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Rice yellow mottle virus stress responsive genes from susceptible and tolerant rice genotypes.

Ventelon-Debout M, Tranchant-Dubreuil C, Nguyen TT, Bangratz M, Siré C, Delseny M, Brugidou C - BMC Plant Biol. (2008)

Bottom Line: The effects of viral infection involve concomitant plant gene variations and cellular changes.RSR transcripts on rice chromosomes 4 and 10 were found to be not randomly distributed.This combined map provides a new tool for exploring molecular mechanisms underlying the RYMV/rice interaction.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR5096, IRD 911 Avenue Agropolis, BP54501, 34394 Montpellier, France. mventelon@yahoo.fr

ABSTRACT

Background: The effects of viral infection involve concomitant plant gene variations and cellular changes. A simple system is required to assess the complexity of host responses to viral infection. The genome of the Rice yellow mottle virus (RYMV) is a single-stranded RNA with a simple organisation. It is the most well-known monocotyledon virus model. Several studies on its biology, structure and phylogeography have provided a suitable background for further genetic studies. 12 rice chromosome sequences are now available and provide strong support for genomic studies, particularly physical mapping and gene identification.

Results: The present data, obtained through the cDNA-AFLP technique, demonstrate differential responses to RYMV of two different rice cultivars, i.e. susceptible IR64 (Oryza sativa indica), and partially resistant Azucena (O. s. japonica). This RNA profiling provides a new original dataset that will enable us to gain greater insight into the RYMV/rice interaction and the specificity of the host response. Using the SIM4 subroutine, we took the intron/exon structure of the gene into account and mapped 281 RYMV stress responsive (RSR) transcripts on 12 rice chromosomes corresponding to 234 RSR genes. We also mapped previously identified deregulated proteins and genes involved in partial resistance and thus constructed the first global physical map of the RYMV/rice interaction. RSR transcripts on rice chromosomes 4 and 10 were found to be not randomly distributed. Seven genes were identified in the susceptible and partially resistant cultivars, and transcripts were colocalized for these seven genes in both cultivars. During virus infection, many concomitant plant gene expression changes may be associated with host changes caused by the infection process, general stress or defence responses. We noted that some genes (e.g. ABC transporters) were regulated throughout the kinetics of infection and differentiated susceptible and partially resistant hosts.

Conclusion: We enhanced the first RYMV/rice interaction map by combining information from the present study and previous studies on proteins and ESTs regulated during RYMV infection, thus providing a more comprehensive view on genes related to plant responses. This combined map provides a new tool for exploring molecular mechanisms underlying the RYMV/rice interaction.

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Azucena (A.) and IR64 (B.) cDNA-AFLP display from non-stressed leaves (lane 1), wounded leaves (lane 2), and RYMV inoculated leaves harvested at 3 dpi for Azucena/2 dpi for IR64 (lane 3), 5 dpi (lane 4) and 7 dpi (lane 5). This five lanes set represented amplification by one particular primer combination. Arrows represented differential bands.
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Figure 2: Azucena (A.) and IR64 (B.) cDNA-AFLP display from non-stressed leaves (lane 1), wounded leaves (lane 2), and RYMV inoculated leaves harvested at 3 dpi for Azucena/2 dpi for IR64 (lane 3), 5 dpi (lane 4) and 7 dpi (lane 5). This five lanes set represented amplification by one particular primer combination. Arrows represented differential bands.

Mentions: We analyzed the transcript profiling using the cDNA-AFLP technique on two different rice cultivars: IR64 (O. s. indica) highly susceptible to the RYMV, and Azucena (O. s. japonica) tolerant to the RYMV. We looked at different time points after infection: 2, 5, 7 days post inoculation (dpi) for IR64 and 3, 5, 7 dpi for Azucena. The kinetics gave a similar pattern of virus content in infected leaves of both cultivars (Figure 1). Non infected IR64 and Azucena leaves were used as control at the first point of the kinetic for the both cultivars, and IR64 and Azucena wounded leaves without RYMV were harvested at the first point of the kinetic for internal control since the virus infection was mechanically done. A section of a typical AFLP gel is shown on Figure 2. Changing patterns of gene expression were revealed using more than 20 000 cDNA fragments from both IR64 and Azucena cultivars. The resulting AFLP products ranged in length from 40 base pairs (bp) to 500 bp, and 60 to 100 bands were observed for each of the 256 primer combinations on the gel. Only bands with a present-absent pattern were considered. The cDNA-AFLP screen identified 353 cDNA fragments corresponding to differentially accumulated transcripts during the first week of RYMV infection for Azucena, and 232 cDNA fragments for IR64. One hundred sixty two (46%) of the AFLP-cDNA fragments corresponded to up-regulated transcripts and 78 (22%) to down-regulated transcripts for Azucena, and 74 (21%) to wound-regulated and RYMV-regulated transcripts (transcripts with a variation of accumulation observed in wounded leaves and an opposite variation observed in infected leaves). On the contrary, 88 (38%) of cDNA fragments corresponded to up-regulated transcripts for IR64, 91 (39%) to down-regulated transcripts, and only 23 (10%) to wound-regulated and RYMV-regulated transcripts (Figure 3).


