一种绿豆柱头外露突变体的转录组分析

doi:10.3724/SP.J.1006.2024.34080

作物学报 ›› 2024, Vol. 50 ›› Issue (4): 957-968.doi: 10.3724/SP.J.1006.2024.34080

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

一种绿豆柱头外露突变体的转录组分析

宋梦媛¹^,²(), 郭中校¹, 苏禹霏¹^,², 邓昆鹏¹, 兰天娇¹, 程钰鑫¹, 包淑英¹, 王桂芳¹, 窦金光¹, 姜泽锴¹^,², 王明海¹^,^*(), 徐宁¹^,^*()

¹吉林省农业科学院作物资源研究所 / 作物种质资源吉林省实验室, 吉林公主岭 136100
²吉林农业大学农学院, 吉林长春 130118

收稿日期:2023-05-09 接受日期:2023-09-13 出版日期:2024-04-12 网络出版日期:2023-10-07
通讯作者: * 徐宁, E-mail: xunig2008@163.com;王明海, E-mail: shiyongdou@163.com
作者简介:E-mail: smyuan2023@163.com
基金资助:
吉林省农业科技创新工程项目(CXGC2021ZY131);吉林省农业科技创新工程项目(CXGC2021TD111);财政部和农业农村部国家现代农业产业技术体系建设专项(CARS-08-Z8)

Transcriptome analysis of a stigma exsertion mutant in mungbean

SONG Meng-Yuan¹^,²(), GUO Zhong-Xiao¹, SU Yu-Fei¹^,², DENG Kun-Peng¹, LAN Tian-Jiao¹, CHENG Yu-Xin¹, BAO Shu-Ying¹, WANG Gui-Fang¹, DOU Jin-Guang¹, JIANG Ze-Kai¹^,², WANG Ming-Hai¹^,^*(), XU Ning¹^,^*()

¹Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences / Jilin Provincial Laboratory of Crop Germplasm Resources, Gongzhuling 136100, Jilin, China
²College of Agronomy, Jilin Agricultural University, Changchun 130118, Jilin, China

Received:2023-05-09 Accepted:2023-09-13 Published:2024-04-12 Published online:2023-10-07
Contact: * E-mail: xunig2008@163.com; E-mail: shiyongdou@163.com
Supported by:
Agricultural Science and Technology Innovation Program of Jilin Province(CXGC2021ZY131);Agricultural Science and Technology Innovation Program of Jilin Province(CXGC2021TD111);China Agriculture Research System of MOF and MARA(CARS-08-Z8)

摘要/Abstract

摘要：

柱头外露作为提高作物异交率、制种纯度和降低制种成本的优良性状, 在杂交制种中得到了广泛的利用。绿豆是一种闭花授粉的作物, 被报道的柱头外露突变体很少。通过对冀绿7号的化学诱变, 发现了1个柱头外露突变体se2, 为明确该突变体柱头外露的分子机制, 对该突变体及其野生型冀绿7号即将开放的花蕾进行了转录组测序(RNA-seq)分析。根据差异倍数|log₂(Fold Change)|≥1, P≤0.05的标准筛选, 在se2中共得到572个差异表达基因(differentially expressed genes, DEGs), 其中262个DEGs上调, 310个DEGs下调。在基因本体(gene ontology, GO)数据库中, 差异表达基因显著富集到代谢和生物合成等生物过程, 定位在质外体和细胞壁、细胞膜等区域, 与结合、氧化还原等分子功能有关。在京都基因与基因组百科全书(kyoto encyclopedia of genes and genome, KEGG)数据库中, 差异表达基因显著富集在植物激素信号传导、次生代谢物生物合成等通路。功能注释发现许多有关细胞壁合成和代谢、细胞分裂和细胞扩张、植物激素相关的基因, 因此推测se2突变体中龙骨瓣的细胞分裂、细胞扩张以及植物激素信号传导过程受到影响, 从而导致了柱头外露。本研究为今后探究绿豆柱头外露的分子机制以及该性状在绿豆杂种优势中的利用奠定了基础。

关键词: 绿豆, 柱头外露, 突变体, 转录组, 高通量测序, 杂种优势

Abstract:

