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

Abstract

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

CLC Number:

S827.2

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.

Figures/Tables 10

Fig. 1

Table 1

Summary of sequencing data and alignment results"

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

Table 1

Fig. 2

Fig. 3

Table 2

Fig. 4

Fig. 5

Fig. 6

Fig. 7

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

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