基于简化基因组测序(Super-GBS)的子午岭黑山羊保种群遗传结构评估

doi:10.11843/j.issn.0366-6964.2024.10.009

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (10): 4334-4345.doi: 10.11843/j.issn.0366-6964.2024.10.009

基于简化基因组测序(Super-GBS)的子午岭黑山羊保种群遗传结构评估

苟想珍¹(), 杨军祥¹, 赵子惠¹, 冯玲霞¹, 陈万辉¹, 李玉洁², 张忠钰², 马克岩³, 蒋东平⁴, 常嵘⁵, 文亚洲⁶, 王珂¹^,*(), 马友记³^,*()

1. 甘肃省畜牧兽医研究所/农业农村部畜禽资源(羊)评价利用重点实验室, 平凉 744000
2. 华池县畜牧兽医站, 庆阳 745000
3. 甘肃农业大学动物科学技术学院, 兰州 730070
4. 白银市平川区畜牧兽医技术服务中心, 白银 730900
5. 张掖市甘州区动物卫生监督所, 张掖 734000
6. 甘肃省绵羊繁育技术推广站, 张掖 734000

收稿日期:2024-03-25 出版日期:2024-10-23 发布日期:2024-11-04
通讯作者: 王珂,马友记 E-mail:gxz1621@sina.com;592374483@qq.com;yjma@gsau.edu.cn
作者简介:苟想珍(1978-), 女, 甘肃通渭人, 硕士生, 正高级畜牧师, 主要从事羊遗传育种与繁殖的研究, E-mail: gxz1621@sina.com
基金资助:
甘肃省自然基金重点项目(22JR5RA759);甘肃省重点人才项目(2023RCXM67)

Evaluation of the Population Structure of the Ziwuling Black Goat Based on Super-GBS

Xiangzhen GOU¹(), Junxiang YANG¹, Zihui ZHAO¹, Lingxia FENG¹, Wanhui CHEN¹, Yujie LI², Zhongyu ZHANG², Keyan MA³, Dongping JIANG⁴, Rong CHANG⁵, Yazhou WEN⁶, Ke WANG¹^,*(), Youji MA³^,*()

1. Key Laboratory of Livestock and Poultry Resources (Goat) Evaluation and Utilization of Ministry of Agriculture and Rural Affairs, Animal Husbandry and Veterinary Research Institute of Gansu, Pingliang 744000, China
2. Station of Huachi County Animal Science and Veterinary, Qingyang 745000, China
3. College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
4. Pingchuan District Animal Husbandry and Veterinary Technical Service Center, Baiyin 730900, China
5. Animal Health Supervision Institute of Ganzhou District, Zhangye 734000, China
6. Gansu Sheep Breeding Technology Extension Station, Zhangye 734000, China

Received:2024-03-25 Online:2024-10-23 Published:2024-11-04
Contact: Ke WANG, Youji MA E-mail:gxz1621@sina.com;592374483@qq.com;yjma@gsau.edu.cn

摘要/Abstract

摘要：

旨在分析子午岭黑山羊的群体遗传多样性和亲缘关系以及家系结构，为子午岭黑山羊的保护和利用提供依据。本研究通过简化基因组测序(super-genotyping by sequencing，Super-GBS)技术对99只(10公/89母)成年子午岭黑山羊进行全基因组SNP检测。利用Plink软件计算观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC)、核苷酸多样性(Pi)、有效等位基因数(Ne)及次要等位基因频率(MAF)等6项遗传多样性指标；GCTA软件进行主成分分析及基因组亲缘关系G矩阵构建；Plink软件构建IBS遗传距离矩阵，R语言绘制热图；PHYLP构建系统发育树；detect RUNS工具检测ROH。结果表明，99只子午岭黑山羊个体共检测到996 042个SNPs。子午岭黑山羊群体的PIC、Pi、Ne及MAF值分别是0.161、0.193、1.295、0.130，且Ho(0.167)低于He(0.192)，说明子午岭黑山羊群体遗传多样性较低。G矩阵和IBS遗传距离结果均表明子午岭黑山羊群体间大部分个体间亲缘关系较远。主成分分析结果揭示子午岭黑山羊群体内部不存在明显分化，系统发育树结果说明子午岭黑山羊群体公羊可大致分为6个家系，所有家系公羊数量较少。子午岭黑山羊群体的近交系数F_ROH为0.049 6，说明子午岭黑山羊群体内部近交程度相对较低。综上所述，子午岭黑山羊群体遗传多样性较低，大部分个体间亲缘关系较远，群体内近交程度较低，后期应注意后代的选育，避免血统流失。

