基于转录组和WGCNA筛选丝瓜果长和果径发育调控相关基因

doi:10.3864/j.issn.0578-1752.2023.22.012

中国农业科学 ›› 2023, Vol. 56 ›› Issue (22): 4506-4522.doi: 10.3864/j.issn.0578-1752.2023.22.012

基于转录组和WGCNA筛选丝瓜果长和果径发育调控相关基因

陈敏氡(), 王彬, 刘建汀, 李永平, 白昌辉, 叶新如, 裘波音, 温庆放(), 朱海生()

福建省蔬菜遗传育种重点实验室/福建省蔬菜工程技术研究中心/福建省农业科学院作物研究所，福州 350013

收稿日期:2023-04-10 接受日期:2023-09-05 出版日期:2023-11-16 发布日期:2023-11-17
通信作者: 朱海生，E-mail：zhs0246@163.com。
温庆放，E-mail：fjvrc@163.com
联系方式: 陈敏氡，E-mail：1053870789@qq.com。
基金资助:
福建省自然科学基金(2021J01494); 福建省农业科学院英才项目(YC2021004); 福建省农业科学院科技创新团队项目(CXTD2021003-1); 国家大宗蔬菜产业技术体系福州综合试验站项目(CARS-23-G51); 福建省种业创新与产业化工程项目(zycxny2021009); 福建省农业高质量发展超越“5511”协同创新工程项目(XTCXGC2021003)

Screening Regulatory Genes Related to Luffa Fruit Length and Diameter Development Based on Transcriptome and WGCNA

CHEN MinDong(), WANG Bin, LIU JianTing, LI YongPing, BAI ChangHui, YE XinRu, QIU BoYin, WEN QingFang(), ZHU HaiSheng()

Fujian Key Laboratory of Vegetable Genetics and Breeding/Fujian Engineering Research Center for Vegetables/Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013

Received:2023-04-10 Accepted:2023-09-05 Published:2023-11-16 Online:2023-11-17

摘要/Abstract

摘要：

【目的】鉴定丝瓜果长和果径发育基因共表达模块并筛选关键调控基因，为后续丝瓜果形控制的分子机制研究提供理论依据。【方法】以丝瓜9个发育阶段（开花前2 d以及花后0、2、4、6、8、10、15和20 d）果实为研究材料，测定各阶段的果长和果径，利用WGCNA方法联合分析转录组与果长和果径数据，鉴定与果长和果径发育相关的共表达基因模块，筛选关键调控基因。【结果】利用WGCNA鉴定出14个共表达模块，与果长和果径显著相关（相关系数的绝对值=0.9）的共表达模块有2个，显著正相关的模块为Turquoise模块，显著负相关的模块为Lightpink4模块。KEGG富集分析发现，Turquoise模块显著富集在内吞作用和苯丙烷生物合成通路，与果实膨大、伸长调控密切相关，可作为研究丝瓜果长和果径的关键基因模块。根据Turquoise模块内基因的连接度以及功能注释，筛选出10个关键调控基因，包括木葡聚糖内转葡糖基酶/水解酶基因XTH23、肌动蛋白解聚因子基因ADF2、伴侣蛋白基因DnaJ10、扩展蛋白基因（EXPA1、EXPA4和EXLA5）、驱动蛋白基因Kinesin-13A、生长素反应基因SAUR21和Aux/IAA11。RT-qPCR结果显示，10个调控基因的表达量均在果实进入快速生长期（花后8 d）后显著升高，增加倍数约为2—50倍。通过构建基因互作网络，发现部分调控基因与WRKY、bHLH和HSF转录因子家族存在互作关系。【结论】获得了丝瓜果长和果径基因共表达重要模块Turquoise模块，筛选到10个调控基因可作为丝瓜果形控制的潜在候选基因，并发现丝瓜果长和果径的发育调控主要涉及细胞壁的重构、细胞的发育与分化、生长素的调控等过程。

关键词: 转录组, WGCNA, 丝瓜, 果长, 果径, 调控基因

Abstract:

