基于WGCNA的辣椒抗疫病关键基因的挖掘

doi:10.16420/j.issn.0513-353x.2024-0996

摘要/Abstract

摘要：

辣椒疫病是由辣椒疫霉菌侵染引起的一种极具破坏性的土传病害，严重制约辣椒生产。目前辣椒抗疫病的分子机制尚不清楚，抗性基因的挖掘和功能分析是抗病育种的基础和前提。通过前期筛选，获得了对辣椒疫霉菌1、2和3号生理小种均表现免疫性的辣椒高代自交系ZCM334，该品系在接菌后，所有植株没有任何感病症状。在接菌后不同时间点（0、12、24和48 h）采集ZCM334和感病材料Early Calwonder的根部样本，并进行转录组测序和加权基因共表达网络分析（weighted gene co-expression network analysis，WGCNA）。共鉴定到17个共表达模块，其中4个与ZCM334抗疫病性呈显著正相关。功能富集分析结果显示，上述4个模块中的基因主要富集在植物激素信号转导、糖酵解、葡萄糖生成以及脂肪酸降解等代谢通路。对这4个模块作相关性分析，预测出12个可能与辣椒抗疫病相关的核心基因，其中包括6个已知功能基因（CA06g02420、CA06g08970、CA01g15560、CA09g14900、CA09g14910和CA09g15310）和6个新基因（novel.5608、novel.2732、novel.3300、novel.752、novel.2181和novel.12038），并构建了基因调控网络。qRT-PCR分析发现，这12个核心基因在ZCM334中显著高表达，且在接菌后24或48 h表达量最高。

关键词: 辣椒, 辣椒疫霉菌, 抗病性, 基因共表达网络, 基因挖掘, 核心基因, 代谢通路

Abstract:

Phytophthora blight is a highly destructive soil-borne disease caused by Phytophthora capsici Leonian，which seriously limits pepper production. At present，the molecular mechanism of pepper’s resistance to phytophthora blight is unclear，and the excavation and functional analysis of resistance genes are the basis and prerequisite for phytophthora blight-resistant breeding. A high- generation inbred line ZCM334 of pepper was obtained through preliminary screening，which is immune to physiological races 1，2，and 3 of P. capsici. After inoculation，all plants showed no signs of infection. Transcriptome sequencing and weighted gene co-expression network analysis（WGCNA）were performed on the roots of ZCM334 and susceptible material Early Calwonder at different stages（0，12，24，and 48 h）before and after inoculation. A total of 17 co-expression modules were identified，and 4 modules were screened for significant positive correlation with the resistance to phytophthora blight of ZCM334. The functional enrichment analysis results showed that the target module genes were mainly enriched in metabolic pathways such as plant hormone signal transduction，glycolysis，glucose production，and fatty acid degradation. Correlation analysis was conducted on these four modules to predict 12 hub genes that may be related to pepper resistance to phytophthora blight，including 6 known functional genes（CA06g02420，CA06g08970，CA01g15560，CA09g14900，CA09g14910，and CA09g15310）and 6 new genes（novel.5608，novel.2732，novel.3300，novel.752，novel.2181，and novel.12038），and a gene regulatory network was constructed. qRT-PCR analysis revealed that these 12 hub genes were highly expressed in ZCM334，with the highest expression levels observed 24 or 48 hours after inoculation.

Key words: pepper, Phytophthora capsici, disease resistance, gene co-expression network, gene mining, hub gene, metabolic pathway

石凤岩, 魏美君, 王秀雪, 张曦, 邹春蕾. 基于WGCNA的辣椒抗疫病关键基因的挖掘[J]. 园艺学报, 2026, 53(1): 257-274.

SHI Fengyan, WEI Meijun, WANG Xiuxue, ZHANG Xi, ZOU Chunlei. Discovery of Key Genes for Pepper Resistance to Phytophthora Blight Based on WGCNA[J]. Acta Horticulturae Sinica, 2026, 53(1): 257-274.