Stigma exsertion has been widely used in hybrid breeding as an excellent trait to improve crop outcrossing rate, seed purity, and seed production cost. As a closed-pollinated crop, few stigma exsertion mutants have been reported in mungbean. A stigma exsertion mutant se2 was discovered in mungbean variety Jilyu 7 after chemical mutagination. In order to clarify the molecular mechanism of stigma exsertion, transcription-sequencing (RNA-seq) analysis was conducted on the next day's opening buds of se2 and its wild type Jilyu 7. A total of 572 differentially expressed genes (DEGs) were obtained in se2, among which 262 DEGs were up-regulated and 310 DEGs were down-regulated, based on the screening criteria of difference multiplier |log₂(Fold Change)| ≥1 and P ≤ 0.05. In GO database, differentially expressed genes were significantly enriched in biological processes such as metabolism and biosynthesis, and localized in regions such as apoplast, cell walls, and membranes, and mainly associated with molecular functions such as binding and redox. In the kyoto encyclopedia of genes and genome (KEGG) database, differentially expressed genes were significantly enriched in plant hormone signal transduction and biosynthesis of secondary metabolites. Functional annotation revealed many genes related to cell wall synthesis and metabolism, cell division and cell expansion, and plant hormones. Therefore, we hypothesized that cell division, cell expansion, and plant hormone signaling processes of the keel flap in se2 mutants were affected, leading to stigma exsertion. This study laid a foundation for future investigations into the molecular mechanism of stigma exsertion in mungbean and its application in heterosis.

Key words: mungbean, stigma exsertion, mutant, transcriptome, high-throughput sequencing, heterosis

宋梦媛, 郭中校, 苏禹霏, 邓昆鹏, 兰天娇, 程钰鑫, 包淑英, 王桂芳, 窦金光, 姜泽锴, 王明海, 徐宁. 一种绿豆柱头外露突变体的转录组分析[J]. 作物学报, 2024, 50(4): 957-968.

SONG Meng-Yuan, GUO Zhong-Xiao, SU Yu-Fei, DENG Kun-Peng, LAN Tian-Jiao, CHENG Yu-Xin, BAO Shu-Ying, WANG Gui-Fang, DOU Jin-Guang, JIANG Ze-Kai, WANG Ming-Hai, XU Ning. Transcriptome analysis of a stigma exsertion mutant in mungbean[J]. Acta Agronomica Sinica, 2024, 50(4): 957-968.

图/表 10

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表1

表2

图2

图3

图4

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图6

表3

细胞分裂和细胞扩张相关的差异表达基因"

