Expression analysis of rooting-related genes between different clones of Eucalyptus urophylla in tissue culture

doi:10.12302/j.issn.1000-2006.202108006

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2023, Vol. 47 ›› Issue (4): 114-122.doi: 10.12302/j.issn.1000-2006.202108006

Expression analysis of rooting-related genes between different clones of Eucalyptus urophylla in tissue culture

LIAO Huanqin(), YANG Huixiao, XU Fang, PAN Wen, ZHANG Weihua, CHEN Xinyu, ZHU Baozhu, XU Bin, WANG Yuxia, YANG Xiaohui()

Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization,Guangdong Academy of Forestry, Guangdong 510520, China

Received:2021-08-04 Revised:2021-12-16 Online:2023-07-30 Published:2023-07-20

Abstract

Abstract:

【Objective】This study was designed to examine differences in gene expression between Eucalyptus urophylla clones cultivated on the same medium and at different growth periods in order to provide genetic information for the analyses of differences in root development.【Method】 We used two E. urophylla clones grown in the same rooting medium with contrasting differences in rooting initiation but with the same generation of subcultures. We performed transcriptome sequencing analysis using 2 mm length stem tissue from the base of each clone on 0, 1, 4 and 6 d when apparent morphological differences occurred in clone base following fast rooting initiation. We further identified the differentially expressed genes (DEGs) that caused rooting differences between clones using gene differential expression analysis, cluster analysis, GO analysis and KEGG analysis.【Result】A total of 20 287 DEGs were obtained, which were significantly grouped into four subclusters. Among them, the number of DEGs with an increasing expression pattern in fast rooting initiation clone was much higher than that in slow rooting initiation clone, and the number of DEGs with less expression change between 1 and 0 d in slow rooting initiation clone were much higher than those in fast rooting initiation clone. After being transferred to IBA medium, the GO analysis showed that DEGs of subcluster 17 were significantly enriched in cell cycle-related pathways in the fast rooting initiation clone, while significantly enriched in the stress resistance-related pathways in the slow rooting initiation clone. The KEGG analysis showed that DEGs in the slow rooting initiation clone were enriched in more biological pathways, while DEGs involved in ribosome were only significantly enriched in the fast rooting initiation clone. DEGs involved in glycolysis, gluconeogenesis, secondary metabolites biosynthesis and oxidative phosphorylation were significantly enriched in the slow rooting initiation clone. A total of 202 DEGs were significantly enriched in the plant hormone signal transduction pathway. There were significant differences between the two clones on the expression levels of DEGs encoding AUX/IAA in the auxin signal transduction pathway, DEGs encoding CRE1 in the cytokinin signal transduction pathway and transcription factor in the gibberellin signal transduction pathway.【Conclusion】The two clones of E. urophylla differ in gene expression during root development after they were transferred to the rooting medium. Expression of the same DEGs varies between the slow rooting initiation clone and the fast rooting initiation clone, resulting in functional variations between the clones including the production of auxin, gibberellin and cytokinin.

Key words: Eucalyptus urophylla, tissue culture, rooting, transcriptome sequencing analysis, KEGG analysis

CLC Number:

S718.46

LIAO Huanqin, YANG Huixiao, XU Fang, PAN Wen, ZHANG Weihua, CHEN Xinyu, ZHU Baozhu, XU Bin, WANG Yuxia, YANG Xiaohui. Expression analysis of rooting-related genes between different clones of Eucalyptus urophylla in tissue culture[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2023, 47(4): 114-122.

Figures/Tables 7

Table 1

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基因gene	引物序列primer sequence
LOC104442334	F:5'-ATGACGATTACGGCTACAC-3'
	R:5'-AAGACGACGCTGAACAAG-3'
LOC104432357	F:5'-TCCTTGTGCCTATGATGATG-3'
	R:5'-CCAGTCTCGTTCTCGTATG-3'
LOC104433019	F:5'-TCAGGAGAGGAGGACAGA-3'
	R:5'-GATAAGTGGTTCGGAAGAGT-3'
LOC104438220	F:5'-TGTCAGATAATCGCTTCCAA-3'
	R:5'-TTCAATCCGCATCAGTTCA-3'
18srRNA	F:5'-ACACGGGGAGGTAGTGACAA-3'
	R:5'-CCTCCAATGGATCCTCGTTA-3'

比较组别 compared libraries	上调DEGs数 up-regulated DEGs	下调DEGs数 down-regulated DEGs	总DEGs total DEGs
D0 vs D1	3 666	3 430	7 096
D0 vs D4	4 300	3 131	7 431
D0 vs D6	4 334	2 842	7 176
E0 vs E1	3 384	2 631	6 015
E0 vs E4	4 015	2 154	6 169
E0 vs E6	4 470	2 535	7 005
D0 vs E0	4 186	4 113	8 299
D1 vs E1	4 509	4 082	8 591
D4 vs E4	4 114	3 774	7 888
D6 vs E6	4 003	3 892	7 895

Expression analysis of rooting-related genes between different clones of Eucalyptus urophylla in tissue culture

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