图/表 10

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差异表达基因 DEGs ID	正向引物（5′-3′）Forward primer	反向引物（5′-3′）Reverse primer
novel.12038	TGATCCAACTTTACCGATAACGAA	GTTGTCCAGACTCCAGAAGATGTT
CA06g02420	GGAGCACTTATCAGGGAGGTATC	ACATCAAAAATACGTGCCCATAG
novel.2732	CCAAACTCTTTCCTCAAAATCCA	GTGGCAAAGAAATAATAGACTCACATA
novel.3300	AAGGCTCCGTTTTCTCTGACC	TTTGGAATAGGACTTGATGCGA
novel.5608	TGAAAATGTATTGGCGTGCTG	ATGTAGTTGGCAAGTCGGGTAA
CA01g15560	GGAGACAAGTCCCAGGGTGAG	ATCCCAGTCGGAAAATCATAGTT
novel.752	CTTAGTCCCTTTTTGTTTGCGT	CTGCTCACCCTGAACCCTTTAG
CA06g08970	GGTAGTTGACTTTCCTTCGGTAGC	CCAAATGACAAGAATACCCAAGG
novel.2181	TCGTTTATGTGTTCTTGATTTTGC	TGAAACCAGCAGGAGGATTGA
CA09g14910	GTGTGAGTTTGGCTTCAATGGA	TGGATTCAGATAAGTTCTTGCCC
CA09g14900	ATCATCCTATTGTTTGGAGAGACC	AATAACCTTGTTGCCGAAGTAATC
CA09g15310	CTGCCATTCCTACTTATGCTTGTG	GTTCTGCCTTGCCCTTTTCA
Actin	GACGTGACCTAACTGATAACCTGAT	CTCTCAGCACCAATGGTAATAACTT

差异表达基因 DEGs ID	正向引物（5′-3′）Forward primer	反向引物（5′-3′）Reverse primer
novel.12038	TGATCCAACTTTACCGATAACGAA	GTTGTCCAGACTCCAGAAGATGTT
CA06g02420	GGAGCACTTATCAGGGAGGTATC	ACATCAAAAATACGTGCCCATAG
novel.2732	CCAAACTCTTTCCTCAAAATCCA	GTGGCAAAGAAATAATAGACTCACATA
novel.3300	AAGGCTCCGTTTTCTCTGACC	TTTGGAATAGGACTTGATGCGA
novel.5608	TGAAAATGTATTGGCGTGCTG	ATGTAGTTGGCAAGTCGGGTAA
CA01g15560	GGAGACAAGTCCCAGGGTGAG	ATCCCAGTCGGAAAATCATAGTT
novel.752	CTTAGTCCCTTTTTGTTTGCGT	CTGCTCACCCTGAACCCTTTAG
CA06g08970	GGTAGTTGACTTTCCTTCGGTAGC	CCAAATGACAAGAATACCCAAGG
novel.2181	TCGTTTATGTGTTCTTGATTTTGC	TGAAACCAGCAGGAGGATTGA
CA09g14910	GTGTGAGTTTGGCTTCAATGGA	TGGATTCAGATAAGTTCTTGCCC
CA09g14900	ATCATCCTATTGTTTGGAGAGACC	AATAACCTTGTTGCCGAAGTAATC
CA09g15310	CTGCCATTCCTACTTATGCTTGTG	GTTCTGCCTTGCCCTTTTCA
Actin	GACGTGACCTAACTGATAACCTGAT	CTCTCAGCACCAATGGTAATAACTT