基因编号 Gene ID	上调/下调 Up/down	基因名称 Gene name	描述 Description
jg13552	Down	Laccase-15	漆酶15 Laccase-15
jg12507	Down	Laccase-2	漆酶2 Laccase-2
jg17193	Down	Laccase-4	漆酶4 Laccase-4
jg15432	Down	callose synthase 8	推测的胼胝质合酶8 Putative callose synthase 8
jg25641	Down	PE6/PME6	可能的果胶甲酯酶6/抑制剂6 Probable pectinesterase/pectinesterase inhibitor 6
jg33131	Up	PMEI 18/PME4	果胶甲酯酶/果胶甲酯酶抑制剂18 Pectinesterase/pectinesterase inhibitor 18
jg11460	Down	NAO	乙酰鸟氨酸脱酰基酶 Acetylornithine deacetylase
jg13187	Up	CEL1	纤维素酶1 Cellulase 1
jg21473	Down	XTH-7	木葡聚糖内转糖苷酶/水解酶7 XTH-7
jg24723	Up	XTH-16	木葡聚糖内转糖苷酶/水解酶16 XTH-16
jg20410	Down	XTH-22		木葡聚糖内转糖苷酶/水解酶22 XTH-22
jg20409	Down	XTH-22		木葡聚糖内转糖苷酶/水解酶22 XTH-22
jg20407	Down	XTH-23		木葡聚糖内转糖苷酶/水解酶23 XTH-23
jg20408	Down	XTH-23		木葡聚糖内转糖苷酶/水解酶23 XTH-23
jg12255	Up	XTH-31		木葡聚糖内转糖苷酶/水解酶31 XTH-31
jg11149	Down	GDP-fucose protein O-fucosyltransferase		GDP-fucose O-岩藻糖基转移酶 GDP-fucose protein O-fucosyltransferase
jg9115	Up	MYB46		转录因子MYB46 Transcription factor MYB46
jg17738	Down	GDPDL4		甘油磷酸二酯磷酸二酯酶GDPDL4 Glycerophosphodiester phosphodiesterase-like 4
jg23957	Down	1,3-beta-glucanase 7		1,3-β-葡聚糖内水解酶7 1,3-beta-glucan endohydrolase 7
jg9059	Up	Beta-glucosidase 12		β-葡萄糖苷酶12 Beta-glucosidase 12
jg16663	Up	Beta-1,3-endoglucanase 8		β-1.3内切葡聚糖酶8 Beta-1,3-endoglucanase 8
jg23043	Down	RAY1		β-阿拉伯呋喃糖基转移酶 Beta-arabinofuranosyltransferase RAY1
jg36915	Down	Cell wall beta-fructosidase 1		细胞壁β-果糖苷酶1 Cell wall beta-fructosidase 1
jg21315	Up	Probable aspartyl protease		可能的天冬氨酰蛋白酶At4g16563 Probable aspartyl protease At4g16563
jg17593	Down	Aspartyl protease family protein 2		天冬氨酰蛋白酶家族蛋白2 Aspartyl protease family protein 2
jg39446	Down	LRX/Extensin 6		富含亮氨酸重复延伸蛋白样蛋白6 Leucine-rich repeat extensin-like protein 6
jg15038	Down	IRX14H		β-1,4-木糖基转移酶IRX14H Probable beta-1,4-xylosyltransferase IRX14H
jg12968	Down	EXPLA2		扩展蛋白EXPLA2 Expansin-like A2
jg19405	Down	EXORDIUM		蛋白EXORDIUM Protein EXORDIUM
jg19402	Down	EXORDIUM		蛋白EXORDIUM Protein EXORDIUM
jg19404	Down	EXORDIUM		蛋白EXORDIUM Protein EXORDIUM
jg20020	Down	COBRA-Like protein 7		COBRA样蛋白7 COBRA-like protein 7
jg29779	Down	Sec3b		囊泡转运复合体亚基Sec3B Exocyst complex component SEC3B
jg15257	Down	KIN-6		驱动蛋白KIN-6 Kinesin-like protein KIN-6
jg15248	Down	KIN-6		驱动蛋白KIN-6 Kinesin-like protein KIN-6
jg35033	Down	KIN-7M		驱动蛋白KIN-7M Kinesin-like protein KIN-7M
jg14893	Up	KIN-5C		驱动蛋白KIN-5C Kinesin-like protein KIN-5C
jg33119	Down	DUF1005		未知功能蛋白DUF1005 Protein of unknown function DUF1005
jg33683	Up	BTB/POZ domain		BTB/POZ结构域蛋白 BTB/POZ domain-containing protein
jg15199	Down	PICKLE/CHR5		CHD3型染色质重塑因子PICKLE CHD3-type chromatin-remodeling factor PICKLE
jg15252	Down	PICKLE/CHR6		CHD3型染色质重塑因子PICKLE CHD3-type chromatin-remodeling factor PICKLE
jg2927	Up	EBP1		ERBB3结合蛋白1 ERBB-3 BINDING PROTEIN 1
jg13226	Down	CCR4		丝氨酸/苏氨酸蛋白激酶样蛋白CCR4 Serine/threonine-protein kinase-like protein CCR4
jg15053	Down	PAS1		肽基脯氨酰顺反异构酶 Peptidyl-prolyl cis-trans isomerase PASTICCINO1
jg15144	Up	SLAH3		S型阴离子通道3 S-type anion channel SLAH3
jg19729	Down	SLAH1		S型阴离子通道1 S-type anion channel SLAH1
jg25789	Down	SKOR		外向整流K+通道SKOR Stelar K(+) outward rectifying channel
jg17957	Down	CLC-e		氯离子通道蛋CLC-e Chloride channel protein CLC-e

表3

表4

植物激素相关的差异表达基因"

