基于SNP芯片的固原鸡遗传结构与保种效果分析

doi:10.3969/j.issn.1004-1524.20230185

浙江农业学报 ›› 2024, Vol. 36 ›› Issue (7): 1530-1536.DOI: 10.3969/j.issn.1004-1524.20230185

基于SNP芯片的固原鸡遗传结构与保种效果分析

张海洋¹(), 黄宣¹, 周薇¹, 向鑫¹, 马玉芳², 尹兆正¹^,^*()

1.浙江大学动物科学学院,浙江杭州 310058
2.宁夏好水川食品有限公司,宁夏固原 756099

收稿日期:2023-02-21 出版日期:2024-07-25 发布日期:2024-08-05
作者简介:张海洋(1997—),男,河南信阳人,硕士,主要从事家禽遗传育种与繁殖研究。E-mail: 22017062@zju.edu.cn
通讯作者: *尹兆正,E-mail: yzhzh@zju.edu.cn
基金资助:
宁夏回族自治区重点研发计划(2021BBF02018)

Analysis of genetic structure and conservation effect of Guyuan chicken based on SNP chip

ZHANG Haiyang¹(), HUANG Xuan¹, ZHOU Wei¹, XIANG Xin¹, MA Yufang², YIN Zhaozheng¹^,^*()

1. College of Animal Science, Zhejiang University, Hangzhou, 310058, China
2. Ningxia Haoshuichuan Food Co., Ltd., Guyuan 756099, Ningxia, China

Received:2023-02-21 Online:2024-07-25 Published:2024-08-05

摘要/Abstract

摘要：

了解固原鸡的保种效果,为更好地保护和利用固原鸡这一重要地方种质资源提供参考和帮助。从固原鸡群体中随机采集公鸡、母鸡各30只血样,采用“京芯一号”55K芯片技术对固原鸡进行保种分析。结果显示,固原鸡群体有效含量为8.9,多态标记比例为0.828,期望杂合度为0.360,观测杂合度为0.359,说明该群体遗传变异较小,整齐度较高;G矩阵表明该群体中存在近亲交配的趋势;在检测到的1 431个长纯合片段(runs of homozygosity, ROH)中,ROH长度在50~100 Mb的个体数量最多,占比达36.67%,该群体平均近交系数为0.11。结合基因组亲缘关系分析和聚类分析结果,现有30只公鸡样本可以划分为10个家系,其中25只母鸡分别划入不同家系,另外5只母鸡和所检测的公鸡亲缘关系系数均小于0.1,亲缘关系都比较远,因此,将它们归入了“其他”分类中。综上所述,该保种固原鸡群体遗传变异较小,选育程度较高,为降低群体的近交增量,后期的保种过程中需考虑亲缘关系再进行配种。

关键词: 固原鸡, 保种分析, SNP芯片, 亲缘关系

Abstract:

In order to understand the conservation effect of Gujun chicken and provide reference and help for better protection and utilization of Gujun chicken, an important local germplasm resource. Blood samples of 30 roosters and 30 hens were randomly collected from Guyuan chicken population, and the conservation of Guyuan chicken was analyzed by “Jingxin No.1” 55K chip technology. The results showed that the effective population size was 8.9, the proportion of polymorphic markers was 0.828, the expected heterozygosity was 0.360, and the observed heterozygosity was 0.359, which indicated that the genetic variation of the population was small and the uniformity was high; and the G matrix showed that there was a trend of inbreeding in the population; Among the 1 431 runs of homozygosity (ROH), the number of individuals with ROH between 50 Mb and 100 Mb was the largest, accounting for 36.67%, and the average inbreeding coefficient was 0.11. According to the results of genetic relationship analysis and cluster analysis, the 30 roosters were divided into 10 families, of which 25 hens were divided into different families, and the kinship coefficients between the other 5 hens and the tested cocks were all less than 0.1, so they were classified as “others”. To sum up, the genetic variation of the conserved Guyuan chicken population was small and the breeding degree was high, in order to reduce the inbreeding increment of the population, it was necessary to consider the genetic relationship before mating in the later conservation process.

Key words: Guyuan chicken, species conservation analysis, SNP chip, genetic relationship

中图分类号:

S831.2

张海洋, 黄宣, 周薇, 向鑫, 马玉芳, 尹兆正. 基于SNP芯片的固原鸡遗传结构与保种效果分析[J]. 浙江农业学报, 2024, 36(7): 1530-1536.

ZHANG Haiyang, HUANG Xuan, ZHOU Wei, XIANG Xin, MA Yufang, YIN Zhaozheng. Analysis of genetic structure and conservation effect of Guyuan chicken based on SNP chip[J]. Acta Agriculturae Zhejiangensis, 2024, 36(7): 1530-1536.