基因 Gene ID	模块 Model	染色体 Chromosome	基因功能描述 Gene description
CA08g08840	黄色Yellow	8	转录延伸因子SPT5同源物 Transcription elongation factor SPT5 homolog
novel.7197	黄色Yellow	7	RNA介导的DNA聚合酶同源物 RNA-directed DNA polymerase homolog
novel.5036	黄色Yellow	5	植物细胞内Ras相关的LRR蛋白 Plant intracellular Ras-group-related LRR protein
novel.6147	黄色Yellow	6	细胞分化蛋白 RCD1 Cell differentiation protein RCD1
novel.12038	黄色Yellow	12	环核苷酸门控离子通道蛋白（CNGC） Cyclic nucleotide-gated ion channel protein（CNGC）
novel.11518	黄色Yellow	12	微管蛋白α-3链 Tubulin alpha-3 chain
novel.2994	黄色Yellow	3	未知功能蛋白 Unknown protein
novel.5893	黄色Yellow	6	线粒体腺嘌呤核苷酸转运蛋白ADNT1 Mitochondrial adenine nucleotide transporter ADNT1
novel.1012	黄色Yellow	1	未知功能蛋白 Unknown protein
novel.1435	黄色Yellow	2	未鉴定的线粒体蛋白 Uncharacterized mitochondrial protein
CA06g02420	粉色Pink	6	晚疫病抗性蛋白 Late blight resistance protein
novel.10180	粉色Pink	10	细胞分裂素核苷5'-单磷酸磷酸核糖水解酶 Cytokinin riboside 5'-monophosphate phosphoribohydrolase
novel.2732	粉色Pink	3	F-box蛋白CPR30 Box protein CPR30
novel.5609	粉色Pink	6	未知功能蛋白 Unknown protein
novel.3300	粉色Pink	3	细胞色素P450 Cytochrome P450
CA09g02700	粉色Pink	9	聚泛素 Polyubiquitin
novel.5608	粉色Pink	6	晚疫病抗性蛋白 Late blight resistance protein
novel.5677	粉色Pink	6	未知功能蛋白 Unknown protein
novel.6307	粉色Pink	6	未知功能蛋白 Unknown protein
novel.9637	粉色Pink	10	RNA介导的DNA聚合酶同源物 RNA-directed DNA polymerase homolog
CA01g15560	洋红色Magenta	1	DEAD-box ATP依赖性RNA解旋酶 DEAD-box ATP-dependent RNA helicase
novel.646	洋红色Magenta	1	RNA导向的DNA聚合酶同源物 RNA-directed DNA polymerase homolog
CA12g10000	洋红色Magenta	12	未知功能蛋白 Unknown protein
novel.752	洋红色Magenta	1	E4泛素连接酶 E4 ubiquitin ligase
CA11g05420	洋红色Magenta	11	α-淀粉酶3 α-amylase 3
CA06g21380	洋红色Magenta	6	胚胎发育晚期丰富蛋白 Late embryogenesis abundant protein
CA06g08970	洋红色Magenta	6	高亲和力硝酸盐转运蛋白 High affinity nitrate transporter
CA08g08430	洋红色Magenta	8	剪接因子SF3a60同源物 Splicing factor SF3a60 homolog
CA05g20820	洋红色Magenta	5	N6腺苷甲基转移酶亚基METTL14 N6-adenosine-methyltransferase subunit METTL14
novel.2181	洋红色Magenta	2	泛素结合酶 Ubiquitin-conjugating enzyme
CA09g14910	棕褐色Tan	9	早期结节样蛋白（ENODL） Early nodulin-like proteins（ENODL）
CA07g12450	棕褐色Tan	7	未知功能蛋白 Unknown protein
novel.3819	棕褐色Tan	4	蛋白酶抑制剂 Proteinase inhibitor
CA06g13600	棕褐色Tan	6	非活性聚合物 Inactive poly
CA09g14900	棕褐色Tan	9	萜烯合成酶 Terpene synthase
CA03g37000	棕褐色Tan	3	丙氨酸氨基转移酶 Alanine aminotransferase
novel.3991	棕褐色Tan	4	未知功能蛋白 Unknown protein
CA02g14150	棕褐色Tan	2	EP1样糖蛋白 EP1-like glycoprotein
CA12g11100	棕褐色Tan	12	甾醇3-β-葡萄糖基转移酶 Sterol 3-β-glucosyltransferase
CA09g15310	棕褐色Tan	9	早期结节样蛋白（ENODL） Early nodulin-like proteins（ENODL）

