Screening Genes Related to Male Sterile in Welsh Onion（Allium fistulosum L.） Based on Transcriptomic Profiling and WGCNA

doi:10.13560/j.cnki.biotech.bull.1985.2024-0276

Abstract

Abstract:

【Objective】The aim of this study is to identify the co-expression modules of male sterile Welsh onion（Allium fistulosum L.）and to screen key hub genes, so as to provide deeper insights into the molecular mechanisms of male sterile in the Welsh onion. 【Method】Twenty-four cDNA libraries were constructed and sequenced for different development stages of flower buds from the male-sterile（MS）plants and male-fertile（MF）plants. Then weighted gene co-expression network analysis（WGCNA）was performed to reveal the key modules and hub genes. 【Result】A total of eighteen co-expression modules were identified based on 8,320 genes, among which three modules（blue, midnightblue, and black）were significantly correlated with pollen abortion of the MS plant. Functional enrichment analysis suggested that several pathways associated with the “phenylpropanoid biosynthesis” “cutin, suberine, and wax biosynthesis” “starch and sucrose metabolism” “alpha-linolenic acid metabolism” and “fatty acid elongation” were found to be involved in pollen abortion of the MS plant. By considering gene significance and intramodular connectivity, several hub genes including atpB, TPS9, TPD1, and BHLH35, were identified, which might play key roles in pollen development of the Welsh onion. Then hub genes related to pollen development response were verified for quantitative real-time PCR（RT-qPCR）analysis, and the expression patterns of RNA-Seq and RT-qPCR were very consistent. 【Conclusion】Three key modules of male sterile Welsh Onion are obtained, and hub genes like atpB, TPS9, and TPD1 are identified. It is found that the pollen abortion of the MS plant mainly is involved the processes of phenylpropanoid biosynthesis, cutin, suberine, and wax biosynthesis, starch and sucrose metabolism, alpha-Linolenic acid metabolism, and fatty acid elongation.

Key words: Welsh onion, male sterile, weighted gene co-expression network analysis, RNA-Seq, hub gene

YUE Li-xin, WANG Qing-hua, LIU Ze-zhou, KONG Su-ping, GAO Li-min. Screening Genes Related to Male Sterile in Welsh Onion（Allium fistulosum L.） Based on Transcriptomic Profiling and WGCNA[J]. Biotechnology Bulletin, 2024, 40(9): 212-224.

Figures/Tables 9

References 49

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基因ID Gene ID	基因名称Gene name	正向引物Forward sequence（5'-3'）	反向引物Reverse sequence（5'-3'）
AfisC2G08595	TPS9	CGCTCTGGTTTGGCATCATCC	ACAACGGCAGGTTCCTTAACAAG
AfisC2G08419	TPD1	GTTGAAGGCAAACCAGAGTACAGAG	GCTCGACACTGCTTAGACCATAAC
AfisC3G06496	OPR1	GCCCAAACGCTTTCTCTTAAATGTC	AGCCTGAACCTGAACCTCCTTC
AfisC4G05057	ATPG	ACGAGAGGAATGAGAAGATGAAGTC	AACACGGTAGCAGCAACAGATC
AfisC4G00897	BHLH35	ATGCCAACTACTGGGAAACCAAGC	TTGTTGTTCCTTCAGGCGAGCTG
AfisC7G05890	APX8	AGGTGGTGGTGGTGGTTACAG	TCTAGTTCCTCCAGTTTCCATCGG
AfisC7G05387	atpB	CATCAGCGAAATGTTGGATCAAGAC	GTGTTGTTATGCGAACCATTCAGAC
	Actin	ACACGGCCTGGATAGCAACAT	AGAGCAGTATTCCCAAGCATT