图/表 7

参考文献 19

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分析内容 Analysis content	软件 Software	基因型数据质控标准 Quality control standards of genotype data
P_N	Plink(V1.90)+R	使用常染色体上的位点,SNP检出率≥90% Using loci on autosomes, SNP detection rate≥ 90%
PIC	Plink(V1.90)+ R	个体检出率大于等于90%,哈迪温伯格P值≥0.000 001 Individual detection rate≥90%, Hardy Weinberg P-value≥ 0.000 001
有效等位基因数 Number of effective allele	Plink(V1.90)+ R	使用常染色体上的位点 Using loci on autosomes
N_e	SNeP(V1.1)+ R	SNP检出率≥90% SNP detection rate≥90%
H_e,H_o	Plink(V1.90)+ R	个体检出率大于等于90% Individual detection rate≥90%
G矩阵分析G matrix analysis	GCTA(V1.94)+ R	最小等位基因频率(MAF)≥0.01 Minimum allele frequency (MAF)≥0.01
IBS遗传距离分析 IBS genetic distance analysis	Plink(V1.90)+ R	哈迪温伯格P值≥0.000 001 Hardy Weinberg P-value≥0.000 001
F_ROH	Plink(V1.90)+R	使用常染色体上的位点,SNP检出率≥90%,个体检出率≥90% Using loci on autosomes, SNP detection rate (call rate)≥90%, individual detection rate≥90%

分析内容 Analysis content	软件 Software	基因型数据质控标准 Quality control standards of genotype data
P_N	Plink(V1.90)+R	使用常染色体上的位点,SNP检出率≥90% Using loci on autosomes, SNP detection rate≥ 90%
PIC	Plink(V1.90)+ R	个体检出率大于等于90%,哈迪温伯格P值≥0.000 001 Individual detection rate≥90%, Hardy Weinberg P-value≥ 0.000 001
有效等位基因数 Number of effective allele	Plink(V1.90)+ R	使用常染色体上的位点 Using loci on autosomes
N_e	SNeP(V1.1)+ R	SNP检出率≥90% SNP detection rate≥90%
H_e,H_o	Plink(V1.90)+ R	个体检出率大于等于90% Individual detection rate≥90%
G矩阵分析G matrix analysis	GCTA(V1.94)+ R	最小等位基因频率(MAF)≥0.01 Minimum allele frequency (MAF)≥0.01
IBS遗传距离分析 IBS genetic distance analysis	Plink(V1.90)+ R	哈迪温伯格P值≥0.000 001 Hardy Weinberg P-value≥0.000 001
F_ROH	Plink(V1.90)+R	使用常染色体上的位点,SNP检出率≥90%,个体检出率≥90% Using loci on autosomes, SNP detection rate (call rate)≥90%, individual detection rate≥90%

家系编号 Family number	公鸡 Rooster	母鸡 Hen
1	M1,M2,M5,M6,M11,M18,M26,M20	F2,F5,F6,F20,F21,F22,F24,F29,F31,F32,F33,F36
2	M8,M19,M30,M21,M14,M22,M29	F12,F1,F17,F9,F13,F3,F4,F5,F31,F7,F14,F36
3	M9,M28,M11	F23,F36,F2,F31,F14,F20,F29
4	M29,M30,M4	F1,F6,F36,F31,F7,F14
5	M4,M24,M27,M31,M15,M29	F1,F6,F36,F21,F20,F17,F3,F12,F13,F27,F19,F31,F7,F14,F32
6	M12,M16,M25	F24,F18,F23,F27,F13,F9,F19,F7
7	M3,M10,M17,M20,M6,M22,M13,M15,M11	F5,F33,F20,F36,F31,F21
8	M6,M17,M20,M3,M5,M7,M1,M21,M22	F32,F2,F6,F21,F29,F5,F33,F20,F23,F24
9	M11,M13,M15,M18,M10,M9,M22,M21,M4	F1,F6,F36,F23,F2,F31,F14,F20,F21,F32,F29,F5
10	M14,M21,M22,M19,M15,M3,M20	F5,F33,F20,F21,F9
其他Other		F10,F8,F11,F16,F30

家系编号 Family number	公鸡 Rooster	母鸡 Hen
1	M1,M2,M5,M6,M11,M18,M26,M20	F2,F5,F6,F20,F21,F22,F24,F29,F31,F32,F33,F36
2	M8,M19,M30,M21,M14,M22,M29	F12,F1,F17,F9,F13,F3,F4,F5,F31,F7,F14,F36
3	M9,M28,M11	F23,F36,F2,F31,F14,F20,F29
4	M29,M30,M4	F1,F6,F36,F31,F7,F14
5	M4,M24,M27,M31,M15,M29	F1,F6,F36,F21,F20,F17,F3,F12,F13,F27,F19,F31,F7,F14,F32
6	M12,M16,M25	F24,F18,F23,F27,F13,F9,F19,F7
7	M3,M10,M17,M20,M6,M22,M13,M15,M11	F5,F33,F20,F36,F31,F21
8	M6,M17,M20,M3,M5,M7,M1,M21,M22	F32,F2,F6,F21,F29,F5,F33,F20,F23,F24
9	M11,M13,M15,M18,M10,M9,M22,M21,M4	F1,F6,F36,F23,F2,F31,F14,F20,F21,F32,F29,F5
10	M14,M21,M22,M19,M15,M3,M20	F5,F33,F20,F21,F9
其他Other		F10,F8,F11,F16,F30

基于SNP芯片的固原鸡遗传结构与保种效果分析

Analysis of genetic structure and conservation effect of Guyuan chicken based on SNP chip

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