北京黑猪全基因组ROH检测和选择信号分析

doi:10.11843/j.issn.0366-6964.2024.09.009

摘要/Abstract

摘要：

旨在基于长纯合片段(ROH)和选择信号iHS分析北京黑猪群体的遗传结构，挖掘与经济性状相关的候选基因。本研究的对象为北京黑猪群体，平均日龄为210 d。对729头北京黑猪的illumina Porcine 50K芯片数据进行质控和填充后，进行ROH和iHS的分析。本研究选择参与组成ROHs的前1%的SNPs作为ROH岛的阈值，将超过此阈值的区域称为ROH岛。保留标准化的|iHS|值中排在前1%的所有SNPs位点，将位点上下游各延伸200 kb作为选择信号iHS得到的强受选择区域。将选择信号的强受选择区域与ROH岛重叠的区段定为本研究的候选区域。本研究最终保留724个体和45 585个SNPs，通过ROH分析共识别到10个ROH岛，这些岛内包含449个SNPs。iHS分析的结果显示，保留得分排在前1%的位点后，共有376个强受选择位点。最终，在iHS的强受选择区域与ROH岛的5个重叠区域内注释到18个基因，其中包括一些已知的影响猪肉质和生长发育过程的基因。本研究分析了北京黑猪群体ROH的分布，并结合选择信号，揭示了北京黑猪受选择的位点和候选基因，该研究结果为深入探讨北京黑猪的群体特性及经济性状的遗传机制提供重要参考。

关键词: 北京黑猪, 芯片数据, ROH, iHS

Abstract:

This study aimed to investigate the genetic structure of the Beijing black pigs based on runs of homozygosity (ROH) and selection signals|iHS|analysis and to identify candidate genes related to economic traits. The subjects of this study were Beijing black pigs, with an average age of 210 days. After quality control and imputation of the illumina Porcine 50K chip data from 729 Beijing black pigs, the ROH and|iHS|were analyzed. In this study, the threshold for ROH islands was set at the SNPs that constituted the top 1% of ROHs, and regions exceeding this threshold were termed ROH islands. All SNPs in the top 1% of standardized |iHS| values were retained, and the areas extending 200 kb upstream and downstream of these SNPs were considered as the strong selection regions obtained by the iHS. The overlapping areas between the strong selection regions of the selection signals and the ROH islands were defined as the candidate regions for this study. In this study, 724 individuals and 45 585 SNPs were retained, and a total of 10 ROH islands containing 449 SNPs were identified by ROH analysis, and the results of|iHS|analysis showed that a total of 376 strongly selected SNPs were retained after the top 1% SNPs with the highest score were retained. In the end, a total of 18 genes in the overlapping regions of the 5 strongly selected regions of |iHS| and ROH islands were annotated, including some genes known to affect pork quality and growth and development. This study analyzed the distribution of ROH in the Beijing black pigs and revealed potential selected SNPs and candidate genes combined with selection signals. The results provide an important reference for further exploring the population characteristics and genetic mechanisms of economic traits of Beijing black pigs.

Key words: Beijing black pig, chip data, ROH, iHS

中图分类号:

S828.2

田晶晶, 王晓庆, 李棉燕, 王海玲, 吴启钿, 王立贤, 张龙超, 赵福平. 北京黑猪全基因组ROH检测和选择信号分析[J]. 畜牧兽医学报, 2024, 55(9): 3833-3842.

Jingjing TIAN, Xiaoqing WANG, Mianyan LI, Hailing WANG, Qitian WU, Lixian WANG, Longchao ZHANG, Fuping ZHAO. Analysis of the Whole Genome Run of Homozygosity (ROH) and Selection Signal in Beijing Black Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(9): 3833-3842.

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ROH分类 Type of ROH	数量 Number	百分比/% Percentage	均值/Mb Mean	总长度/Mb Total length	长度百分比/% Length percentage
1~5 Mb	28 315	59.99	3.07	86 848.9	28.68
5~10 Mb	11 869	25.15	6.88	81 660.9	26.97
10~20 Mb	4 994	10.58	13.59	67 863.5	22.41
20~40 Mb	1 604	3.40	26.69	42 818.2	14.14
>40 Mb	419	0.89	56.40	23 630.1	7.80

染色体 Chromosome	起始位点/bp Start	终止位点/bp End	SNPs数目 SNPs number	基因数目 Gene number
1	59 620 943	61 060 616	24	2
1	61 246 160	63 012 075	34	2
1	266 123 073	266 123 073	1	1
13	1 967 845	4 228 022	69	16
15	25 472 091	29 112 719	119	2
5	16 390 314	17 316 265	26	8
6	4 546 603	8 502 813	112	20
7	69 872 560	74 920 040	57	12
8	122 505 268	122 951 435	6	0
9	9 902 154	10 035 783	1	2

F_ROH	F_ROH-total	F_ROH1-5	F_ROH5-10	F_ROH10-20	F_ROH20-40	F_ROH>40
均值 Mean	0.185	0.053	0.050	0.041	0.026	0.014

候选区域 Candidate region	基因 Gene
5:16 804 202-17 204 202	SLC4A8、SCN8A、FIGNL2
6:4 749 263-7 182 078	HSBP1、CDH13、HSD17B2、SDR42E1、PLCG2、CMIP、GAN、BCO1、PKD1L2
6:7 326 054-8 502 813	CDYL2、DYNLRB2、U6、MAF
15:25 472 091-27 498 595	GYPC、CNTNAP5
15:28 664 951-29 064 951	NA

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