基因ID Gene ID	基因名称Gene name	正向引物Forward sequence（5'-3'）	反向引物Reverse sequence（5'-3'）
AfisC2G08595	TPS9	CGCTCTGGTTTGGCATCATCC	ACAACGGCAGGTTCCTTAACAAG
AfisC2G08419	TPD1	GTTGAAGGCAAACCAGAGTACAGAG	GCTCGACACTGCTTAGACCATAAC
AfisC3G06496	OPR1	GCCCAAACGCTTTCTCTTAAATGTC	AGCCTGAACCTGAACCTCCTTC
AfisC4G05057	ATPG	ACGAGAGGAATGAGAAGATGAAGTC	AACACGGTAGCAGCAACAGATC
AfisC4G00897	BHLH35	ATGCCAACTACTGGGAAACCAAGC	TTGTTGTTCCTTCAGGCGAGCTG
AfisC7G05890	APX8	AGGTGGTGGTGGTGGTTACAG	TCTAGTTCCTCCAGTTTCCATCGG
AfisC7G05387	atpB	CATCAGCGAAATGTTGGATCAAGAC	GTGTTGTTATGCGAACCATTCAGAC
	Actin	ACACGGCCTGGATAGCAACAT	AGAGCAGTATTCCCAAGCATT

基因名称Gene name	模块 Module	基因描述 Gene description	GO注释 GO term	KEGG通路 KEGG pathway
CYT1	Blue	甘露糖-1-磷酸鸟苷酸转移酶1 Mannose-1-phosphate guanylyl transferase 1	甘露糖-1-磷酸鸟苷酸转移酶活性Mannose-1-phosphate guanylyl transferase activity GDP-甘露糖生物合成过程GDP-mannose biosynthetic process L-抗坏血酸的生物合成过程L-ascorbic acid biosynthetic process 纤维素生物合成过程Cellulose biosynthetic process	氨基糖和核苷酸糖代谢 Amino sugar and nucleotide sugar metabolism 果糖和甘露糖代谢途径 Fructose and mannose metabolism
TPS9	Blue	α海藻糖合成酶 9 Alpha-trehalose-phosphate synthase[UDP-forming]9	海藻糖生物合成过程Trehalose biosynthetic process 去磷酸化Dephosphorylation 转移酶活性，转移糖基Transferase activity, transferring glycosyl groups 海藻糖代谢对逆境胁迫的响应Trehalose metabolism in response to stress	淀粉和蔗糖代谢 Starch and sucrose metabolism
atpB	Blue	ATP合成酶β亚基 ATP synthase subunit beta	ATP结合ATP binding ATP合成偶联质子转运ATP synthesis coupled proton transport 质子转移ATP合酶复合体，催化核心F（1）Proton-transporting ATP synthase complex, Catalytic core F（1）质子转移ATP合酶活性，旋转机制Proton-transporting ATP synthase activity, rotational mechanism	氧化磷酸化 Oxidative phosphorylation
TPD1	Midnightblue	绒毡层决定因子蛋白 Protein TAPETUM DETERMINANT 1	细胞命运决定Cell fate determination 花药发育Anther development	_
ATPG	Midnightblue	ATP合酶亚基b' ATP synthase subunit b'	ATP结合ATP binding 质子跨膜转运蛋白活性Proton transmembrane transporter activity ATP合成偶联质子转运ATP synthesis coupled proton transport 膜的整体成分Integral component of membrane 质子转移ATP合酶复合体，催化核心F（o）Proton-transporting ATP synthase complex, coupling factor F（o）	氧化磷酸化 Oxidative phosphorylation
APX8	Midnightblue	L-抗坏血酸过氧化物酶8 L-ascorbate peroxidase 8	对活性氧的响应Response to reactive oxygen species 过氧化物酶活性Peroxidase activity L-抗坏血酸过氧化物酶活性L-ascorbate peroxidase activity 细胞对氧化应激的反应Cellular response to oxidative stress 过氧化氢分解过程Hydrogen peroxide catabolic process	谷胱甘肽代谢 Glutathione metabolism
OPR1	Black	12-氧代二烯酸还原酶1 12-oxophytodienoate reductase 1	茉莉酸生物合成过程Jasmonic acid biosynthetic process 12-氧植二烯酸还原酶活性12-oxophytodienoate reductase activity 脂氧化物生物合成过程Oxylipin biosynthetic process	α-亚油酸代谢 Alpha-Linolenic acid metabolism
LOX6	Black	脂氧合酶6 Lipoxygenase 6	茉莉酸生物合成过程Jasmonic acid biosynthetic process 脂氧化物生物合成过程Oxylipin biosynthetic process 脂质氧化Lipid oxidation 亚油酸13S-脂氧合酶活性Linoleate 13S-lipoxygenase activity	亚油酸代谢 Linoleic acid metabolism

