基于SNP芯片信息分析西藏四个本地牛种的血统组成

doi:10.11843/j.issn.0366-6964.2024.10.012

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (10): 4377-4390.doi: 10.11843/j.issn.0366-6964.2024.10.012

基于SNP芯片信息分析西藏四个本地牛种的血统组成

马龙刚¹(), 刘楠², 尼玛群宗², 王欣³, 陆健⁴, 毛华明⁵, 陈功⁶, 旦增欧珠², 拉巴次仁², 张楠², 于福清⁴, 王雅春¹^,*()

1. 中国农业大学动物科学技术学院, 北京 100193
2. 西藏自治区动物疫病预防控制中心, 拉萨 850009
3. 北京奶牛中心, 北京 100192
4. 全国畜牧总站, 北京 100125
5. 云南农业大学动物科学技术学院, 昆明 650201
6. 北京交通大学生命科学与生物工程研究院, 北京 100044

收稿日期:2024-04-07 出版日期:2024-10-23 发布日期:2024-11-04
通讯作者: 王雅春 E-mail:13369452684@163.com;wangyachun@cau.edu.cn
作者简介:马龙刚(1996-), 男, 甘肃天水人, 硕士, 主要从事分子及数量遗传学研究, E-mail: 13369452684@163.com
基金资助:
西藏自治区重点研发计划(CGZH2023000257);国家现代农业产业技术体系(CARS-36);；西藏自治区区域协同创新专项(QYXTZX-LS2021-01)

Study on the Genetic Composition of Four Local Tibetan Cattle Breeds Based on SNP Chip Analysis

Longgang MA¹(), Nan LIU², MA Qunzong NI², Xin WANG³, Jian LU⁴, Huaming MAO⁵, Gong CHEN⁶, ZENG Ouzhu DAN², BA Ciren LA², Nan ZHANG², Fuqing YU⁴, Yachun WANG¹^,*()

1. College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
2. Animal Disease Prevention and Control Center of Tibet Autonomous Region, Lhasa 850009, China
3. Beijing Dairy Cattle Center, Beijing 100192, China
4. National Animal Husbandry Station, Beijing 100125, China
5. College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
6. Institute of Life Science and Bioengineering, Beijing JiaoTong University, Beijing 100044, China

Received:2024-04-07 Online:2024-10-23 Published:2024-11-04
Contact: Yachun WANG E-mail:13369452684@163.com;wangyachun@cau.edu.cn

摘要/Abstract

摘要：

旨在探究西藏4个本地牛种的遗传结构和血统组成。本研究以22头高原荷斯坦牛与20头高原娟姗牛以及45头美国婆罗门牛、46头云南瘤牛和11头婆罗门牛为参照标准品种，待测样品为4个西藏本地品种的177头牛。通过Illumina GGP100K芯片杂交获取所有待测个体的SNPs数据，利用MEGA X和Admixture等软件对SNPs进行遗传结构与血统组成分析。结果表明，西藏牛较其他西藏本地牛种与高原荷斯坦牛和高原娟姗牛有更近的遗传关系；部分樟木牛和阿沛甲咂牛将西藏牛分为两个大群；日喀则驼峰牛与云南瘤牛遗传关系更近。在日喀则驼峰牛群体中，高原牛血统比例超过90%，在阿沛甲咂牛与西藏牛群体中，高原牛血统也超过了50%，仅在樟木牛群体中，高原牛血统比例为33.15%。其次，在樟木牛群体中，瘤牛血统占比高达18.27%，在阿沛甲咂牛、西藏牛与日喀则驼峰牛群体中，瘤牛血统较少(5%)。在阿沛甲咂牛群体内有高达35.94%的普通牛血统，在樟木牛群体内，奶牛血统高达48.58%。本研究对西藏本地牛种今后的杂交扩繁和横交固定提供了重要指导作用，也为阿沛甲咂牛与樟木牛两个濒危品种的资源保护和利用提供了理论参考。

关键词: 阿沛甲咂牛, 樟木牛, 西藏牛, 日喀则驼峰牛, SNPs数据, 遗传结构, 血统组成

Abstract:

The study aimed to explore the genetic structure and bloodline composition of 4 local cattle breedings in Tibet. In this study, 22 plateau Holstein cattle, 20 plateau Jersey cattle, 45 American Brahmin cattle, 46 Yunnan Zebu and 11 Brahmen cattle as reference breeds, the samples to be tested were 177 cattle of 4 local breeds in Tibet. SNPs data were obtained by Illumina GGP100K chip hybridization, and the genetic structure and bloodline composition of SNPs were analyzed by MEGA X and Admixture. The results showed that Tibetan cattle had a closer genetic relationship with plateau Holstein cattle and plateau Jersey cattle than other local cattle breeds in Tibet. Some Zhangmu cattle and Apeijia cattle divided Tibetan cattle into two large subpopulations; There was a close genetic relationship between Shigatse hump cattle and Yunnan Zebu. In the Shigatse hump cattle population, the proportion of plateau cattle bloodline was more than 90%, in the Apaijia cattle population and Tibet cattle population, the proportion of plateau cattle bloodline was more than 50%, only in the Zhangmu cattle population, the proportion of plateau cattle bloodline was 33.15%. Secondly, bos indicus bloodline accounted for 18.27% in Zhangmu cattle population, while bos indicus bloodline was less (5%) in Apaijiza cattle, Tibet cattle and Shigatse hump cattle population. There were 35.94% dairy cattle bloodline in Apaijia population and 48.58% dairy cattle bloodline in Zhangmu population. This study provided important guidance for the future cross-breeding and cross-fixing of the native cattle species in Tibet, and also provided theoretical reference for the conservation and utilization of the resources of the two endangered breeds of Apaijiza cattle and Zhangmu cattle.

Key words: Apejiaza cattle, Zhangmu cattle, Tibetan cattle, Shigatse hump cattle, SNPs data, genetic structure, bloodline composition

中图分类号:

S823.2

马龙刚, 刘楠, 尼玛群宗, 王欣, 陆健, 毛华明, 陈功, 旦增欧珠, 拉巴次仁, 张楠, 于福清, 王雅春. 基于SNP芯片信息分析西藏四个本地牛种的血统组成[J]. 畜牧兽医学报, 2024, 55(10): 4377-4390.

Longgang MA, Nan LIU, MA Qunzong NI, Xin WANG, Jian LU, Huaming MAO, Gong CHEN, ZENG Ouzhu DAN, BA Ciren LA, Nan ZHANG, Fuqing YU, Yachun WANG. Study on the Genetic Composition of Four Local Tibetan Cattle Breeds Based on SNP Chip Analysis[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(10): 4377-4390.

图/表 9

表 1

图 1

图 2

图 3

表 2

阿沛甲咂牛种血统组成统计"

样本编号 Number of samples	高原牛血统 Plateau cattle bloodline	奶牛血统HO&JS Dairy cattle bloodline	瘤牛血统YL&PLM&APLM Bos indicus bloodline
XZ_XZ130A1	0.591 808	0.337 569	0.070 623
XZ_XZ131A2	0.650 873	0.349 117	0.000 010
XZ_XZ132A3	0.635 391	0.278 572	0.086 037
XZ_XZ133A4	0.625 004	0.264 077	0.110 919
XZ_XZ134A5	0.599 911	0.297 645	0.102 445
XZ_XZ135A6	0.595 588	0.291 839	0.112 573
XZ_XZ136A7	0.559 761	0.440 229	0.000 010
XZ_XZ137A8	0.464 256	0.525 932	0.009 813
XZ_XZ138A9	0.505 470	0.494 520	0.000 010
XZ_XZ139A10	0.621 555	0.378 435	0.000 010
XZ_XZ140A11	0.629 386	0.325 753	0.044 861
XZ_XZ141A12	0.578 619	0.421 371	0.000 010
XZ_XZ142A13	0.568 924	0.431 066	0.000 010
XZ_XZ143A14	0.630 678	0.296 967	0.072 355
XZ_XZ144A15	0.615 776	0.376 662	0.007 563
XZ_XZ145A16	0.603 238	0.306 934	0.089 828
XZ_XZ146A17	0.615 065	0.384 925	0.000 010
XZ_XZ147A18	0.560 493	0.439 497	0.000 010
XZ_XZ148A19	0.591 752	0.383 408	0.024 840
XZ_XZ149A20	0.614 305	0.310 690	0.075 005
XZ_XZ150A21	0.464 667	0.535 323	0.000 010
XZ_XZ151A22	0.499 923	0.500 067	0.000 010
XZ_XZ152A23	0.580 664	0.406 541	0.012 794
XZ_XZ153A24	0.584 292	0.342 017	0.073 691
XZ_XZ154A25	0.584 141	0.415 849	0.000 010
XZ_XZ155A26	0.602 120	0.358 702	0.039 178
XZ_XZ156A27	0.612 105	0.387 885	0.000 010
XZ_XZ157A28	0.618 876	0.245 122	0.136 002
XZ_XZ158A29	0.610 937	0.309 870	0.079 193
XZ_XZ159A30	0.638 190	0.327 481	0.034 328
XZ_XZ140A11	0.591 614	0.371 062	0.037 325
XZ_XZ160A31	0.579 055	0.256 812	0.164 134
XZ_XZ161A32	0.604 542	0.334 637	0.060 821
XZ_XZ162A33	0.650 543	0.295 178	0.054 279
XZ_XZ163A34	0.580 946	0.286 235	0.132 819
XZ_XZ164A35	0.597 039	0.376 766	0.026 195
XZ_XZ165A36	0.585 410	0.326 809	0.087 781
XZ_XZ166A37	0.641 904	0.358 086	0.000 010
XZ_XZ167A38	0.622 421	0.245 618	0.131 961
XZ_XZ168A39	0.591 808	0.337 569	0.070 623

