脂质组与转录组联合揭示南阳牛不同肌肉组织脂质特征的差异表达模式

doi:10.3864/j.issn.0578-1752.2025.06.014

摘要/Abstract

摘要：

【目的】肌内脂质的组成与含量是影响风味和嫩度的重要因素，与牛肉品质紧密相关。通过比较南阳牛背最长肌与里脊组织脂质特征和基因表达模式，鉴定调控南阳牛不同肌肉组织脂质特征的潜在候选基因，为优质牛肉分子育种提供理论依据。【方法】选用生长环境和遗传背景相同的成年南阳牛背最长肌和里脊组织为试验材料，采用气相色谱质谱联用（gas chromatography-mass spectrometry，GC-MS）、液相色谱质谱联用（liquid chromatography mass spectrometry，LC-MS）与转录组测序技术（RNA sequencing，RNA-seq），构建肌肉组织的脂质图谱与基因表达谱，鉴定差异脂质分子（differential lipid molecules, DLMs）和差异表达基因（differentially expressed genes, DEGs），进行功能富集分析及蛋白质互作网络分析（protein-protein interaction network, PPI）筛选潜在候选基因，并采用实时荧光定量PCR技术（real-time fluorescence quantitative PCR，RT-qPCR）进行表达水平验证。【结果】在肌肉组织间共检测到19种脂肪酸，其中C18:0、C14:1n5和C16:1n7的含量在组织间存在显著差异。共检测到2 106种脂质分子，其中磷脂酰胆碱（phosphatidylcholine，PC）、甘油三酯（triacylglycerols，TG）和磷脂酰乙醇胺（phosphatidylethanolamine，PE）为主要成分。通过差异分析在肌肉组织间共筛选到39种DLMs和3 424个DEGs，经受试者工作特征曲线（receiver operating characteristic curve，ROC）分析鉴定到13种DLMs（如：DG（16:0_18:1）、DG（18:0_18:1）、DG（18:0_18:2））可作为组织间的潜在脂质生物标志物。PPI和MCODE分析获得3个与脂质代谢密切相关的核心基因模块，通路富集分析显示，DEGs与DLMs共同参与肌醇磷酸代谢、甘油酯代谢和甘油磷脂代谢通路。整合分析鉴定到19个调控脂质特征差异的潜在候选基因，其中7个基因（PLCG2、SYNJ1、LPIN1、DGKZ、DGAT1、LPL和SELENOI）居于通路中的关键位置，对DLMs具有直接调控作用。RT-qPCR结果显示6个脂质候选基因的表达趋势与RNA-seq结果一致。【结论】在南阳牛背最长肌与里脊组织间鉴定到13种潜在脂质生物标志物，筛选到19个潜在候选基因参与脂质特征调控的关键代谢通路，为今后进一步探究南阳牛脂质差异形成的调控机制及优质牛肉分子育种提供理论基础。

关键词: 南阳牛, 脂质生物标志物, 脂质组, 转录组, 候选基因

Abstract:

【Objective】 The composition and content of intramuscular lipids are important factors affecting flavor and tenderness of beef, and are closely related to beef quality. In this study, by comparing the lipid characteristics and gene expression patterns of longissimus dorsi muscle and tenderloin tissue of Nanyang cattle, the potential candidate genes regulating lipid characteristics of different muscle tissues in Nanyang cattle were identified. 【Method】 The longissimus dorsi muscle and tenderloin tissues of adult Nanyang cattle with the same growth environment and genetic background were selected as experimental materials, and then the lipid profile and gene expression profile of muscle tissue were constructed by gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS) and transcriptome sequencing (RNA-seq) to identify differential lipid molecules (DLMs) and differentially expressed genes (DEGs) between different tissues. Functional enrichment analysis and protein-protein interaction network (PPI) were performed to screen potential candidate genes, and real-time fluorescent quantitative PCR (RT-qPCR) was used to verify their expression levels. 【Result】 In this study, 19 kinds of fatty acids were detected in muscle tissue, among which the content of C18:0, C14:1n5 and C16:1n7 were significantly different between tissues. A total of 2 106 lipid molecules were detected, of which Phosphatidylcholine (PC), Triacylglycerols (TG) and Phosphatidylethanolamine (PE) were the main components. A total of 39 DLMs and 3,424 DEGs were screened between two muscle tissues by difference analysis. According to receiver operating characteristic curve (ROC) analysis, 13 DLMs (e.g. DG(16:0_18:1), DG(18:0_18:1), DG(18:0_18:2)) could be used as potential lipid biomarkers between tissues. PPI and MCODE analysis obtained three core gene modules closely related to lipid metabolism. Pathway enrichment analysis showed that DEGs and DLMs were involved in Inositol phosphate metabolism, Glycerolipid metabolism and Glycerophospholipid metabolism. Integration analysis identified 19 potential candidate genes with different lipid characteristics, among which 7 genes (PLCG2, SYNJ1, LPIN1, DGKZ, DGAT1, LPL and SELENOI) were located in key positions in the pathway, and had direct regulatory effects on DLMs. RT-qPCR showed that the expression trend of six candidate genes was consistent with that of RNA-seq. 【Conclusion】 In this study, 13 potential lipid biomarkers were identified and 19 potential candidate genes were screened for the key metabolic pathways involved in the regulation of lipid characteristics between longissimus dorsi muscle and tenderloin tissue for Nanyang cattle, which provided a theoretical basis for further exploration of the regulatory mechanism for lipid difference formation in Nanyang cattle and molecular breeding for high-quality beef.

Key words: Nanyang cattle, lipid biomarkers, lipidome, transcriptome, candidate gene

高岩浩, 王婷婷, 白卫卫, 杜兴杰, 刘贤, 秦本源, 付彤, 孙宇, 高腾云, 张天留. 脂质组与转录组联合揭示南阳牛不同肌肉组织脂质特征的差异表达模式[J]. 中国农业科学, 2025, 58(6): 1239-1258.

GAO YanHao, WANG TingTing, BAI WeiWei, DU XingJie, LIU Xian, QIN BenYuan, FU Tong, SUN Yu, GAO TengYun, ZHANG TianLiu. The Combination of Lipidome and Transcriptome Revealed the Differential Expression Patterns of Lipid Characteristics in Different Muscle Tissues for Nanyang Cattle[J]. Scientia Agricultura Sinica, 2025, 58(6): 1239-1258.

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基因 Gene symbol	序列号 Accession number	引物序列 Primer sequence (5'-3')	产物长度 Product length (bp)
GAPDH	NM_001034034.2	F:ATGCTGGTGCTGAGTATGTG R:GTGTCGCTGTTGAAGTCG	604
LPL	NM_001075120.1	F:GCCGCAGACAGGATTACAGG R:CCAGGAATGAGGTGGCAAGT	107
ETNK1	XM_002687736.6	F:GCTACCACCACTTTCTGGGA R:TGTTATCCCACTGTACCGCC	292
DGKZ	NM_001278652.1	F:TTTTCGGGCACAGGAAAGC R:GGGACACTGATTTCAGCATCTT	231
LYPLA1	NM_001034688.2	F:CACTGCCTTTACTGTGGATTGC R:TACACAAGGCCTCTTGGTGG	293
GPCPD1	XM_002692364.7	F:GATCTCGGACAACCCCCATT R:GGCTGTTCAGGCATCCAATC	241
PCYT1A	NM_001105052.2	F:GTGCTGGTATATGGGTGCCT R:TTGTCACTCTTGCTCGCTGG	166

组别 Group	n	最大值 Maximum (%)	最小值 Minimum (%)	平均值 Average(%)	P值 P value
背最长肌 Longissimus_dorsi	5	10.63	9.46	9.97±0.006	0.208318
里脊 Tenderloin	5	15.65	9.38	13.18±3.338	0.208318

