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

Abstract

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

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

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

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