表 2

表 3

表 4

西藏牛种血统组成统计"

样本编号 Number of samples	高原牛血统 Plateau cattle bloodline	奶牛血统HO&JS Dairy cattle bloodline	瘤牛血统YL&PLM&APLM Bos indicus bloodline
XZ_XZ10X1	0.622 872	0.308 491	0.068 637
XZ_XZ11X2	0.633 158	0.363 321	0.003 521
XZ_XZ12X3	0.646 045	0.327 586	0.026 369
XZ_XZ13X4	0.635 350	0.279 115	0.085 535
XZ_XZ14X5	0.638 679	0.325 750	0.035 571
XZ_XZ15X6	0.603 639	0.315 973	0.080 389
XZ_XZ16X7	0.609 889	0.233 567	0.156 543
XZ_XZ17X8	0.652 039	0.329 176	0.018 785
XZ_XZ18X9	0.635 890	0.307 220	0.056 890
XZ_XZ19X10	0.631 742	0.335 706	0.032 552
XZ_XZ20X11	0.611 872	0.388 118	0.000 010
XZ_XZ21X12	0.594 332	0.405 658	0.000 010
XZ_XZ22X13	0.572 545	0.427 445	0.000 010
XZ_XZ23X14	0.637 320	0.312 323	0.050 358
XZ_XZ24X15	0.630 524	0.305 918	0.063 558
XZ_XZ25X16	0.633 546	0.306 382	0.060 072
XZ_XZ26X17	0.613 711	0.288 301	0.097 987
XZ_XZ27X18	0.404 625	0.595 365	0.000 010
XZ_XZ28X19	0.642 301	0.337 137	0.020 562
XZ_XZ29X20	0.631 345	0.304 976	0.063 678
XZ_XZ30X21	0.630 991	0.320 005	0.049 004
XZ_XZ31X22	0.615 252	0.264 151	0.120 597
XZ_XZ32X23	0.611 422	0.304 258	0.084 320
XZ_XZ33X24	0.517 562	0.482 428	0.000 010
XZ_XZ34X25	0.459 532	0.513 612	0.026 856
XZ_XZ35X26	0.527 868	0.472 122	0.000 010
XZ_XZ36X27	0.623 479	0.306 017	0.070 504
XZ_XZ37X28	0.435 248	0.483 450	0.081 302
XZ_XZ38X29	0.616 798	0.383 192	0.000 010
XZ_XZ39X30	0.577 093	0.422 897	0.000 010
XZ_XZ40XD1	0.325 353	0.674 637	0.000 010
XZ_XZ41XD2	0.600 257	0.399 733	0.000 010
XZ_XZ42XD3	0.430 266	0.569 724	0.000 010
XZ_XZ43XD4	0.405 176	0.594 814	0.000 010
XZ_XZ44XD5	0.374 860	0.625 130	0.000 010
XZ_XZ45XD6	0.385 590	0.614 400	0.000 010
XZ_XZ46X40	0.432 893	0.567 097	0.000 010
XZ_XZ47X41	0.625 818	0.279 362	0.094 819
XZ_XZ48X42	0.622 711	0.377 279	0.000 010
XZ_XZ49X43	0.391 394	0.608 596	0.000 010
XZ_XZ50X44	0.283 703	0.716 287	0.000 010
XZ_XZ51X45	0.383 231	0.616 759	0.000 010
XZ_XZ52X46	0.359 128	0.640 862	0.000 010
XZ_XZ53X47	0.610 206	0.389 784	0.000 010
XZ_XZ54X48	0.603 838	0.396 152	0.000 010
XZ_XZ55X49	0.587 840	0.337 553	0.074 607
XZ_XZ56X50	0.466 024	0.533 966	0.000 010
XZ_XZ57X51	0.616 003	0.327 261	0.056 736
XZ_XZ58X52	0.638 859	0.331 216	0.029 925
XZ_XZ59X53	0.610 792	0.345 997	0.043 211
XZ_XZ60X54	0.577 660	0.422 330	0.000 010
XZ_XZ61X55	0.433 269	0.566 721	0.000 010
XZ_XZ62X56	0.465 059	0.534 931	0.000 010
XZ_XZ63X57	0.414 089	0.585 901	0.000 010
XZ_XZ64X58	0.423 080	0.576 910	0.000 010
XZ_XZ65X59	0.445 328	0.554 662	0.000 010
XZ_XZ66X60	0.441 022	0.558 968	0.000 010
XZ_XZ67X61	0.355 537	0.644 453	0.000 010
XZ_XZ68X62	0.430 559	0.569 431	0.000 010
XZ_XZ69X63	0.428 978	0.571 012	0.000 010
XZ_XZ70X64	0.514 546	0.485 444	0.000 010

