基于转录组测序解析南瓜子叶黄化的分子机理

doi:10.3969/j.issn.1004-1524.2023.01.10

浙江农业学报 ›› 2023, Vol. 35 ›› Issue (1): 90-102.DOI: 10.3969/j.issn.1004-1524.2023.01.10

基于转录组测序解析南瓜子叶黄化的分子机理

熊兴伟(), 王艺琴, 田怀志, 张素勤, 耿广东()

贵州大学农学院,贵州贵阳 550025

收稿日期:2022-03-30 出版日期:2023-01-25 发布日期:2023-02-21
通讯作者: *耿广东,E-mail:genggd213@163.com
作者简介:熊兴伟(1996—),男,侗族,贵州石阡人,硕士研究生,主要从事蔬菜生理生态与生物技术研究。E-mail:gdxxwei@163.com
基金资助:
贵州省科技计划(黔科合成果〔2021〕一般063);贵州省科技计划(黔科合成果〔2020〕1Z002号);国家重点研发计划(2021YFD1100301)

Molecular mechanisms of chlorophyll-reduced cotyledon based on transcriptome sequencing in pumpkin

XIONG Xingwei(), WANG Yiqin, TIAN Huaizhi, ZHANG Suqin, GENG Guangdong()

College of Agriculture, Guizhou University, Guiyang 550025, China

Received:2022-03-30 Online:2023-01-25 Published:2023-02-21

摘要/Abstract

摘要：

为研究南瓜叶色黄化突变的机制,挖掘黄化相关关键基因,试验以南瓜自然黄化突变体为试材,通过高通量RNA测序(RNA-seq)对苗期子叶进行转录组分析。结果表明:从检测的26 445个表达基因中鉴定出12 687个差异表达基因(DEGs),包括6 444个上调基因,6 243个下调基因;其中2 321个DEGs是转录因子编码基因。选取14个与光合色素密切相关的DEGs进行实时荧光定量PCR(qRT-PCR)分析,发现它们的基因表达水平与转录组测序结果一致。经KEGG富集分析,发现卟啉和叶绿素(Chl)生物合成、光系统Ⅰ、光系统Ⅱ、光合作用-天线蛋白、电子传递和F型ATP酶相关基因的表达显著下调。谷氨酰-tRNA还原酶、镁离子螯合酶、叶绿素a加氧酶基因异常表达,血红素代谢相关基因表达上调抑制了Chl合成;β-胡萝卜素3-羟基酶促进了类胡萝卜素生成;另外,光合作用过程受阻也反馈抑制Chl合成,Chl合成受阻和类胡萝卜素合成受促导致南瓜叶色黄化。研究结果为南瓜黄化突变的分子机制提供了新的见解,为关键基因功能分析和南瓜育种奠定了基础。

关键词: 南瓜, 黄化突变体, 叶绿素, 转录组, 基因表达

Abstract:

In order to explore the mechanisms of chlorophyll-reduced mutation and excavate its key genes, pumpkin natural chlorophyll-reduced seedling was used as test material, and the transcriptome of the cotyledon was analyzed by high-throughput RNA sequencing (RNA-seq). The results showed that 12 687 differentially expressed genes (DEGs) were identified from 26 445 expressed genes, including 6 444 up-regulated genes and 6 243 down-regulated genes. Among them, 2 321 DEGs were transcription factor genes. Fourteen DEGs closely related to photosynthetic pigments were selected for qRT-PCR analysis. It was found that their expression level was consistent with the transcriptome data. KEGG enrichment analysis showed that the expression levels of biosynthesis of porphyrin and chlorophyll (Chl), photosystem Ⅰ, photosystem Ⅱ, photosynthesis antenna protein, electron transport, and F-type ATPase related genes were significantly down-regulated. Abnormal expression of glutamyl tRNA reductase, magnesium chelatase, and chlorophyll a oxygenase, and up-regulated expression of heme-related genes inhibited Chl synthesis. β-carotenoid 3-hydroxylase promoted carotenoid synthesis. In addition, feedback of photosynthesis inhibition also reduced Chl synthesis. The inhibition of Chl synthesis and the promotion of carotenoid synthesis led to pumpkin leaf etiolation. It laid a new foundation for the molecular analysis of pumpkin mutation and gene function.

Key words: pumpkin, chlorophyll-reduced mutant, chlorophyll, transcriptome, gene expression

中图分类号:

S642.1

熊兴伟, 王艺琴, 田怀志, 张素勤, 耿广东. 基于转录组测序解析南瓜子叶黄化的分子机理[J]. 浙江农业学报, 2023, 35(1): 90-102.

XIONG Xingwei, WANG Yiqin, TIAN Huaizhi, ZHANG Suqin, GENG Guangdong. Molecular mechanisms of chlorophyll-reduced cotyledon based on transcriptome sequencing in pumpkin[J]. Acta Agriculturae Zhejiangensis, 2023, 35(1): 90-102.

图/表 13

图1 南瓜黄化苗 A,MB21M黄化苗;B,MB21CK绿苗对照。

Fig.1 Chlorophyll-reduced seedlingof pumpkin A, Chlorophyll-reduced seedling MB21M; B, Control green seedling MB21CK.

