Identification and Expression Analysis of miRNA Related to Bacterial Wilt Resistance in Tomato

doi:10.13560/j.cnki.biotech.bull.1985.2022-1241

Abstract

Abstract:

To elucidate the regulatory relationship of miRNA-targets in the bacterial wilt response of tomato（Solanum lycopersicum）, sRNA sequencing was performed in resistant and susceptible tomato inbred lines with Ralstonia solanacearum vs mock inoculation. In all, 112.76 M high-quality reads were generated in eight libraries. A total of 336 miRNA including 193 novel miRNAs were identified. Among them, 31 differentially expressed miRNAs targeted the regulatory expressions of 575 genes. In total, 556 target genes were annotated in metabolic pathways such as defense response, plant-pathogen interaction, and plant hormone signal transduction. In addition to typical TATA-box and CAAT-box with the transcriptional initiation role, as well as W-box and TC-rich repeats related to biotic stress, there were also hormone, light, abiotic stress, wound and other response elements in the promoters. RT-qPCR confirmed that six pairs of miRNA-targets had three bacterial wilt response patterns in tomato, i.e., positive-negative, negative-positive and negative-negative. These results preliminarily revealed the miRNAs may respond to the bacterial wilt disease by target gene expression in tomato.

Key words: tomato, Ralstonia solanacearum, miRNA, target gene, expression regulation

SHI Jian-lei, ZAI Wen-shan, SU Shi-wen, FU Cun-nian, XIONG Zi-li. Identification and Expression Analysis of miRNA Related to Bacterial Wilt Resistance in Tomato[J]. Biotechnology Bulletin, 2023, 39(5): 233-242.

Figures/Tables 9

References 34

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基因 Gene	序列 Sequence（5'-3'）	引物 Primer（5'-3'）
SlU6	GTCCCTTCGGGGACATCCGATAAAATTGGAACGATACAGAGAAGATTAGCATGGCCCCTGCGCAAGGATGACACGCACAAATCGAGAAATGGTCCAAAATTTT	F: GGGACATCCGATAAAATTGG R: TTGGACCATTTCTCGATTTGT
novel_miR_13	GGCGGAUGUAGCCAAGUGGA	RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGTCCACTT F: ACACTCCAGCTGGGGGCGGATGTAGCC
sly-miR172c	AGAATCTTGATGATGCTGCAG	RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTGCAGC F: ACACTCCAGCTGGGAGAATCTTGATGAT
sly-miR172d	GGAATCTTGATGATGCTGCAG	RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTGCAGC F: ACACTCCAGCTGGGGGAATCTTGATGAT
sly-miR396a-5p	TTCCACAGCTTTCTTGAACTG	RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCAGTTCAA F: ACACTCCAGCTGGGTTCCACAGCTTTC
		All R: TGGTGTCGTGGAGTCG

基因 Gene	序列 Sequence（5'-3'）	引物 Primer（5'-3'）
SlU6	GTCCCTTCGGGGACATCCGATAAAATTGGAACGATACAGAGAAGATTAGCATGGCCCCTGCGCAAGGATGACACGCACAAATCGAGAAATGGTCCAAAATTTT	F: GGGACATCCGATAAAATTGG R: TTGGACCATTTCTCGATTTGT
novel_miR_13	GGCGGAUGUAGCCAAGUGGA	RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGTCCACTT F: ACACTCCAGCTGGGGGCGGATGTAGCC
sly-miR172c	AGAATCTTGATGATGCTGCAG	RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTGCAGC F: ACACTCCAGCTGGGAGAATCTTGATGAT
sly-miR172d	GGAATCTTGATGATGCTGCAG	RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTGCAGC F: ACACTCCAGCTGGGGGAATCTTGATGAT
sly-miR396a-5p	TTCCACAGCTTTCTTGAACTG	RT: CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCAGTTCAA F: ACACTCCAGCTGGGTTCCACAGCTTTC
		All R: TGGTGTCGTGGAGTCG

样本Library	净读数Clean reads/M	净碱基数Clean bases/Gb	GC含量GC content/%	Q30/%	无注释Unannotated	比对读数Mapped reads
RC02	14.31	0.32	41.86	95.26	10.81	7.08
RC14	16.69	0.38	42.34	95.26	11.86	7.68
RT06	12.93	0.30	42.68	95.61	8.85	5.72
RT18	10.84	0.24	41.95	95.57	7.92	5.11
SC04	14.57	0.33	42.10	95.68	10.22	7.31
SC16	16.54	0.37	43.15	95.75	10.79	7.77
ST08	11.32	0.26	42.76	95.55	7.68	5.14
ST20	15.56	0.35	41.62	95.77	11.52	7.75

样本Library	净读数Clean reads/M	净碱基数Clean bases/Gb	GC含量GC content/%	Q30/%	无注释Unannotated	比对读数Mapped reads
RC02	14.31	0.32	41.86	95.26	10.81	7.08
RC14	16.69	0.38	42.34	95.26	11.86	7.68
RT06	12.93	0.30	42.68	95.61	8.85	5.72
RT18	10.84	0.24	41.95	95.57	7.92	5.11
SC04	14.57	0.33	42.10	95.68	10.22	7.31
SC16	16.54	0.37	43.15	95.75	10.79	7.77
ST08	11.32	0.26	42.76	95.55	7.68	5.14
ST20	15.56	0.35	41.62	95.77	11.52	7.75

样本 Library	已知miRNA Known miRNA	新miRNA Novel miRNA	总数 Total	新miRNA百分率 Novel miRNA percentage/%
RC02	134	193	327	59.02
RC14	138	193	331	58.31
RT06	136	192	328	58.54
RT18	132	190	322	59.01
SC04	137	193	330	58.48
SC16	136	193	329	58.66
ST08	134	193	327	59.02
ST20	136	193	329	58.66
Total	143	193	336	57.44