【Objective】 The aim of this study was to identify the co expression modules of luffa fruit length and diameter development and to screen key regulatory genes, so as to provide the theoretical basis for subsequent research on the molecular mechanism of fruit shape control in luffa. 【Method】 The luffa fruits in 9 fruit development stages (2 days before anthesis, and 0, 2, 4, 6, 8, 10, 15, and 20 days after anthesis) were applied as research materials. The fruit length and diameter of each stage were measured. The WGCNA method was used to jointly analyze transcriptome and fruit length and diameter data, to identify co-expressed gene modules of fruit length and diameter development, and to screen out key regulatory genes.【Result】A total of 14 co expression modules were identified by WGCNA, among which two modules (Turquoise and Lightpink4) were significantly correlated with fruit length and diameter (absolute value of correlation coefficient=0.9); Turquoise module was significantly positively correlated, while Lightpink4 module was significantly negatively correlated. KEGG enrichment analysis found that the Turquoise module was significantly enriched in endocytosis and phenylpropanoid biosynthesis pathways, which were closely related to fruit enlargement and growth regulation, and could be used as a key gene module for studying fruit length and diameter in luffa. According to the connectivity and functional annotation of genes in Turquoise module, ten key regulatory genes were screened, including xyloglucan endotransglucosylase/hydrolase gene XTH23, actin-depolymerizing factor gene ADF2, chaperone protein gene DnaJ10, expansin gene (EXPA1, EXPA4 and EXLA5), kinesin gene kinesin-13A, auxin response genes SAUR21, and Aux/IAA11. The RT-qPCR results showed that the expression levels of ten regulatory genes significantly increased after the fruit entered the rapid growth period (8 day after anthesis), with an increase of 2-50 times approximately. Through constructing a gene interaction network, it was found that some candidate genes interacted with the WRKY, bHLH, and HSF transcription factor families.【Conclusion】The Turquoise module, an important co expression module of luffa fruit length and diameter was obtained, and ten potential candidate genes for luffa fruit shape control were screened. It was found that luffa fruit length and diameter development regulation mainly involved the processes of cell wall reconstruction, cell development and differentiation, and auxin regulation.

Key words: transcriptome, WGCNA, Luffa cylindrica L., fruit length, fruit diameter, regulatory genes

陈敏氡, 王彬, 刘建汀, 李永平, 白昌辉, 叶新如, 裘波音, 温庆放, 朱海生. 基于转录组和WGCNA筛选丝瓜果长和果径发育调控相关基因[J]. 中国农业科学, 2023, 56(22): 4506-4522.

CHEN MinDong, WANG Bin, LIU JianTing, LI YongPing, BAI ChangHui, YE XinRu, QIU BoYin, WEN QingFang, ZHU HaiSheng. Screening Regulatory Genes Related to Luffa Fruit Length and Diameter Development Based on Transcriptome and WGCNA[J]. Scientia Agricultura Sinica, 2023, 56(22): 4506-4522.

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基因ID Gene ID	上游引物 Upstream primer（5'-3'）	下游引物 Downstream primer（5'-3'）
Maker00007620	GAACCAGCCGATGAGGAT	TAGGACGCAGTGAAGGGA
Maker00033581	TGATTTCGACTTTGTTACTG	TGAATCTGTCTTTGGAGC
Maker00000726	CAGATGGACGAGTTTGTG	TCCCGAGTTCCTTAGCAG
Maker00000768	ATGCTCTTCCCAACGACA	CCTGATTCCTCCCTGCTT
Maker00039481	TCGCAGCCAATCTTTCAG	ACCGCCCACGTTTGTTAT
Maker00026031	GCCTTGGTTTCCTCTGTT	TGTTCCATAGCCTTGACTG
Maker00009740	GCCCTCCGAACTACGCTCTT	TGAACCTGATTCCTCCCTGT
Maker00024997	TTTCTTCAGTTCCGTCTATT	TCTGCAACCCTTCTACCC
Maker00001372	TTTCAAGGACCTGCTAAG	ATAGTCAAGCCTCCCATA
Maker00038241	GCGATTCCGCACGCAAGA	TCCACGAAGCGACGACGAG
18sRNA	GCTTGGGTGCTCGACAAACT	TCCACAGAGCAATGTCAATGG

基因名 Gene ID	染色体 Chromosome	基因功能描述 Gene description	基因连通性在Turquoise模块的排名 Gene connectivity in turquoise module ranking
Maker00007620	2	木葡聚糖内转葡糖基酶/水解酶23 Xyloglucan endotransglucosylase/hydrolase protein 23 (XTH23)	1
Maker00033581	5	肌动蛋白解聚因子2 Actin-depolymerizing factor 2 (ADF2)	4
Maker00000726	8	伴侣蛋白DnaJ10 Chaperone protein DnaJ10 (DnaJ10)	7
Maker00026031	7	扩展蛋白A1 Expansin-A1 (EXPA1)	50
Maker00009740	7	扩展蛋白A4 Expansin-A4 (EXPA4)	155
Maker00024997	12	驱动蛋白13A Kinesin-13A (Kinesin-13A)	266
Maker00000768	8	扩展蛋白A4 Expansin-A4 (EXPA4)	351
Maker00039481	10	类扩展蛋白A5 Expansin-like-A5 (EXLA5)	373
Maker00001372	8	生长素反应蛋白SAUR21 Auxin-responsive protein SAUR21 (SAUR21)	416
Maker00038241	12	生长素反应蛋白IAA11 Auxin-responsive protein IAA11 (AUX/IAA11)	453

基于转录组和WGCNA筛选丝瓜果长和果径发育调控相关基因

Screening Regulatory Genes Related to Luffa Fruit Length and Diameter Development Based on Transcriptome and WGCNA

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