表1 qRT-PCR所用特异引物

Table 1 Specific primers used for qRT-PCR

差异表达基因ID ID of differential expressed genes	正向引物 Forward primer(5'→3')	反向引物 Reverse primer(5'→3')
CmaCh14G018600	ATCTCCGCTCCGTTCCTCTGTC	GCTTCGGTTCCGATTTTCCATTTGG
CmaCh11G001420	ATCCGAGTTGAAGCACATCCAATCC	TCGCCTGAGCATTTCGTCACATAC
CmaCh10G000130	CTCACAGGAGTAACAGTCTGCGATG	AATATCACTGGCGAAGACGATGGC
CmaCh03G010210	GAAGGCTGAGGGAGTGAACAAGAAC	TCCAGGGTGTAAGTTAGGCGAGTC
CmaCh07G007390	GCTGGTGGAAGAGGTGATGAAGAAG	AGATGGCTGAACGCTCTCAAACAC
CmaCh18G003280	CGAGACTTGGACCTGCCCTTAAAG	CTGATTCTTTCGCCCTGGCTACG
CmaCh11G018510	TCAGTTGTCAAGCCACGAGTATTCC	GAAGCCCAATAGCACCCAGAAGAAG
CmaCh19G009550	GCGAAGGGAAAGGGCGTTAAGG	CAACATGGTAGCAGTGGGAAGGC
CmaCh14G016960	AACCCTCTTCACCCCATCTCTCTC	AAGATGCGGCAGGCTTGATGAG
CmaCh05G007770	GCCACTGAAGAACCCAAGCCTAAG	CCTGGTCAACTGTTACAACCGATCC
CmaCh12G009820	TTGGCCCCAAGAGAGGTACTAAGG	AACCGTGACAACAGATCCAACATCC
CmaCh13G003520	TCCTCCCTCTCCTCTCCTTCCTC	TGAACCTTCCGCCGAATGAACG
CmaCh19G004980	GCAGAGGCGGATGTCATCTTCAC	CACATGGCTCGACGTTCCTTGG
CmaCh07G012230	TTGCTAATGCTGCTGCTCTTCCG	AACGAATGGTGCTACAGTCGATACG
18S	TCGGGATCGGAGTAATGA	TTCGCAGTTGTTCGTCTT

图2 两个南瓜样本的相关性热图 r1、r2、r3分别表示3次重复。

Fig.2 Correlation heat map of two pumpkin samples r1, r2, and r3 represented three repetitions, respectively.

图3 南瓜黄化苗突变体中差异表达基因的数量 A,组间差异表达基因维恩图;B,突变体中差异表达基因数量。

Fig.3 Number of differentially expressed genes in pumpkin chlorophyll-reduced mutant

表2 qRT-PCR验证基因的名称与相对表达水平

Table 2 Name and relative expression level of genes verified by qRT-PCR

基因ID Gene ID	基因名称 Gene name	相对表达水平 Relative expression level
基因ID Gene ID	基因名称 Gene name	RNA-seq	qRT-PCR
CmaCh14G018600	HCAR	96.92	0.92
CmaCh11G001420	chlP, bchP	43.16	1.15
CmaCh10G000130	bchM,chlM	181.12	2.69
CmaCh03G010210	psbO	564.12	21.51
CmaCh07G007390	psbO	467.19	19.25
CmaCh18G003280	psbQ	471.95	27.78
CmaCh11G018510	MYBP/petC	200.09	12.41
CmaCh19G009550	petC	428.96	42.18
CmaCh14G016960	psaD	442.07	52.54
CmaCh05G007770	psaE	104.02	1.88
CmaCh12G009820	psaE	592.67	69.60
CmaCh13G003520	psaO	576.34	37.67
CmaCh19G004980	hemA	104.80	1.15
CmaCh07G012230	psbE	6.40	0.26

图4 qRT-PCR和转录组数据的相关性

Fig.4 Correlation of data from qRT-PCR and transcriptome analysis

图5 差异基因GO分类 1,生物粘附;2,生物调节;3,细胞过程;4,排毒;5,发育过程;6,生长;7,免疫系统过程;8,物种间相互作用;9,定位;10,移动;11,代谢过程;12,多生物过程;13,多细胞组织过程;14,氮利用;15,繁殖;16,生殖过程;17,对刺激的反应;18,节律过程;19,信号转导;20,细胞解剖实体;21,细胞内;22,含蛋白质复合物;23,抗氧化剂活性;24,结合;25,受体活性;26,催化活性;27,分子载体活性;28,分子功能调节器;29,分子传感器活性;30,营养库活性;31,蛋白质折叠伴侣;32,蛋白质标签;33,小分子传感器活性;34,结构分子活性;35,毒素活性;36,转录调节活性;37,翻译调节活性;38,载体活性。