关键词: 子午岭黑山羊, 简化基因组测序, 群体结构, 遗传多样性, 家系结构, 亲缘关系

Abstract:

This study aimed to assess the genetic diversity and population structure of the Ziwuling black goat, laying the groundwork for the preservation and utilization of this breed. The whole-genome SNP analysis of a total of 99 adult Ziwuling black goats (10 males and 89 females) was performed by super-genotyping by sequencing(super-GBS). Genetic diversity parameters including observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), nucleotide diversity (Pi), effective allele number (Ne), and minor allele frequency (MAF) were calculated using Plink software. Principal component analysis and construction of genetic relationship G matrix were conducted using GCTA software. IBS genetic distance matrix was built using Plink software, and a heatmap was plotted using R language. A phylogenetic tree was constructed using PHYLP, while runs of homozygosity (ROH) were detected using the detect RUNS tool. A total of 996 042 SNPs were detected in the 99 individuals of Ziwuling black goats. The PIC, Pi, Ne, and MAF values of Ziwuling black goats were 0.161, 0.193, 1.295, 0.130, respectively, indicating a relatively low genetic diversity with Ho(0.167) lower than He(0.192). Both the G matrix and IBS genetic distance results showed that most individuals in the Ziwuling black goat population had distant genetic relationships. The principal component analysis revealed no obvious differentiation within the Ziwuling black goat population, while the phylogenetic tree indicated that the rams could be roughly divided into 6 lineages, with few rams in each lineage. The inbreeding coefficient F_ROH of the Ziwuling black goat population was 0.049 6, suggesting a relatively low level of inbreeding within the population. In conclusion, the genetic diversity of the Ziwuling black goat population is relatively low, with most individuals having distant kinship relations and a low level of inbreeding within the group. It is recommended to pay attention to the breeding of offspring in order to avoid loss of genetic diversity in the future.

Key words: Ziwuling black goat, Super-GBS, population structure, genetic diversity, family structure, kinship

中图分类号:

S827.2

苟想珍, 杨军祥, 赵子惠, 冯玲霞, 陈万辉, 李玉洁, 张忠钰, 马克岩, 蒋东平, 常嵘, 文亚洲, 王珂, 马友记. 基于简化基因组测序(Super-GBS)的子午岭黑山羊保种群遗传结构评估[J]. 畜牧兽医学报, 2024, 55(10): 4334-4345.

Xiangzhen GOU, Junxiang YANG, Zihui ZHAO, Lingxia FENG, Wanhui CHEN, Yujie LI, Zhongyu ZHANG, Keyan MA, Dongping JIANG, Rong CHANG, Yazhou WEN, Ke WANG, Youji MA. Evaluation of the Population Structure of the Ziwuling Black Goat Based on Super-GBS[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(10): 4334-4345.

图/表 10

图 1

表 1

测序数据和比对结果统计表"