基因 Gene ID	模块 Model	染色体 Chromosome	基因功能描述 Gene description
CA08g08840	黄色Yellow	8	转录延伸因子SPT5同源物 Transcription elongation factor SPT5 homolog
novel.7197	黄色Yellow	7	RNA介导的DNA聚合酶同源物 RNA-directed DNA polymerase homolog
novel.5036	黄色Yellow	5	植物细胞内Ras相关的LRR蛋白 Plant intracellular Ras-group-related LRR protein
novel.6147	黄色Yellow	6	细胞分化蛋白 RCD1 Cell differentiation protein RCD1
novel.12038	黄色Yellow	12	环核苷酸门控离子通道蛋白（CNGC） Cyclic nucleotide-gated ion channel protein（CNGC）
novel.11518	黄色Yellow	12	微管蛋白α-3链 Tubulin alpha-3 chain
novel.2994	黄色Yellow	3	未知功能蛋白 Unknown protein
novel.5893	黄色Yellow	6	线粒体腺嘌呤核苷酸转运蛋白ADNT1 Mitochondrial adenine nucleotide transporter ADNT1
novel.1012	黄色Yellow	1	未知功能蛋白 Unknown protein
novel.1435	黄色Yellow	2	未鉴定的线粒体蛋白 Uncharacterized mitochondrial protein
CA06g02420	粉色Pink	6	晚疫病抗性蛋白 Late blight resistance protein
novel.10180	粉色Pink	10	细胞分裂素核苷5'-单磷酸磷酸核糖水解酶 Cytokinin riboside 5'-monophosphate phosphoribohydrolase
novel.2732	粉色Pink	3	F-box蛋白CPR30 Box protein CPR30
novel.5609	粉色Pink	6	未知功能蛋白 Unknown protein
novel.3300	粉色Pink	3	细胞色素P450 Cytochrome P450
CA09g02700	粉色Pink	9	聚泛素 Polyubiquitin
novel.5608	粉色Pink	6	晚疫病抗性蛋白 Late blight resistance protein
novel.5677	粉色Pink	6	未知功能蛋白 Unknown protein
novel.6307	粉色Pink	6	未知功能蛋白 Unknown protein
novel.9637	粉色Pink	10	RNA介导的DNA聚合酶同源物 RNA-directed DNA polymerase homolog
CA01g15560	洋红色Magenta	1	DEAD-box ATP依赖性RNA解旋酶 DEAD-box ATP-dependent RNA helicase
novel.646	洋红色Magenta	1	RNA导向的DNA聚合酶同源物 RNA-directed DNA polymerase homolog
CA12g10000	洋红色Magenta	12	未知功能蛋白 Unknown protein
novel.752	洋红色Magenta	1	E4泛素连接酶 E4 ubiquitin ligase
CA11g05420	洋红色Magenta	11	α-淀粉酶3 α-amylase 3
CA06g21380	洋红色Magenta	6	胚胎发育晚期丰富蛋白 Late embryogenesis abundant protein
CA06g08970	洋红色Magenta	6	高亲和力硝酸盐转运蛋白 High affinity nitrate transporter
CA08g08430	洋红色Magenta	8	剪接因子SF3a60同源物 Splicing factor SF3a60 homolog
CA05g20820	洋红色Magenta	5	N6腺苷甲基转移酶亚基METTL14 N6-adenosine-methyltransferase subunit METTL14
novel.2181	洋红色Magenta	2	泛素结合酶 Ubiquitin-conjugating enzyme
CA09g14910	棕褐色Tan	9	早期结节样蛋白（ENODL） Early nodulin-like proteins（ENODL）
CA07g12450	棕褐色Tan	7	未知功能蛋白 Unknown protein
novel.3819	棕褐色Tan	4	蛋白酶抑制剂 Proteinase inhibitor
CA06g13600	棕褐色Tan	6	非活性聚合物 Inactive poly
CA09g14900	棕褐色Tan	9	萜烯合成酶 Terpene synthase
CA03g37000	棕褐色Tan	3	丙氨酸氨基转移酶 Alanine aminotransferase
novel.3991	棕褐色Tan	4	未知功能蛋白 Unknown protein
CA02g14150	棕褐色Tan	2	EP1样糖蛋白 EP1-like glycoprotein
CA12g11100	棕褐色Tan	12	甾醇3-β-葡萄糖基转移酶 Sterol 3-β-glucosyltransferase
CA09g15310	棕褐色Tan	9	早期结节样蛋白（ENODL） Early nodulin-like proteins（ENODL）