Fig.5 The GO terms of the DEGs 1, Biological adhesion; 2, Biological regulation; 3, Cell process; 4, Detoxification; 5, Development process; 6, Growth; 7, Immune system process; 8, Interspecies interactions between organisms; 9, Localization; 10, Locomotion; 11, Metabolic process; 12, Multi-organism process; 13, Multicellular organization process; 14, Nitrogen utilization; 15, Reproduction; 16, Reproductive process; 17, Response to stimulus; 18, Rhythmic process; 19, Signaling; 20, Cellular anatomical entity; 21, Intracellular; 22, Protein-containing complex; 23, Antioxide activity; 24, Binding; 25, Cargo receptor activity; 26, Catalytic activity; 27, Molecular carrier activity; 28, Molecular function regulator; 29, Molecular transducer activity; 30, Nutrient reservoir activity; 31, Protein folding chaperone; 32, Protein tag; 33, Small molecule sensor activity; 34, Structural molecular activity; 35, Toxin activity; 36, Transcriptional regulatory activity; 37, Translational regulatory activity; 38, Transporter activity.

图6 差异基因GO富集气泡图 1,蛋白丝氨酸/苏氨酸激酶活性;2,细胞氨基酸代谢过程;3,丝氨酸家族氨基酸代谢过程;4,磷酸转移酶活性,醇基为受体;5,α-氨基酸代谢过程;6,蛋白激酶活性;7,催化活性,作用于蛋白质;8,激酶活性;9,腺苷酸结合;10,腺苷基核糖核苷酸结合;11,ATP结合;12,碳水化合物衍生物结合;13,阴离子结合;14,嘌呤核苷酸结合;15,核苷磷酸结合;16,小分子结合;17,嘌呤核糖核苷三磷酸结合;18,嘌呤核糖核苷酸结合;19,核糖核苷酸结合;20,核苷酸结合。

Fig.6 Bubble chart of DEG GO enrichment 1, Protein serine/threonine kinase activity; 2, Cellular amino acid metabolic process; 3, Serine family amino acid metabolic process; 4, Phosphotransferase activity, alcohol group as acceptor; 5, Alpha-amino acid metabolic process; 6, Protein kinase activity; 7, Catalytic activity, acting on a protein; 8, Kinase activity; 9, Adenyl nucleotide binding; 10, Adenyl ribonucleotide binding; 11, ATP binding; 12, Carbohydrate derivative binding; 13, Anion binding; 14, Purine nucleotide binding; 15, Nucleoside phosphate binding; 16, Small molecule binding; 17, Purine ribonucleoside triphosphate binding; 18, Purine ribonucleotide binding; 19, Ribonucleotide binding; 20, Nucleotide binding.

图7 差异基因KEGG富集气泡图 1,自噬-其他;2,植物激素信号转导;3,2-氧代羧酸代谢;4,碳代谢;5,硫胺素代谢;6,苯丙氨酸,酪氨酸和色氨酸生物合成;7,精氨酸生物合成;8,磷酸戊糖途径;9,过氧物酶体;10,丁酸代谢;11,光合作用-天线蛋白;12,MAPK信号通路-植物;13,甘氨酸,丝氨酸和苏氨酸的代谢;14,硫代谢;15,吞噬体;16,卟啉和叶绿素代谢;17,内质网中的蛋白质加工;18,丙氨酸、天冬氨酸和谷氨酸代谢;19,蛋白酶体;20,氨基酸生物合成。

Fig.7 Bubble chart of DEG KEGG pathways 1, Autopophagy-other; 2, Plant hormone signal transduction; 3, 2-Oxyxy arboxylic acid metabolism; 4, Carbon metabolism; 5, Thiamine metabolism; 6, Phenylalanine, tyrosine and tryptophan biosynthesis; 7, Arginine biosynthesis; 8, Pentose phosphate pathway; 9, Peroxisome; 10, Butyrate metabolism; 11, Photosynthesis-antenna proteins; 12, MAPK signaling pathway-plant; 13, Glycine, serine and threonine metabolism; 14, Sulfur metabolism; 15, Phagosome; 16, Porphyrin and chlorophyll metabolism; 17, Protein processing in endoplasmic reticulum; 18, Alanine, aspartate, and glutamate metabolism; 19, Proteasome; 20, Biosynthesis of amino acids.

图8 DEGs所属转录因子家族分类

Fig.8 Classification of transcription factor families to which the DEGs belong

图9 卟啉与叶绿素合成途径 A,ALA合成;B,原卟啉Ⅸ和血红素合成;C,叶绿素合成。红色指示上调基因,绿色指示下调基因,下同。

Fig.9 Porphyrin and chlorophyll synthesis pathways A, ALA synthesis; B, Proporphyrin and heme synthesis; C, Chlorophyll synthesis. Red color indicated up-regulated genes, and green color showed down-regulated genes. The same as below.

图10 类胡萝卜素生物合成途径

Fig.10 Pathways of carotenoid biosynthesis

图11 光合作用途径

Fig.11 Photosynthesis pathway

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基于转录组测序解析南瓜子叶黄化的分子机理

Molecular mechanisms of chlorophyll-reduced cotyledon based on transcriptome sequencing in pumpkin

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