基于转录组测序技术鉴别影响莱芜猪滴水损失的关键基因

doi:10.11843/j.issn.0366-6964.2025.03.015

Abstract

Abstract:

This study aimed to identify key genes affecting drip loss in Laiwu pigs to improve pork quality and reduce economic loss caused by drip. Twenty-eight Laiwu pigs, including 19 boars and 9 sows with carcass weight of (72.30±1.26) kg, were selected as experimental animals. The meat quality traits, including 48 h drip loss, meat color, intramuscular fat content, and pH, were measured. RNA sequencing was conducted on the longissimus dorsi muscle tissue of these pigs. Then, differentially expressed genes (DEGs) were detected based on the criteria of log₂(fold change) ≥1 and an adjusted P≤0.01 between groups with high and low drip loss. Each group included three boars and one sow. By combining correlation analysis between DEGs and drip loss, as well as protein-protein interaction (PPI) analysis, the candidate genes influencing drip loss in Laiwu pigs were further identified. The results indicated that drip loss was significantly negatively correlated with the intramuscular fat content and the a^* value of meat color at both 1 h and 24 h post-mortem (P < 0.05) in Laiwu pigs. A total of 166 DEGs were identified between the high and low drip loss groups. These DEGs were significantly enriched in Gene Ontology (GO) terms and pathways related to cardiovascular system development and function, cytoskeleton and motility, and protein regulation and function. Correlation analysis using the 28 individuals revealed that 110 of the 166 DEGs were significantly correlated with drip loss (P < 0.05). Among the top ten of the most significantly correlated DEGs, two genes, KLF2 and IGF2, were identified, whose functions were reported to be related to drip loss. Furthermore, PPI analysis of DEGs identified two proteins, which were encoded by UBR1 and TTBK2, having the highest number of interactions with other proteins, and the mRNA expression levels of the two genes were significantly correlated with drip loss (P < 0.05). These gene functions were also reported closely related to drip loss in previous studies. Therefore, by combining the results of DEG analysis, correlation analysis, and PPI analysis, KLF2, IGF2, UBR1 and TTBK2 were identified as candidate genes affecting drip loss. This study lays the ground for elucidating the molecular mechanisms underlying the drip loss in pigs and offers valuable insights for the improvement of meat quality traits in pigs.

Key words: Laiwu pig, drip loss, RNA sequencing, meat quality traits, candidate genes

CLC Number:

S828.2

JIA Wanli, WANG Jiying, LI Jingxuan, WANG Yanping, GENG Liying, ZHANG Chuansheng, ZHAO Xueyan. Identification of Key Genes Affecting Drip Loss in Laiwu Pigs Based on Transcriptome Sequencing Technology[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(3): 1134-1146.

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References 43

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性状 Trait	平均值±标准误 Mean±Standard error	中位数 Median	最小值 Minimum value	最大值 Maximum value	变异系数/% Coefficient of variation
胴体重/kg Carcass weight	72.30±1.26	6.64	72.48	60.00	83.10
亮度L1 Lightness L1	43.74±0.60	44.20	38.53	49.75	7.31
红度a1 Redness a1	16.19±0.43	15.97	11.89	20.19	14.02
黄度b1 Yellowness b1	8.95±0.20	8.93	6.73	10.98	11.86
亮度L24 Lightness L24	45.49±0.91	44.73	37.80	60.83	10.60
红度a24 Redness a24	17.62±0.36	17.29	13.72	20.97	10.70
黄度b24 Yellowness b24	9.41±0.24	9.29	7.31	12.03	13.41
1小时pH pH₁_h	6.69±0.05	6.76	6.15	7.18	3.89
24小时pH pH₂₄_h	6.47±0.06	6.47	5.73	6.95	4.61
肌内脂肪含量/% Intramuscular fat content	8.82±0.80	8.10	3.19	18.57	48.20
48小时滴水损失/% 48 h drip loss(DL48h)	1.44±0.14	1.30	0.49	3.97	52.17

项目 Item	平均值 Mean	最小值 Minimum value	最大值 Maximum value	标准差 Standard deviation
原始读段/bp Raw reads	45 781 549.43	41 020 608	51 117 088	442 854.90
去冗余片段/bp Clean reads	44 329 938.71	40 346 978	49 275 354	458 787.63
总比对率/% Total mapping rate	95.13	92.63	96.65	0.19
单一比对率/% Unique mapping rate	92.04	89.71	93.04	0.17
碱基数/G Base count	6.65	6.05	7.39	0.07
碱基质量分值/% (Q20) Base quality score (Q20)	98.04	97.14	98.47	0.07
碱基质量分值/% (Q30) Base quality score (Q30)	94.56	92.50	95.74	0.18

项目 Item	低滴水损失组 DL-L	高滴水损失组 DL-H	P值 P-value
胴体重/kg Carcass weight	65.68±2.02	73.34±3.10	0.091 6
亮度L1 Lightness L1	40.91±1.32	44.86±0.98	0.056 5
红度a1 Redness a1	18.58±0.94	13.78±0.98	0.012 3^*
黄度b1 Yellowness b1	8.69±0.55	8.55±0.18	0.826 6
亮度L24 Lightness L24	46.04±1.70	42.71±3.09	0.391 1
红度a24 Redness a24	19.61±0.60	16.21±0.87	0.021 1^*
黄度b24 Yellowness b24	9.56±0.35	8.84±0.85	0.480 4
1小时pH pH_{1 h}	6.98±0.07	6.78±0.03	0.060 9
24小时pH pH_{24 h}	6.68±0.03	6.63±0.16	0.795 3
肌内脂肪含量/% Intramuscular fat content	11.93±1.90	5.10±0.62	0.031 2^*
48小时滴水损失/% 48 h drip loss(DL48 h)	0.61±0.07	2.88±0.37	0.007 6^**

