豫农黑猪生长相关性状的拷贝数变异全基因组关联分析研究

doi:10.11843/j.issn.0366-6964.2025.03.013

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (3): 1110-1119.doi: 10.11843/j.issn.0366-6964.2025.03.013

豫农黑猪生长相关性状的拷贝数变异全基因组关联分析研究

吴嘉浩¹^,²(), 吴姿仪¹^,²(), 窦腾飞¹^,², 白利瑶¹, 张永前²^,³, 董联合²^,³, 李鹏飞²^,³, 李新建¹^,⁴, 韩雪蕾¹, 李秀领¹^,²^,*()

1. 河南农业大学动物科技学院, 郑州 450046
2. 河南浚县生猪科技小院, 鹤壁 456285
3. 河南省谊发牧业有限责任公司, 鹤壁 456285
4. 海南省农业科学院, 三亚 572025

收稿日期:2024-08-26 出版日期:2025-03-23 发布日期:2025-04-02
通讯作者: 李秀领 E-mail:m17630413022@163.com;W17746978907@163.com;xiulingli@henau.edu.cn
作者简介:吴嘉浩(2001-)，男，河南驻马店人，硕士，主要从事动物遗传育种与繁殖研究，E-mail: m17630413022@163.com
吴姿仪(1999-)，女，河南驻马店人，硕士，主要从事动物遗传育种与繁殖研究，E-mail: W17746978907@163.com
第一联系人：
吴嘉浩和吴姿仪为同等贡献作者
基金资助:
国家重点研发计划(2021YFD1301201)；河南高等学校重点科研项目(23A230012；25CY014)；河南省农业良种联合攻关项目(2022020101)

Genome-wide Association Study of Copy Number Variation in Growth-Related Traits of Yunong-Black Pigs

WU Jiahao¹^,²(), WU Ziyi¹^,²(), DOU Tengfei¹^,², BAI Liyao¹, ZHANG Yongqian²^,³, DONG Lianhe²^,³, LI Pengfei²^,³, LI Xinjian¹^,⁴, HAN Xuelei¹, LI Xiuling¹^,²^,*()

1. College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
2. Henan Xun County Swine Science and Technology Courtyard, Hebi 456285, China
3. Henan Yifa Animal Husbandry Co., Ltd, Hebi 456285, China
4. Hainan Academy of Agricultural Sciences, Sanya 572025, China

Received:2024-08-26 Online:2025-03-23 Published:2025-04-02
Contact: LI Xiuling E-mail:m17630413022@163.com;W17746978907@163.com;xiulingli@henau.edu.cn

摘要/Abstract

摘要：

旨在检测豫农黑猪全基因组拷贝数变异(copy number variations，CNVs)，鉴定豫农黑猪生长相关性状候选基因。本研究收集了豫农黑猪2~5世代种群的生长相关性状数据(包括体长、体高、胸围、管围、腿臀围、背膘厚和眼肌深度)，共807头猪(母猪738头，公猪69头)，体重范围为95~105 kg。随后采集该试验群体耳组织样本利用中芯一号50K SNP芯片进行基因分型，并使用PennCNV软件对基因型数据进行CNV检测，通过重叠CNV融合法构建拷贝数变异区域(copy number variable regions, CNVRs)图谱。而后使用Plink软件对生长相关性状进行CNV的全基因组关联分析(genome-wide association study, GWAS)。结果，在18条常染色体上共鉴定到1 432个CNVs，合并为232个CNVRs，其中CNV大小范围为2.7 kb至2.2 Mb，CNVR大小范围为4.5 kb至2.2 Mb，共覆盖56.4 Mb，占常染色体基因组的2.50%。通过GWAS分析，发现1个CNV在全基因组水平上与胸围性状显著相关，7个CNV在染色体水平上分别与胸围、管围和背膘厚性状显著相关，胸围性状中显著性最高的CNV也与管围性状显著相关。其中，位于17号染色体上的CLDN23基因与背膘厚显著相关，推测其可能在肌肉发育或脂肪沉积中起重要调控作用。本研究结果为豫农黑猪基因组CNV的功能提供新见解，并为进一步分子标记辅助选择在豫农黑猪新品种培育中提供了重要的理论支持。

关键词: 豫农黑猪, 生长性状, 拷贝数变异, 全基因组关联性分析(GWAS)