表 4

表 5

日喀则驼峰牛种血统组成统计"

样本编号 Number of samples	高原牛血统 Plateau cattle bloodline	奶牛血统HO&JS Dairy cattle bloodline	瘤牛血统YL&PLM&APLM Bos indicus bloodline
XZ_XZ72T2	0.999 980	0.000 010	0.000 010
XZ_XZ73T3	0.922 479	0.057 603	0.019 918
XZ_XZ74T4	0.831 484	0.120 605	0.047 911
XZ_XZ75T5	0.680 514	0.181 640	0.137 846
XZ_XZ76T6	0.798 369	0.152 918	0.048 714
XZ_XZ77T7	0.976 787	0.023 203	0.000 010
XZ_XZ78T8	0.999 980	0.000 010	0.000 010
XZ_XZ79T9	0.807 248	0.139 684	0.053 068
XZ_XZ80T10	0.999 980	0.000 010	0.000 010
XZ_XZ81T11	0.999 980	0.000 010	0.000 010
XZ_XZ82T12	0.999 977	0.000 013	0.000 010
XZ_XZ83T13	0.882 359	0.117 631	0.000 010
XZ_XZ84T14	0.884 968	0.104 265	0.010 767
XZ_XZ85T15	0.963 772	0.036 218	0.000 010
XZ_XZ86T16	0.863 891	0.073 225	0.062 884
XZ_XZ87T17	0.999 980	0.000 010	0.000 010
XZ_XZ89T19	0.852 990	0.127 367	0.019 643
XZ_XZ90T20	0.883 743	0.102 123	0.014 133
XZ_XZ91T21	0.953 611	0.046 379	0.000 010
XZ_XZ92T22	0.620 491	0.232 930	0.146 578
XZ_XZ93T23	0.915 620	0.084 370	0.000 010
XZ_XZ94T24	0.930 951	0.069 039	0.000 010
XZ_XZ95T26	0.921 803	0.078 187	0.000 010
XZ_XZ96T28	0.999 980	0.000 010	0.000 010
XZ_XZ97T29	0.926 863	0.073 127	0.000 010
XZ_XZ98T30	0.908 525	0.091 465	0.000 010
XZ_XZ99T31	0.999 980	0.000 010	0.000 010
XZ_XZ100T32	0.594 266	0.286 145	0.119 589
XZ_XZ101T33	0.969 662	0.030 328	0.000 010
XZ_XZ102T34	0.952 904	0.025 523	0.021 572
XZ_XZ103T35	0.856 997	0.142 993	0.000 010
XZ_XZ104T36	0.979 404	0.020 586	0.000 010
XZ_XZ105T37	0.941 707	0.058 283	0.000 010
XZ_XZ106T38	0.999 980	0.000 010	0.000 010
XZ_XZ107T39	0.999 980	0.000 010	0.000 010
XZ_XZ108T40	0.874 609	0.125 381	0.000 010
XZ_XZ109T41	0.822 893	0.177 097	0.000 010
XZ_XZ110T42	0.993 389	0.006 601	0.000 010
XZ_XZ111T43	0.962 979	0.037 011	0.000 010
XZ_XZ112T44	0.953 058	0.046 932	0.000 010
XZ_XZ113T45	0.928 898	0.071 092	0.000 010
XZ_XZ114T46	0.807 205	0.176 474	0.016 321
XZ_XZ115T47	0.916 653	0.081 226	0.002 121
XZ_XZ116T48	0.999 980	0.000 010	0.000 010
XZ_XZ117T49	0.880 538	0.072 113	0.047 349
XZ_XZ118T51	0.900 973	0.099 017	0.000 010
XZ_XZ119T52	0.927 356	0.072 634	0.000 010
XZ_XZ120T53	0.838 603	0.086 573	0.074 824
XZ_XZ121T54	0.794 682	0.205 308	0.000 010
XZ_XZ122T55	0.922 265	0.061 969	0.015 767
XZ_XZ123T56	0.972 426	0.027 564	0.000 010
XZ_XZ124T57	0.646 169	0.224 953	0.128 878
XZ_XZ125T59	0.999 980	0.000 010	0.000 010
XZ_XZ126T60	0.956 114	0.043 876	0.000 010
XZ_XZ127T61	0.818 665	0.103 817	0.077 518
XZ_XZ128T62	0.921 174	0.078 816	0.000 010
XZ_XZ129T63	0.943 591	0.056 399	0.000 010

