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

Abstract

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

CLC Number:

S828.2

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.

Figures/Tables 6

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Table 1

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

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