Abstract:

This study aimed to detect genome-wide copy number variations (CNVs) in Yunong-black pigs and identify candidate genes associated to growth-related traits in this breed. Growth-related traits were collected from 807 Yunong-black pigs (738 sows and 69 boars) across four generations (2rd-5th generation), with body weight range of 95 to 105 kg. The measured traits included body length (BL), body height (BH), chest circumference (CC), cannon bone circumference (CBC), legs buttocks circumference (LBC), backfat thickness (BF), and loin muscle depth (LMD). Ear tissue samples from the experimental population were genotyped using the "Zhongxin-1"50K SNP chip, and CNV detection was performed using PennCNV software. The CNV regions (CNVRs) were identified by merging overlapping CNVs and genome-wide association analysis (GWAS) was conducted using Plink software to examine associations between CNVs and growth-related traits. A total of 1 432 CNVs were identified on 18 autosomes and merged into 232 CNVRs. The CNVs ranged in size from 2.7 kb to 2.2 Mb, while CNVRs spanned from 4.5 kb to 2.2 Mb, covering 56.4 Mb or 2.50% of the autosomal genome. GWAS identified one CNV was associated with CC at the genome-wide significance level, and seven CNVs showed suggestive associated with CC, CBC and BF. The CNV most strongly associated with CC also showed a strong association with CBC. Additionally, the CLDN23 gene on SSC17 was significantly associated with BF, suggesting its potential role in regulating muscle development or fat deposition. This study provides new insights into the functional implications of CNVs in the Yunong-black pig, and offering valuable theoretical support for implement molecular marker-assisted selection in Yunong-black pigs breeding programs.

Key words: Yunong-black pigs, growth traits, copy number variation, genome-wide association study(GWAS)

中图分类号:

S828.2

吴嘉浩, 吴姿仪, 窦腾飞, 白利瑶, 张永前, 董联合, 李鹏飞, 李新建, 韩雪蕾, 李秀领. 豫农黑猪生长相关性状的拷贝数变异全基因组关联分析研究[J]. 畜牧兽医学报, 2025, 56(3): 1110-1119.

WU Jiahao, WU Ziyi, DOU Tengfei, BAI Liyao, ZHANG Yongqian, DONG Lianhe, LI Pengfei, LI Xinjian, HAN Xuelei, LI Xiuling. Genome-wide Association Study of Copy Number Variation in Growth-Related Traits of Yunong-Black Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(3): 1110-1119.

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染色体 Chromosome	CNVR数目 CNVR count	CNVR长度/kb Length of CNVR	最小长度/kb Minimum size	最大长度/kb Maximum size	平均长度/kb Average size
1	18	4 246.27	9.30	1 465.44	235.90
2	18	4 847.94	31.11	704.46	269.33
3	18	5 953.04	43.95	1 141.00	330.72
4	9	3 649.12	28.24	2 222.16	405.46
5	9	2 699.64	41.88	652.15	299.96
6	15	5 653.12	13.28	1 563.56	376.87
7	14	1 070.91	45.11	185.55	76.49
8	18	4 063.80	14.50	873.32	225.77
9	13	1 818.76	10.60	452.26	139.90
10	6	889.36	19.00	317.20	148.23
11	12	2 350.00	32.19	497.58	195.83
12	8	1 665.53	54.34	701.22	208.19
13	23	6 613.98	15.95	1 160.06	287.56
14	12	2 644.65	21.94	1 106.14	220.39
15	19	4 416.32	21.63	1 758.26	232.44
16	9	1 762.76	33.94	633.51	195.86
17	5	1 319.47	117.65	509.60	263.89
18	6	719.50	56.86	225.78	119.92

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豫农黑猪生长相关性状的拷贝数变异全基因组关联分析研究

Genome-wide Association Study of Copy Number Variation in Growth-Related Traits of Yunong-Black Pigs

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性状Trait	染色体SSC	物理位置/bp Position	候选基因Candidate gene
CC	1	157 232 630~157 498 487	/
CC	11	35 411 663~35 472 493	/
CBC	1	157 232 630~157 498 487	/
CBC	3	99 462 180~99 539 999	/
BF	15	110 808 122~110 878 014	/
BF	17	319 640~693 319	CLDN23