脂质分子 Lipid molecule	脂质离子 Lipid ion	亚类 Subclass	质荷比 m/z	时间 Time （min）	P值 P value	VIP值 VIP value	丰度高/丰度低 High-abundance/Low-abundance
DG(16:0_18:1)	DG(16:0_18:1)+NH4	DG	612.5561505	13.08173	0.0053	2.64	丰度高 High-abundance
DG(18:0_18:1)	DG(18:0_18:1)+NH4	DG	640.5874505	14.18853297	0.0000	3.51	丰度高 High-abundance
DG(18:0_18:2)	DG(18:0_18:2)+NH4	DG	638.5718005	13.12742785	0.0020	3.40	丰度高 High-abundance
DG(37:4)	DG(37:4)+H	DG	631.5296015	13.45720732	0.0005	1.12	丰度高 High-abundance
DG(38:5)	DG(38:5)+H	DG	643.5296015	13.30231755	0.0137	2.13	丰度高 High-abundance
PC(11:0_22:1)	PC(11:0_22:1)+Na	PC	768.5513785	11.21609073	0.0039	2.04	丰度高 High-abundance
PC(35:4)	PC(35:4)+H	PC	768.5537835	11.2368014	0.0034	2.08	丰度高 High-abundance
PE(16:1e_18:2)	PE(16:1e_18:2)-H	PE	698.5130155	10.85689739	0.0088	2.37	丰度高 High-abundance
PE(18:0_18:1)	PE(18:0_18:1)+Na	PE	768.5513785	11.25022966	0.0055	4.24	丰度高 High-abundance
PE(18:0_20:4)	PE(18:0_20:4)-H	PE	766.5392305	11.23645543	0.0002	4.15	丰度高 High-abundance
PE(18:0e)	PE(18:0e)+H	PE	482.3241185	3.510563969	0.0097	2.60	丰度高 High-abundance
PE(18:2e_17:1)	PE(18:2e_17:1)+H	PE	714.5432185	11.53612853	0.0036	1.09	丰度高 High-abundance
SPH(d22:0)	SPH(d22:0)+H	SPH	358.3679555	3.081586854	0.0002	2.84	丰度低 Low-abundance

样品 Sample	原始序列 Raw reads	原始碱基 Raw bases （G）	质控序列 Clean reads	质控碱基 Clean bases （G）	Q20 (%)	Q30 (%)	GC (%)	序列比对率 Ratio of Mapped reads (%)
背最长肌_1 Longissimus_dorsi_1	44427252	6.71	43874518	6.61	96.97	94.64	48.38	97.56
背最长肌_2 Longissimus_dorsi_2	57740820	8.72	57298348	8.63	97.40	95.49	47.28	96.84
背最长肌_3 Longissimus_dorsi_3	57335318	8.66	56890740	8.56	97.39	95.48	50.01	97.37
背最长肌_4 Longissimus_dorsi_4	54104992	8.17	53663454	8.05	97.45	95.59	48.89	97.56
背最长肌_5 Longissimus_dorsi_5	55554150	8.39	55083896	8.22	97.38	95.46	49.48	96.66
里脊_1 Tenderloin_1	56825130	8.58	56433728	8.49	97.44	95.57	47.62	97.53
里脊_2 Tenderloin_2	56261048	8.50	55802264	8.40	97.42	95.53	47.81	97.51
里脊_3 Tenderloin_3	53378910	8.06	52998730	7.97	97.39	95.46	47.92	97.52
里脊_4 Tenderloin_4	53416466	8.07	52949120	7.98	97.23	95.14	47.10	96.86
里脊_5 Tenderloin_5	51869138	7.83	51266774	7.73	97.27	95.22	47.01	98.38
总和 All	540913224	81.69	536261572	80.64	-	-	-	-
平均 Average	54091322.4	8.17	53626157.2	8.06	97.33	95.36	48.15	97.38

通路 Pathway	基因数目 Gene number		脂质数目 Lipid number
通路 Pathway	上调 Up-regulated	下调 Down-regulated	丰度高 High-abundance	丰度低 Low-abundance
肌醇磷酸代谢 Inositol phosphate metabolism	12	6	11	0
甘油酯代谢 Glycerolipid metabolism	12	5	11	2
甘油磷脂代谢 Glycerophospholipid metabolism	17	6	32	0