表 5

表 6

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群体名称 Population name	分组 Group	数量/头 Number	活动区域 Distribution area	数据来源 Data source
西藏牛XZ	XZ	61	拉萨市附近	自测
阿沛甲咂牛AP	XZ	39	工布江达县	自测
日喀则驼峰牛TF	XZ	57	日喀则市	自测
樟木牛ZM	XZ	20	日喀则市樟木镇	自测
荷斯坦牛HO	NN	22	拉萨市	自测
娟姗牛JS	NN	20	拉萨市	自测
云南瘤牛LN	LN	46	云南省	自测
婆罗门牛PLM	LN	11	云南省	自测
美国婆罗门牛APLM	LN	45	/	WIDDE

样本编号 Number of samples	高原牛血统 Plateau cattle bloodline	奶牛血统HO&JS Dairy cattle bloodline	瘤牛血统YL&PLM&APLM Bos indicus bloodline
XZ_XZ1Z1	0.374 161	0.538 873	0.086 966
XZ_XZ2Z2	0.557 966	0.417 791	0.024 243
XZ_XZ3Z3	0.268 150	0.594 257	0.137 593
XZ_XZ4Z4	0.461 712	0.538 278	0.000 010
XZ_XZ5Z5	0.349 663	0.591 801	0.058 537
XZ_XZ6Z6	0.191 895	0.543 071	0.265 034
XZ_XZ7Z7	0.433 616	0.566 374	0.000 010
XZ_XZ8Z8	0.101 796	0.421 195	0.477 009
XZ_ZMN01	0.198 054	0.432 891	0.369 055
XZ_ZMN02	0.397 534	0.586 953	0.015 512
XZ_ZMN03	0.426 174	0.573 816	0.000 010
XZ_ZMN04	0.473 77	0.526 220	0.000 010
XZ_ZMN07	0.323 625	0.603 089	0.073 286
XZ_ZMN09	0.084 154	0.668 482	0.247 364
XZ_ZMN13	0.417 285	0.569 806	0.012 909
XZ_ZMN14	0.297 964	0.607 186	0.094 849
XZ_ZMN15	0.429 561	0.271 353	0.299 086
XZ_ZMN16	0.319 767	0.175 883	0.504 349
XZ_ZMN17	0.306 641	0.129 275	0.564 084
XZ_ZMN18	0.216 045	0.359 326	0.424 629

品种 Breed	血统 Bloodline	均值±标准差 Mean±SD	变异系数% Coefficient of variation
阿沛甲咂牛	高原牛血统	0.592 493±0.043 725	7.38
Apeijiaza cattle	奶牛血统	0.359 366±0.073 970	20.58
	瘤牛血统	0.048 141±0.048 222	100.17
樟木牛Zhangmu cattle	高原牛血统	0.331 480±0.128 460	37.06
	奶牛血统	0.485 800±0.145 540	29.96
	瘤牛血统	0.182 730±0.189 080	103.47
西藏牛Tibet cattle	高原牛血统	0.534 094±0.105 343	19.72
	奶牛血统	0.438 804±0.128 865	29.37
	瘤牛血统	0.027 102±0.037 541	138.52
日喀则驼峰牛	高原牛血统	0.905 323±0.096 382	10.65
Shigatse Humped cattle	奶牛血统	0.075 979±0.067 516	88.86
	瘤牛血统	0.018 698±0.037 191	198.91

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基于SNP芯片信息分析西藏四个本地牛种的血统组成

Study on the Genetic Composition of Four Local Tibetan Cattle Breeds Based on SNP Chip Analysis

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