Rice yellow mottle virus stress responsive genes from susceptible and tolerant rice genotypes.

Ventelon-Debout M, Tranchant-Dubreuil C, Nguyen TT, Bangratz M, Siré C, Delseny M, Brugidou C - BMC Plant Biol. (2008)

Azucena (A.) and IR64 (B.) cDNA-AFLP display from non-stressed leaves (lane 1), wounded leaves (lane 2), and RYMV inoculated leaves harvested at 3 dpi for Azucena/2 dpi for IR64 (lane 3), 5 dpi (lane 4) and 7 dpi (lane 5). This five lanes set represented amplification by one particular primer combination. Arrows represented differential bands.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2275266&req=5

Figure 2: Azucena (A.) and IR64 (B.) cDNA-AFLP display from non-stressed leaves (lane 1), wounded leaves (lane 2), and RYMV inoculated leaves harvested at 3 dpi for Azucena/2 dpi for IR64 (lane 3), 5 dpi (lane 4) and 7 dpi (lane 5). This five lanes set represented amplification by one particular primer combination. Arrows represented differential bands.
Mentions: We analyzed the transcript profiling using the cDNA-AFLP technique on two different rice cultivars: IR64 (O. s. indica) highly susceptible to the RYMV, and Azucena (O. s. japonica) tolerant to the RYMV. We looked at different time points after infection: 2, 5, 7 days post inoculation (dpi) for IR64 and 3, 5, 7 dpi for Azucena. The kinetics gave a similar pattern of virus content in infected leaves of both cultivars (Figure 1). Non infected IR64 and Azucena leaves were used as control at the first point of the kinetic for the both cultivars, and IR64 and Azucena wounded leaves without RYMV were harvested at the first point of the kinetic for internal control since the virus infection was mechanically done. A section of a typical AFLP gel is shown on Figure 2. Changing patterns of gene expression were revealed using more than 20 000 cDNA fragments from both IR64 and Azucena cultivars. The resulting AFLP products ranged in length from 40 base pairs (bp) to 500 bp, and 60 to 100 bands were observed for each of the 256 primer combinations on the gel. Only bands with a present-absent pattern were considered. The cDNA-AFLP screen identified 353 cDNA fragments corresponding to differentially accumulated transcripts during the first week of RYMV infection for Azucena, and 232 cDNA fragments for IR64. One hundred sixty two (46%) of the AFLP-cDNA fragments corresponded to up-regulated transcripts and 78 (22%) to down-regulated transcripts for Azucena, and 74 (21%) to wound-regulated and RYMV-regulated transcripts (transcripts with a variation of accumulation observed in wounded leaves and an opposite variation observed in infected leaves). On the contrary, 88 (38%) of cDNA fragments corresponded to up-regulated transcripts for IR64, 91 (39%) to down-regulated transcripts, and only 23 (10%) to wound-regulated and RYMV-regulated transcripts (Figure 3).

Bottom Line: The effects of viral infection involve concomitant plant gene variations and cellular changes.RSR transcripts on rice chromosomes 4 and 10 were found to be not randomly distributed.This combined map provides a new tool for exploring molecular mechanisms underlying the RYMV/rice interaction.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR5096, IRD 911 Avenue Agropolis, BP54501, 34394 Montpellier, France. mventelon@yahoo.fr

ABSTRACT

Background: The effects of viral infection involve concomitant plant gene variations and cellular changes. A simple system is required to assess the complexity of host responses to viral infection. The genome of the Rice yellow mottle virus (RYMV) is a single-stranded RNA with a simple organisation. It is the most well-known monocotyledon virus model. Several studies on its biology, structure and phylogeography have provided a suitable background for further genetic studies. 12 rice chromosome sequences are now available and provide strong support for genomic studies, particularly physical mapping and gene identification.

Results: The present data, obtained through the cDNA-AFLP technique, demonstrate differential responses to RYMV of two different rice cultivars, i.e. susceptible IR64 (Oryza sativa indica), and partially resistant Azucena (O. s. japonica). This RNA profiling provides a new original dataset that will enable us to gain greater insight into the RYMV/rice interaction and the specificity of the host response. Using the SIM4 subroutine, we took the intron/exon structure of the gene into account and mapped 281 RYMV stress responsive (RSR) transcripts on 12 rice chromosomes corresponding to 234 RSR genes. We also mapped previously identified deregulated proteins and genes involved in partial resistance and thus constructed the first global physical map of the RYMV/rice interaction. RSR transcripts on rice chromosomes 4 and 10 were found to be not randomly distributed. Seven genes were identified in the susceptible and partially resistant cultivars, and transcripts were colocalized for these seven genes in both cultivars. During virus infection, many concomitant plant gene expression changes may be associated with host changes caused by the infection process, general stress or defence responses. We noted that some genes (e.g. ABC transporters) were regulated throughout the kinetics of infection and differentiated susceptible and partially resistant hosts.

Conclusion: We enhanced the first RYMV/rice interaction map by combining information from the present study and previous studies on proteins and ESTs regulated during RYMV infection, thus providing a more comprehensive view on genes related to plant responses. This combined map provides a new tool for exploring molecular mechanisms underlying the RYMV/rice interaction.

Show MeSH
Related in: MedlinePlus