基因ID Gene ID	基因名称 Gene name	差异倍数 Fold change	P值 P-value	染色体 Chromosome	基因描述 Gene description
ENSSSCG00000011363	PRKAR2A	5.920	1.63×10^-11	13	蛋白激酶c AMP依赖的Ⅱ型调节亚基α protein kinase cAMP-dependent type Ⅱ regulatory subunit alpha
ENSSSCG00000039290	MTPN	5.727	1.55×10^-9	18	肌营养蛋白myotrophin
ENSSSCG00000029558	EXTL1	0.172	3.98×10^-9	6	外泌体样糖基转移酶1 exostosin like glycosyltransferase 1
ENSSSCG00000050398	-	5.607	5.70×10^-9	5	-
ENSSSCG00000004980	THSD4	4.182	6.70×10^-9	1	含血小板反应蛋白1型结构域4 thrombospondin type 1 domain containing 4
ENSSSCG00000030921	APOA1	0.293	8.47×10^-9	9	载脂蛋白A1 apolipoprotein A1
ENSSSCG00000014291	AFF4	4.812	9.87×10^-9	2	AF4/FMR2家族成员4 AF4/FMR2 family member 4
ENSSSCG00000017268	PRKCA	3.909	2.01×10^-8	12	蛋白激酶Cα protein kinase C alpha
ENSSSCG00000017791	-	4.414	2.34×10^-8	12	弹弓蛋白磷酸酶2 slingshot protein phosphatase 2
ENSSSCG00000013598	KANK3	0.296	2.44×10^-8	2	KN基序和锚蛋白重复结构域3 KN motif and ankyrin repeat domains 3

类别 Category	项目 Item	编号 ID	描述 Description	P值 P-value	富集基因个数 Enriched gene count
GO	BP	GO: 0003018	循环系统中的血管过程 vascular process in circulatory system	2.60×10^-5	6
		GO: 0001944	脉管系统发育 vasculature development	2.70×10^-5	14
		GO: 0072358	心血管系统发育 cardiovascular system development	2.70×10^-5	14
	CC	GO: 0001725	应力纤维stress fiber	2.05×10^-3	3
		GO: 0097517	收缩型肌动蛋白丝束 contractile actin filament bundle	2.05×10^-3	3
		GO: 0032432	肌动蛋白丝束 actin filament bundle	2.89×10^-3	3
	MF	GO: 0035173	组蛋白激酶活性 histone kinase activity	3.58×10^-3	2
		GO: 0051393	α-辅肌动蛋白结合 alpha-actinin binding	4.28×10^-3	2
		GO: 0005518	胶原结合 collagen binding	4.71×10^-3	3
KEGG		ssc04371	Apelin信号通路 Apelin signaling pathway	2.30×10^-5	8
		ssc04730	长时程抑制 long-term depression	1.20×10^-4	5
		ssc04921	催产素信号通路 oxytocin signaling pathway	1.47×10^-4	7

Identification of Key Genes Affecting Drip Loss in Laiwu Pigs Based on Transcriptome Sequencing Technology

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基因 Gene	相关系数r Correlation coefficient r	相关性P值 Correlation P-value	差异倍数 Fold change	P值 P-value
RBPMS2	-0.656	1.50×10^-4	0.327	5.56×10^-5
KLF2	-0.586	1.04×10^-3	0.373	5.44×10^-5
IGF2	-0.583	1.13×10^-3	0.388	1.89×10^-5
EDRF1	0.583	1.14×10^-3	2.481	1.08×10^-4
DDIT4	-0.574	1.42×10^-3	0.323	5.44×10^-6
GATA2	-0.573	1.45×10^-3	0.353	1.14×10^-4
ENSSSCG00000001341	-0.570	1.54×10^-3	0.384	3.25×10^-6
RHOBTB2	0.570	1.55×10^-3	3.563	1.88×10^-5
TCP11L1	0.568	1.62×10^-3	2.472	1.11×10^-4
ID3	-0.560	1.97×10^-3	0.330	3.55×10^-7

蛋白名称 Protein name	互作程度 Degree	相关系数r Correlation coefficient	相关P值 Correlation P-value	差异倍数 Fold change	差异P值 P-value	基因描述 Gene description
UBR1	3	0.446	1.734×10^-2	2.749	1.021×10^-4	泛素蛋白连接酶E3组分n-识别蛋白1 ubiquitin protein ligase E3 component n-recognin 1
TTBK2	3	0.408	3.118×10^-2	2.681	8.160×10^-5	Tau微管蛋白激酶2 tau tubulin kinase 2
GATA2	2	-0.573	1.447×10^-3	0.353	1.139×10^-4	GATA结合蛋白2 GATA binding protein 2
PDLIM4	2	-0.525	4.121×10^-3	0.359	9.710×10^-5	PDZ和LIM结构域4 PDZ and LIM domain 4
SPG11	2	0.517	4.811×10^-3	2.510	1.033×10^-4	SPG11囊泡转运相关蛋白, Spatacsin SPG11 vesicle trafficking associated, spatacsin
ATMIN	2	0.509	5.704×10^-3	2.412	9.030×10^-5	ATM相互作用蛋白ATM interactor
CHUK	2	0.488	8.443×10^-3	2.679	3.470×10^-5	核因子κB激酶复合物抑制组分 component of inhibitor of nuclear factor kappa B kinase complex
USP24	2	0.425	2.417×10^-2	2.580	8.300×10^-5	泛素特异性肽酶24 ubiquitin specific peptidase 24
ARHGAP35	2	0.396	3.691×10^-2	2.436	5.240×10^-6	Rho GTPase激活蛋白35 Rho GTPase activating protein 35

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