基因编号 Gene ID	上调/下调 Up/down	基因名称 Gene name	描述 Description
jg16675	Down	AUX1-like protein 1	生长素输入载体AUX1 Auxin transporter-like protein 1
jg2587	Down	PIN-Likes 1	生长素输出蛋白PIN-Likes 1 Protein PIN-Likes 1
jg20452	Up	VAN3-binding	VAN3结合蛋白 VAN3-binding protein
jg12839	Up	ARG7	生长素相应蛋白ARG7 Auxin responsive protein
jg28855	Up	SAUR71	生长素响应蛋白SAUR71 Auxin-responsive protein SAUR71
jg13096	Down	CKX6/CKO6	细胞分裂素脱氢酶/氧化酶6 Cytokinin dehydrogenase/oxidase 6
jg33851	Up	ATHB-40	HD-ZIP蛋白ATHB-40 HD-ZIP protein ATHB-40
jg638	Up	ATHB-12	HD-ZIP蛋白 ATHB-12 HD-ZIP protein ATHB-12
jg1095	Up	GA 20-oxidase 2	赤霉素20氧化酶2 Gibberellin 20 oxidase 2
jg18873	Up	GA 20-oxidase 2	赤霉素20氧化酶2 Gibberellin 20 oxidase 2
jg36069	Up	ETR2	乙烯受体ETR2 Ethylene receptor 2
jg36578	Up	ERF106	乙烯响应转录因子ERF106 Ethylene-responsive transcription factor ERF106
jg4916	Up	ERF034	乙烯响应转录因子ERF034 Ethylene-responsive transcription factor ERF034
jg37484	Up	ERF1B	乙烯响应转录因子ERF1B Ethylene-responsive transcription factor 1B
jg38226	Down	PP2C	可能的蛋白磷脂酶 PP2C 49 Probable protein phosphatase 2C 49
jg545	Up	MARD1/SAG102	ABA调节的休眠介质1/衰老相关蛋白SAG102 Mediator of ABA-regulated dormancy1/Senescence-associated protein SAG102
jg20855	Up	AFP3	ABI5结合蛋白3 ABI5-binding protein 3
jg27356	Up	ABR1	乙烯响应因子ABR1 Ethylene-responsive transcription factor ABR1
jg29371	Up	AOS2/P450 74A	丙二烯氧化物合酶2 Allene oxide synthase 2/Cytochrome P450 74A
jg35914	Down	TGA7	转录因子TGA7 Transcription factor TGA7
jg15164	Down	OPP21	双组分响应调节子ORR21 Two-component response regulator ORR21
jg25674	Down	ARR14	双组分响应调节子ARR14 Two-component response regulator ARR14
jg27911	Up	ARR17	双组分响应调节子ARR17 Two-component response regulator ARR17
jg14455	Down	SAP12	锌指结构域应激相关蛋白12 Zinc finger AN1 domain-containing stress-associated protein 12 SAP12
jg14454	Down	SAP12	锌指结构域应激相关蛋白12 Zinc finger AN1 domain-containing stress-associated protein 12 SAP12

表4

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基因编号 Gene ID	正向引物序列 Forward sequence (5'-3')	反向引物序列 Reverse sequence (5'-3')
jg12155	CTTGGATACCATACCTGCGGACATG	CACGAACATCGGCAATTCTGAATGG
jg15370	TGTGGAGCAAGGAGCATCAACAAC	CTTAGCCAAATCCATGTCCCTTCCC
jg17957	CCCGGTGTTGCAACTTCTCT	CATAAGCTTGCGGTGATGCC
novel.24	TGTGTGGTGTCGCAGGTTGTTC	AGCAGTGAGGAGTGGTCCAAGAG
jg25789	CACCTCCCTCTACTTTGCCG	AGCGCCGAGAATCATGTCAA
VrActin	GGCATCCACGAGACAACA	AGCCTCCAATCCAGACAC

样本 Sample	测序总读数 Total reads number	质控后读数 Clean reads number	错误率 Error rate (%)	总比对率 Mapped ratio (%)	Q20碱基百分比 Q20 base percentage (%)	Q30碱基百分比 Q30 base percentage (%)
WT1	44719486	43961678	0.02	96.79	98.10	94.43
WT2	46637862	45775686	0.02	96.86	98.05	94.23
WT3	43888030	42753792	0.03	96.68	97.97	94.08
SE2-1	47065416	46312622	0.02	96.97	98.10	94.33
SE2-2	47644132	46668574	0.02	96.67	98.20	94.61
SE2-3	45688950	44977346	0.03	96.99	98.00	94.11

一种绿豆柱头外露突变体的转录组分析

Transcriptome analysis of a stigma exsertion mutant in mungbean

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