterozygosity (Hp), and linkage disequilibrium (LD). 【Result】A total of 6 905 944 306 clean reads were obtained by genome sequencing from 29 individuals of the two cattle breeds in Guangdong. Average genome coverage and average sequencing depth of each sample were 97.99% and 12.78×, respectively. After integrating the NCBI cattle genome data, 14 664 391 population SNPs were identified. The results of phylogenetic tree, PCA and Admixture showed that a primary division was found between cattle from taurine and indicine. Moreover, indicine cattle split on Chinese and Indian cattle, and Northeast Asian cattle (Hanwoo and Yanbian) and Tibetan cattle separated from European taurine group, while Wenling cattle and Zhoushan cattle differentiated from Chinese indicine group. Lufeng cattle and Leiqiong cattle belonged to pure Chinese indicine cattle. Lufeng cattle and Wannan cattle, Leiqiong cattle and Ji'an cattle showed the closest relationship, respectively. The relationships indicated that Lufeng cattle and Leiqiong cattle in the adjacent areas belonged to two independent breeds. Some Lufeng and Leiqiong individuals were genetically admixed with European taurine and Northeast Asian taurine cattle, and the admixed proportion was high, indicating that these two breeds needed to strengthen the purification and rejuvenation within the population. Compared with European taurine cattle and Korean cattle, for Chinese domestic cattle, LD decay rate was faster, and nucleotide diversity (Pi) and heterozygosity (Hp) were higher, indicating that genetic diversity of Chinese domestic cattle was richer. Compared with other Chinese domestic cattle, LD levels of Lufeng cattle and Leiqiong cattle were lower, heterozygosity (Hp) was higher, and the density distribution of nucleotide diversity (Pi) and heterozygosity (Hp) was more concentrated, indicating that the two cattle breeds were less subject to artificial selection and maintain higher genetic diversity. 【Conclusion】Population structure and genetic diversity of Lufeng cattle and Leiqiong cattle were analyzed by genome-wide SNPs, which provided data support for independent classification and conservation of these two cattle breeds.

Key words: Lufeng cattle, Leiqiong cattle, whole-genome SNPs, population structure

童雄, 罗威, 闵力, 张志飞, 马新燕, 罗成龙, 陈卫东, 徐斌, 李大刚. 基于全基因组SNPs分析陆丰黄牛和雷琼牛的群体结构与遗传多样性特征[J]. 中国农业科学, 2023, 56(14): 2798-2811.

TONG Xiong, LUO Wei, MIN Li, ZHANG ZhiFei, MA XinYan, LUO ChengLong, CHEN WeiDong, XU Bin, LI DaGang. Population Structure and Genetic Diversity of Lufeng Cattle and Leiqiong Cattle Based on Genome-Wide SNPs[J]. Scientia Agricultura Sinica, 2023, 56(14): 2798-2811.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2023.14.014

https://www.chinaagrisci.com/CN/Y2023/V56/I14/2798

图/表 8

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本研究中25个品种121个个体的样本信息"

