豫南黑猪背膘厚度与全基因组拷贝数变异的关联研究

doi:10.11843/j.issn.0366-6964.2025.06.010

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (6): 2639-2648.doi: 10.11843/j.issn.0366-6964.2025.06.010

豫南黑猪背膘厚度与全基因组拷贝数变异的关联研究

吴桐¹(), 王楠¹, 邢雨欣¹, 张犇¹^,², 胡潘阳¹^,², 张海涛³, 朱玉峰¹^,², 吴相哲¹^,², 杨峰¹^,², 李秀领¹^,², 王克君¹^,², 韩雪蕾¹^,², 李新建⁴, 余彤¹^,², 柏峻¹^,², 李改英¹^,²^,*(), 乔瑞敏¹^,²^,*()

1. 河南农业大学动物科技学院, 郑州 450046
2. 河南省猪遗传改良工程技术研究中心, 郑州 450046
3. 河南三高农牧股份有限公司, 信阳 464000
4. 海南省农业科学院, 三亚 571100

收稿日期:2024-10-30 出版日期:2025-06-23 发布日期:2025-06-25
通讯作者: 李改英,乔瑞敏 E-mail:925998286@qq.com;ligaiying@126.com;ruiminqiao@henau.edu.cn
作者简介:吴桐(2004-)，男，河南固始人，学士，主要从事猪遗传育种研究，E-mail：925998286@qq.com
基金资助:
国家自然科学基金联合基金项目(U1904115)；国家重点研发项目(2021YFD1301202)

Association Analysis of Backfat Thickness and Genome-Wide Copy Number Variations in Yunan Black Pigs

WU Tong¹(), WANG Nan¹, XING Yuxin¹, ZHANG Ben¹^,², HU Panyang¹^,², ZHANG Haitao³, ZHU Yufeng¹^,², WU Xiangzhe¹^,², YANG Feng¹^,², LI Xiuling¹^,², WANG Kejun¹^,², HAN Xuelei¹^,², LI Xinjian⁴, YU Tong¹^,², BAI Jun¹^,², LI Gaiying¹^,²^,*(), QIAO Ruimin¹^,²^,*()

1. College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
2. Henan Provincial Engineering and Technology Research Center for Swine Genetic Improvement, Zhengzhou 450046, China
3. Henan Sangao Agriculture and Animal Husbandry Co., Ltd., Xinyang 464000, China
4. Hainan Academy of Agricultural Sciences, Sanya 571100, China

Received:2024-10-30 Online:2025-06-23 Published:2025-06-25
Contact: LI Gaiying, QIAO Ruimin E-mail:925998286@qq.com;ligaiying@126.com;ruiminqiao@henau.edu.cn

摘要/Abstract

摘要：

旨在通过对豫南黑猪进行全基因组拷贝数变异分析及其与背膘厚度进行关联分析，并挖掘影响豫南黑猪背膘厚度的关键拷贝数变异(copy number variation, CNV)及候选基因，为豫南黑猪的遗传改良提供新的育种思路。本研究以120头豫南黑猪核心群个体为研究对象，利用基因组SNP芯片及PennCNV软件进行CNV检测；并使用PennCNV对检测结果进行质量控制；通过合并重叠CNV确定拷贝数变异区域(copy number variation region, CNVR)。使用背膘测定仪对120头豫南黑猪P2点、肩部最厚处、六七肋骨处、最后肋骨处、腰荐结合处的背膘厚度进行测量及对平均背膘厚度进行计算；利用Plink软件对CNV与背膘厚度进行关联分析；利用BioMart和GeneCards注释挖掘影响猪背膘厚度的关键候选基因。共有104个个体符合质控标准，全基因组拷贝数变异分析结果显示，在104个样本中共检测到252个CNV，合并后共62个CNVRs，分布于猪的1~18号常染色体上。全基因组关联分析结果显示，1、8和16号染色体上存在4个与背膘厚度显著关联的位点。在显著关联位点附近共注释到11个候选基因(SOCS6、PTTN、CD226、NR3C2、ARHGAP10、DCLK2、IQCM、CDH9、CDH10、U2和U6)。本研究在120头豫南黑猪核心群个体中通过基因组SNP芯片的拷贝数变异分析，共发现252个CNV，筛选出11个候选基因。11个候选基因中大部分与畜禽生长信号通路有关，分别是SOCS6、NR3C2和CDH10与脂肪沉积过程相关；CD226、U2和U6与肉品质性状和生殖性状相关；ARHGAP10与生长性状和体重调控相关。本研究结果对豫南黑猪的精准育种和背膘厚度相关基因的进一步探索提供了重要参考价值。

关键词: 豫南黑猪, 背膘厚度, 拷贝数变异, 关联分析

Abstract:

The purpose of this study was to analyze the whole genome copy number variation and its association with backfat thickness of Yunan black pigs, and to explore the key copy number variation (CNV) and candidate genes affecting the backfat thickness of Yunan black pigs, so as to provide new breeding ideas for the genetic improvement of Yunan black pigs.In this study, a genome-wide copy number variation (CNV) analysis was conducted on 120 Yunan black pigs from a core breeding population by SNP chip and PennCNV software. Backfat thickness was systematically measured at five anatomical landmarks (P2 point, maximum shoulder thickness, 6th-7th rib interface, last rib, and lumbosacral junction), and the average values were calculated for the association studies. After stringent quality control, 104 individuals were retained for downstream analysis. Using high-density SNP microarrays and PennCNV software, 252 CNVs were identified and further merged into 62 non-overlapping copy number variation regions (CNVRs) distributed across autosomes 1 to 18. Genome-wide association analysis using Plink revealed 4 loci on chromosomes 1, 8, and 16 that exhibited statistically significant correlations with backfat thickness (P < 0.05). Subsequent functional annotation using BioMart and GeneCards databases dentified 11 candidate genes located in proximity to these loci: SOCS6, PTTN, CD226, NR3C2, ARHGAP10, DCLK2, IQCM, CDH9, CDH10, U2 and U6. Functional characterization indicated that these genes are involved in diverse biological pathways: SOCS6, NR3C2 and CDH10 are associated with lipid metabolism and adipocyte differentiation; CD226, U2 and U6 are linked to meat quality attributes and reproductive performance; and ARHGAP10 plays a role in growth regulation and body weight modulation. These findings not only enhance the understanding of the genetic architecture underlying backfat deposition in Yunan black pigs but also provide actionable targets for precision breeding programs aimed at optimizing carcass traits through marker-assisted selection.

Key words: Yunan black pig, backfat thickness, copy number variation, association analysis

中图分类号:

S828.2

吴桐, 王楠, 邢雨欣, 张犇, 胡潘阳, 张海涛, 朱玉峰, 吴相哲, 杨峰, 李秀领, 王克君, 韩雪蕾, 李新建, 余彤, 柏峻, 李改英, 乔瑞敏. 豫南黑猪背膘厚度与全基因组拷贝数变异的关联研究[J]. 畜牧兽医学报, 2025, 56(6): 2639-2648.

WU Tong, WANG Nan, XING Yuxin, ZHANG Ben, HU Panyang, ZHANG Haitao, ZHU Yufeng, WU Xiangzhe, YANG Feng, LI Xiuling, WANG Kejun, HAN Xuelei, LI Xinjian, YU Tong, BAI Jun, LI Gaiying, QIAO Ruimin. Association Analysis of Backfat Thickness and Genome-Wide Copy Number Variations in Yunan Black Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(6): 2639-2648.

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染色体 Chromosome	拷贝数变异区域 Copy number variation region
染色体 Chromosome	CNVR数目 CNVR count	长度/bp Length	染色体占比/% Percentage of chromosomes	均值/bp Average size	最大值/bp Max size	最小值/bp Min size
1	6	419 684	0.153	69 947.333	188 012	12 589
2	5	882 284	0.581	176 456.800	609 138	11 884
3	8	1 115 033	0.839	139 379.125	518 657	14 568
4	1	19 611	0.015	19 611.000	19 611	19 611
5	3	524 569	0.502	174 856.333	434 828	31 410
6	2	179 723	0.105	89 861.500	95 517	84 206
7	4	377 690	0.310	94 422.500	187 907	38 779
8	6	891 973	0.642	148 662.167	455 579	27 728
9	3	265 452	0.190	88 484.000	189 777	25 963
10	1	83 312	0.120	83 312.000	83 312	83 312
11	5	455 969	0.576	91 193.800	271 456	16 937
12	1	7 074	0.011	7 074.000	7 074	7 074
13	3	282 199	0.135	94 066.333	183 842	36 129
14	3	158 815	0.112	52 938.333	62 587	48 045
15	6	457 949	0.326	76 324.833	116 540	34 047
16	2	164 561	0.206	82 280.500	146 652	17 909
17	2	441 155	0.695	220 577.500	342 967	98 188
18	1	3 918	0.007	3 918.000	3 918	3 918

背膘厚表型 Average backfat thickness phenotype	平均值/mm Average size	标准差/mm S.D.	最大值/mm Max size	最小值/mm Min size	变异系数/% C.V
P2点 P2 point	36.058	7.983	53.900	20.700	22.139
肩部最厚处 Maximum shoulder thickness	17.259	3.166	26.900	9.400	18.322
六七肋骨处 6th-7th rib interface	38.243	9.313	60.300	20.700	24.351
最后肋骨处 The last rib	33.218	7.693	53.900	18.200	23.159
腰荐结合处 Lumbosacral junction	21.295	3.506	36.400	13.800	16.463
平均背膘厚 Average backfat thickness	27.504	4.900	40.425	18.000	17.817

背膘厚表型 Average backfat thickness phenotype	染色体 Chromosome	CNV位置/bp Position	类型 Category	CNV长度/bp Length	P值 P-value	候选基因 Candidate gene
腰荐结合处 Lumbosacral junction	1	152 201 203~152 222 760	Gain	21 558	2.7×10^-3	SOCS6, PTTN, CD226
P2点 P2 point	8	79 697 483~79 725 210	Loss	27 728	1.52×10^-3	NR3C2, ARHGAP10, DCLK2, IQCM
肩部最厚处 Maximum shoulder thickness	8	79 697 483~79 725 210	Loss	27 728	6.4×10^-3	NR3C2, ARHGAP10, DCLK2, IQCM
最后肋骨处 The last rib	16	13 214 860~13 232 768	Loss	17 909	1.76×10^-3	CDH9, CDH10, U2, U6

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豫南黑猪背膘厚度与全基因组拷贝数变异的关联研究

Association Analysis of Backfat Thickness and Genome-Wide Copy Number Variations in Yunan Black Pigs

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