Plant Pathology Department


Date of this Version



Rice (2010) 3:22–35 DOI 10.1007/s12284-010-9037-8


Copyright 2019 Springer Science+Business Media, LLC. Open Access licensed.


The beet armyworm (Spodoptera exigua) and the rice water weevil (Lissorhoptrus oryzophilus) are two important insect pests in rice production. To identify insect-responsive genes in rice, we performed a deep transcriptome analysis of Nipponbare rice leaves infested with both beet armyworm and water weevil using massively parallel signature sequencing (MPSS). Many antisense, alternative, and novel transcripts were commonly and specifically induced and suppressed in the infested tissue. Key genes involved in the defense metabolic pathways such as salicylic acid and jasmonic acid biosynthesis pathways were up-regulated in the infested leaves. To validate theMPSS results, we analyzed the transcriptome of the rice leaves infested with water weevils using Solexa’s sequencing-bysynthesis (SBS) method. The MPSS and SBS data were highly correlated (Pearson’s correlation coefficient=0.85), and 83% of genes had similar gene expression in both libraries. Our comprehensive and in-depth survey of the insect-infested libraries provides a rich genomic resource for further analyzing the function of key regulatory genes involved in insect resistance in rice.

Supplementary files are attached below.

Boehm RICE 2010 Deep and Comparative Transcriptome--SUPPL01.ppt (559 kB)
Supplemental Fig. 1 (PPT 559 kb)

Boehm RICE 2010 Deep and Comparative Transcriptome--SUPPL02.xls (31 kB)
Supplemental Table S1--List of Selected Genes for Validation Through RT-PCR Primers (XLS 31 kb)

Boehm RICE 2010 Deep and Comparative Transcriptome--SUPPL03.doc (55 kB)
Supplemental Table S2 (DOC 55 kb)

Boehm RICE 2010 Deep and Comparative Transcriptome--SUPPL04.xls (3339 kB)
Supplemental Table S3--Antisense Novel Genes and Transcripts Alternate Transcripts (XLS 3339 kb)

Boehm RICE 2010 Deep and Comparative Transcriptome--SUPPL05.xls (286 kB)
Supplemental Table S4--TFs and Cis Elements (XLS 286 kb)

Boehm RICE 2010 Deep and Comparative Transcriptome--SUPPL06.xls (1238 kB)
Supplemental Table S5 (XLS 1,238 kb)

Boehm RICE 2010 Deep and Comparative Transcriptome--SUPPL07.xls (3737 kB)
Supplemental Table S6--Final MPSS vs SBS Correlation Analysis (XLS 3737 kb)