品种 Breed	品种代号 Breed code	样本量 Sample size	原产地 Origin region	数据来源 Reference	地理区域 Geographic region
安格斯牛 Angus cattle	Angus	5	英国苏格兰阿伯丁郡 Aberdeenshire, Scotland, UK	STOTHARD et al, 2015^[29]	西欧 West Europe
海福特牛 Hereford cattle	Hereford	6	英国赫里福德郡 Hereford, UK	STOTHARD et al, 2015^[29]	西欧 West Europe
利木赞牛 Limousin cattle	Limousin	1	法国利穆赞大区 Limousin, France	STOTHARD et al, 2015^[29]	中南欧 Central-South Europe
西门塔尔牛 Simmental cattle	Simmental	6	瑞士日内瓦 Geneve, Switzerland	STOTHARD et al, 2015^[29]	中南欧 Central-South Europe
西藏牛 Tibetan cattle	Tibetan	6	中国西藏自治区昌都市 Changdu, Xizang, China	CHEN et al, 2018^[7]	西藏 Tibet
韩牛 Hanwoo cattle	Hanwoo	6	韩国江原道春川市 Chuncheon, Kangwon-do, Korea	SHIN et al, 2014^[30]	东北亚 Northeast Asia
延边牛 Yanbian cattle	Yanbian	1	中国吉林省延边朝鲜族自治州 Yanbian, Jilin, China	CHEN et al, 2018^[7]	东北亚 Northeast Asia
鲁西牛 Luxi cattle	Luxi	5	中国山东省济宁市 Jining, Shandong, China	CHEN et al, 2018^[7]	中国中北部 North-Central China
渤海黑牛 Bohai Black cattle	Bohai	4	中国山东省滨州市 Binzhou, Shandong, China	CHEN et al, 2018^[7]	中国中北部 North-Central China
南阳牛 Nanyang cattle	Nanyang	4	中国河南省南阳市 Nanyang, Henan, China	CHEN et al, 2018^[7]	中国中北部 North-Central China
锦江牛 Jinjiang cattle	Jinjiang	3	中国江西省高安市 Gaoan, Jiangxi, China	CHEN et al, 2018^[7]	中国南部 South China
皖南牛 Wannan cattle	Wannan	5	中国安徽省宣城市 Xuancheng, Anhui, China	CHEN et al, 2018^[7]	中国南部 South China
广丰牛 Guangfeng cattle	Guangfeng	4	中国江西省上饶市 Shangrao, Jiangxi, China	CHEN et al, 2018^[7]	中国南部 South China
吉安牛 Ji’an cattle	Jian	4	中国江西省吉安市 Ji’an, Jiangxi, China	CHEN et al, 2018^[7]	中国南部 South China
雷琼牛 Leiqiong cattle	Leiqiong	3	中国广东省湛江市 Zhanjiang, Guangdong, China	CHEN et al, 2018^[7]	中国南部 South China
雷琼牛 Leiqiong cattle	Leiqiong	17	中国广东省湛江市 Zhanjiang, Guangdong, China	本研究 Present study	中国南部 South China
陆丰黄牛 Lufeng cattle	Lufeng	12	中国广东省汕尾市 Shanwei, Guangdong, China	本研究 Present study	中国南部 South China
文山牛 Wenshan cattle	Wenshan	6	中国云南省文山壮族苗族自治州 Wenshan, Yunnan, China	CHEN et al, 2018^[7]	中国南部 South China
舟山牛 Zhoushan cattle	Zhoushan	6	中国浙江省舟山市 Zhoushan, Zhejiang, China	JIANG et al, 2021^[15]	中国南部 South China
温岭高峰牛 Wenling Hump cattle	Wenling	6	中国浙江省温岭市 Wenling, Zhejiang, China	JIANG et al, 2021^[15]	中国南部 South China
哈里亚娜牛 Hariana cattle	Hariana	1	印度哈里亚纳邦古尔加翁县 Gurgaon, Haryana, India	CHEN et al, 2018^[7]	印巴地区 India-Paksitan
吉尔牛 Gir cattle	Gir	2	印度古吉拉特邦艾哈迈达巴德 Amblash, Gujarat, India	BICKHART et al, 2016^[31]	印巴地区 India-Paksitan
沙希华牛 Sahiwal cattle	Sahiwal	1	巴基斯坦旁遮普省萨希瓦尔 Sahiwal, Punjab, Pakistan	CHEN et al, 2018^[7]	印巴地区 India-Paksitan
内洛尔牛 Nelore cattle	Nelore	1	印度安得拉邦内洛尔县 Nelore, Andhra, India	BICKHART et al, 2016^[31]	印巴地区 India-Paksitan
塔帕卡牛 Tharparkar cattle	Tharparkar	1	巴基斯坦信德省塔帕卡 Tharparkar, Sindh, Pakistan	CHEN et al, 2018^[7]	印巴地区 India-Paksitan
婆罗门牛 Brahman cattle	Brahman	5	印度西孟加拉邦婆罗门 Brahman, West Bengal, India	BICKHART et al, 2016^[31]	印巴地区 India-Paksitan
总计 Total	25品种 25 breeds	121个体 121 individuals

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基于全基因组SNPs分析陆丰黄牛和雷琼牛的群体结构与遗传多样性特征

Population Structure and Genetic Diversity of Lufeng Cattle and Leiqiong Cattle Based on Genome-Wide SNPs

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