样品 Sample	过滤后Reads Clean_Reads	比对率/% Mapped_rate	GC含量/% GC_content	>Q30/%	样品 Sample	过滤后Reads Clean_Reads	比对率/% Mapped_rate	GC含量/% GC_content	>Q30/%
HC001	15723786	99.92	51.06	91.06	HC051	18963572	99.93	51.64	90.83
HC002	11357766	99.92	50.88	90.53	HC052	19947760	99.92	51.10	91.39
HC003	11776480	99.92	51.12	90.13	HC053	18207258	99.91	52.57	91.10
HC004	8818160	99.91	50.54	91.02	HC054	16934562	99.89	50.37	91.30
HC005	13691508	99.90	51.40	90.57	HC055	22493854	99.90	51.76	91.33
HC006	14070242	99.90	51.37	90.56	HC056	19388552	99.91	50.63	91.00
HC007	11397596	99.87	51.89	90.49	HC057	15965320	99.88	50.26	90.00
HC008	16374438	99.93	51.73	90.97	HC058	18326812	99.75	50.55	90.50
HC009	19142758	99.93	51.90	91.68	HC059	17913268	99.90	50.70	90.66
HC010	14507570	99.93	51.53	91.63	HC060	17321590	99.93	50.87	90.86
HC011	17512412	99.88	51.96	91.63	HC061	22150354	99.93	51.48	91.08
HC012	18723236	99.92	52.59	91.13	HC062	18028022	99.89	50.91	91.34
HC013	18372780	99.79	52.16	91.05	HC063	21509706	99.89	51.39	91.45
HC014	18031258	99.93	51.92	91.21	HC064	23344710	99.93	51.61	91.77
HC015	17671448	99.94	52.48	91.57	HC065	20725182	99.80	52.15	90.94
HC016	19278720	99.89	51.66	90.35	HC066	18222938	99.91	51.28	91.23
HC017	25453812	99.90	51.32	91.57	HC067	20333588	99.88	50.74	91.03
HC018	20849468	99.92	51.42	91.80	HC068	18042546	99.91	50.76	90.89
HC019	20523396	99.94	51.48	91.76	HC069	18326404	99.90	50.71	90.62
HC020	20669448	99.93	51.86	91.59	HC070	18589752	99.87	50.82	90.83
HC021	18979926	99.94	51.42	91.48	HC071	18716826	99.92	50.66	90.64
HC022	17176094	99.89	51.00	91.36	HC072	20656610	99.86	51.00	91.18
HC023	19853500	99.93	52.96	90.73	HC073	18896944	99.93	51.08	91.69
HC024	20985560	99.94	52.15	91.68	HC075	17405612	99.93	51.57	91.40
HC025	19509332	99.91	51.83	91.30	HC076	19348882	99.92	50.56	90.56
HC026	17655638	99.93	51.68	91.37	HC077	20191532	99.93	50.92	91.01
HC027	20538096	99.93	51.79	91.46	HC078	18494528	99.94	50.48	90.82
HC028	16601072	99.92	51.67	91.27	HC079	21633892	99.91	51.27	91.64
HC029	13994416	99.86	50.21	90.16	HC081	21762888	99.94	52.23	91.07
HC030	21086732	99.76	52.32	91.76	HC082	18036114	99.91	50.65	91.21
HC031	16866210	99.90	50.56	90.51	HC083	18968968	99.91	51.03	90.59
HC032	14888336	99.93	51.70	91.17	HC084	10063902	99.91	50.20	90.01
HC033	18574256	99.66	51.37	90.66	HC085	18163650	99.93	50.54	90.61
HC034	20713514	99.91	51.14	91.40	HC086	19786304	99.90	50.98	91.35
HC035	18454010	99.78	51.53	91.05	HC087	12033866	99.87	50.47	90.44
HC036	16947634	99.91	51.65	91.69	HC088	12369478	99.93	51.19	90.62
HC037	20557184	99.93	51.84	91.40	HC089	19628806	99.92	50.50	91.09
HC038	18808000	99.92	51.15	91.02	HC090	14673620	99.91	50.66	91.18
HC039	13835644	99.91	50.54	90.40	HC080	7976566	99.92	49.84	89.87
HC040	16613790	99.90	50.42	90.45	HC091	16865222	99.93	50.75	90.91
HC041	17281896	99.92	50.59	90.51	HC092	19915634	99.93	51.78	91.46
HC042	19206896	99.91	50.58	90.66	HC093	18589052	99.80	50.80	91.02
HC043	13187640	99.86	50.37	90.32	HC094	17490238	99.92	50.33	90.81
HC044	17946442	99.75	51.44	91.08	HC095	21047088	99.92	50.91	91.08
HC045	14360856	99.93	51.49	90.76	HC096	18793270	99.93	50.83	90.92
HC046	13624786	99.94	50.90	90.78	HC097	19618062	99.93	51.60	91.33
HC047	17759106	99.80	50.40	90.52	HC098	17986048	99.93	50.69	91.37
HC048	14753076	99.79	50.13	90.27	HC099	15075114	99.92	49.94	89.11
HC049	18989696	99.91	51.77	90.91	HC100	24152032	99.94	51.86	91.71
HC050	15230518	99.91	50.24	90.13

表 1

图 2

图 3

表 2

图 4

图 5

图 6

图 7

图 8

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指标 Index	参数值(平均值) Parameter value (Mean value)
观测杂合度Observed heterozygosity(Ho)	0.000~1.000(0.167)
期望杂合度Expected heterozygosity(He)	0.020~0.500(0.192)
有效等位基因数Effective number of alleles(Ne)	1.020~2.00(1.295)
多态信息含量Polymorphic information content(PIC)	0.020~0.375(0.161)
核苷酸多样性Nucleotide diversity(Pi)	0.020~0.503(0.193)
次要等位基因频率Minor allele frequency(MAF)	0.010~0.5(0.130)

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基于简化基因组测序(Super-GBS)的子午岭黑山羊保种群遗传结构评估

Evaluation of the Population Structure of the Ziwuling Black Goat Based on Super-GBS

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