基因名称Gene name	模块 Module	基因描述 Gene description	GO注释 GO term	KEGG通路 KEGG pathway
CYT1	Blue	甘露糖-1-磷酸鸟苷酸转移酶1 Mannose-1-phosphate guanylyl transferase 1	甘露糖-1-磷酸鸟苷酸转移酶活性Mannose-1-phosphate guanylyl transferase activity GDP-甘露糖生物合成过程GDP-mannose biosynthetic process L-抗坏血酸的生物合成过程L-ascorbic acid biosynthetic process 纤维素生物合成过程Cellulose biosynthetic process	氨基糖和核苷酸糖代谢 Amino sugar and nucleotide sugar metabolism 果糖和甘露糖代谢途径 Fructose and mannose metabolism
TPS9	Blue	α海藻糖合成酶 9 Alpha-trehalose-phosphate synthase[UDP-forming]9	海藻糖生物合成过程Trehalose biosynthetic process 去磷酸化Dephosphorylation 转移酶活性，转移糖基Transferase activity, transferring glycosyl groups 海藻糖代谢对逆境胁迫的响应Trehalose metabolism in response to stress	淀粉和蔗糖代谢 Starch and sucrose metabolism
atpB	Blue	ATP合成酶β亚基 ATP synthase subunit beta	ATP结合ATP binding ATP合成偶联质子转运ATP synthesis coupled proton transport 质子转移ATP合酶复合体，催化核心F（1）Proton-transporting ATP synthase complex, Catalytic core F（1）质子转移ATP合酶活性，旋转机制Proton-transporting ATP synthase activity, rotational mechanism	氧化磷酸化 Oxidative phosphorylation
TPD1	Midnightblue	绒毡层决定因子蛋白 Protein TAPETUM DETERMINANT 1	细胞命运决定Cell fate determination 花药发育Anther development	_
ATPG	Midnightblue	ATP合酶亚基b' ATP synthase subunit b'	ATP结合ATP binding 质子跨膜转运蛋白活性Proton transmembrane transporter activity ATP合成偶联质子转运ATP synthesis coupled proton transport 膜的整体成分Integral component of membrane 质子转移ATP合酶复合体，催化核心F（o）Proton-transporting ATP synthase complex, coupling factor F（o）	氧化磷酸化 Oxidative phosphorylation
APX8	Midnightblue	L-抗坏血酸过氧化物酶8 L-ascorbate peroxidase 8	对活性氧的响应Response to reactive oxygen species 过氧化物酶活性Peroxidase activity L-抗坏血酸过氧化物酶活性L-ascorbate peroxidase activity 细胞对氧化应激的反应Cellular response to oxidative stress 过氧化氢分解过程Hydrogen peroxide catabolic process	谷胱甘肽代谢 Glutathione metabolism
OPR1	Black	12-氧代二烯酸还原酶1 12-oxophytodienoate reductase 1	茉莉酸生物合成过程Jasmonic acid biosynthetic process 12-氧植二烯酸还原酶活性12-oxophytodienoate reductase activity 脂氧化物生物合成过程Oxylipin biosynthetic process	α-亚油酸代谢 Alpha-Linolenic acid metabolism
LOX6	Black	脂氧合酶6 Lipoxygenase 6	茉莉酸生物合成过程Jasmonic acid biosynthetic process 脂氧化物生物合成过程Oxylipin biosynthetic process 脂质氧化Lipid oxidation 亚油酸13S-脂氧合酶活性Linoleate 13S-lipoxygenase activity	亚油酸代谢 Linoleic acid metabolism