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NAC transcription factor family genes are differentially expressed in rice during infections with Rice dwarf virus, Rice black-streaked dwarf virus, Rice grassy stunt virus, Rice ragged stunt virus, and Rice transitory yellowing virus.

Nuruzzaman M, Sharoni AM, Satoh K, Karim MR, Harikrishna JA, Shimizu T, Sasaya T, Omura T, Haque MA, Hasan SM, Ahmad A, Kikuchi S - Front Plant Sci (2015)

Bottom Line: Most of the genes in the NAC subgroups NAC22, SND, ONAC2, ANAC34, and ONAC3 were down-regulated for all virus infections.These results suggested that OsNAC genes might be related to the responses induced by the virus infection.A number of putative cis-elements were identified, which may help to clarify the function of these key genes in network pathways.

View Article: PubMed Central - PubMed

Affiliation: Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences Tsukuba, Japan ; Faculty of Science, Centre for Research for Biotechnology for Agriculture, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia ; Post Harvest Technology, School of Food Science and Technology, University Malaysia Terengganu Kuala Terengganu, Malaysia ; Department of Agronomy and Agricultural Extension, Faculty of Agriculture, University of Rajshahi Rajshahi, Bangladesh.

ABSTRACT
Expression levels of the NAC gene family were studied in rice infected with Rice dwarf virus (RDV), Rice black-streaked dwarf virus (RBSDV), Rice grassy stunt virus (RGSV), Rice ragged stunt virus (RRSV), and Rice transitory yellowing virus (RTYV). Microarray analysis showed that 75 (68%) OsNAC genes were differentially regulated during infection with RDV, RBSDV, RGSV, and RRSV compared with the control. The number of OsNAC genes up-regulated was highest during RGSV infection, while the lowest number was found during RTYV infection. These phenomena correlate with the severity of the syndromes induced by the virus infections. Most of the genes in the NAC subgroups NAC22, SND, ONAC2, ANAC34, and ONAC3 were down-regulated for all virus infections. These OsNAC genes might be related to the health stage maintenance of the host plants. Interestingly, most of the genes in the subgroups TIP and SNAC were more highly expressed during RBSDV and RGSV infections. These results suggested that OsNAC genes might be related to the responses induced by the virus infection. All of the genes assigned to the TIP subgroups were highly expressed during RGSV infection when compared with the control. For RDV infection, the number of activated genes was greatest during infection with the S-strain, followed by the D84-strain and the O-strain, with seven OsNAC genes up-regulated during infection by all three strains. The Os12g03050 and Os11g05614 genes showed higher expression during infection with four of the five viruses, and Os11g03310, Os11g03370, and Os07g37920 genes showed high expression during at least three viral infections. We identified some duplicate genes that are classified as neofunctional and subfunctional according to their expression levels in different viral infections. A number of putative cis-elements were identified, which may help to clarify the function of these key genes in network pathways.

No MeSH data available.


Related in: MedlinePlus

Evaluation of the expression levels of selected DEGs by semi-quantitative RT-PCR during RDV-84 and RDV-O virus infections.
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Figure 3: Evaluation of the expression levels of selected DEGs by semi-quantitative RT-PCR during RDV-84 and RDV-O virus infections.

Mentions: To assess the accuracy of the microarray data, we selected five non-redundant genes that were differentially expressed in response to viral infection and examined the similarity between gene responses observed by microarray and by RT-PCR. Designed primers are shown in Figure 3. Rice actin gene (LOC_Os11g06390) was used for RT-PCR as an internal control, and its expression remained nearly constant under all experimental conditions (Figure 3). We observed that microarray and RT-PCR data, which were calculated based on the median of three repeated measurements, showed good correlation for RDV virus infection compared with the control; in most cases, the up-/down-regulated expression of five selected genes identified by microarray was also detected by RT-PCR (Figure 3). The oligoarray data of our lab have also been confirmed by Satoh et al. (2011, 2013). Hierarchical cluster analysis based on log2 ratio values showed that the OsNAC genes had very diverse expression profiles (red color for up and green color for down-regulation) during all virus infections (Figure S1).


NAC transcription factor family genes are differentially expressed in rice during infections with Rice dwarf virus, Rice black-streaked dwarf virus, Rice grassy stunt virus, Rice ragged stunt virus, and Rice transitory yellowing virus.

Nuruzzaman M, Sharoni AM, Satoh K, Karim MR, Harikrishna JA, Shimizu T, Sasaya T, Omura T, Haque MA, Hasan SM, Ahmad A, Kikuchi S - Front Plant Sci (2015)

Evaluation of the expression levels of selected DEGs by semi-quantitative RT-PCR during RDV-84 and RDV-O virus infections.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4563162&req=5

Figure 3: Evaluation of the expression levels of selected DEGs by semi-quantitative RT-PCR during RDV-84 and RDV-O virus infections.
Mentions: To assess the accuracy of the microarray data, we selected five non-redundant genes that were differentially expressed in response to viral infection and examined the similarity between gene responses observed by microarray and by RT-PCR. Designed primers are shown in Figure 3. Rice actin gene (LOC_Os11g06390) was used for RT-PCR as an internal control, and its expression remained nearly constant under all experimental conditions (Figure 3). We observed that microarray and RT-PCR data, which were calculated based on the median of three repeated measurements, showed good correlation for RDV virus infection compared with the control; in most cases, the up-/down-regulated expression of five selected genes identified by microarray was also detected by RT-PCR (Figure 3). The oligoarray data of our lab have also been confirmed by Satoh et al. (2011, 2013). Hierarchical cluster analysis based on log2 ratio values showed that the OsNAC genes had very diverse expression profiles (red color for up and green color for down-regulation) during all virus infections (Figure S1).

Bottom Line: Most of the genes in the NAC subgroups NAC22, SND, ONAC2, ANAC34, and ONAC3 were down-regulated for all virus infections.These results suggested that OsNAC genes might be related to the responses induced by the virus infection.A number of putative cis-elements were identified, which may help to clarify the function of these key genes in network pathways.

View Article: PubMed Central - PubMed

Affiliation: Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences Tsukuba, Japan ; Faculty of Science, Centre for Research for Biotechnology for Agriculture, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia ; Post Harvest Technology, School of Food Science and Technology, University Malaysia Terengganu Kuala Terengganu, Malaysia ; Department of Agronomy and Agricultural Extension, Faculty of Agriculture, University of Rajshahi Rajshahi, Bangladesh.

ABSTRACT
Expression levels of the NAC gene family were studied in rice infected with Rice dwarf virus (RDV), Rice black-streaked dwarf virus (RBSDV), Rice grassy stunt virus (RGSV), Rice ragged stunt virus (RRSV), and Rice transitory yellowing virus (RTYV). Microarray analysis showed that 75 (68%) OsNAC genes were differentially regulated during infection with RDV, RBSDV, RGSV, and RRSV compared with the control. The number of OsNAC genes up-regulated was highest during RGSV infection, while the lowest number was found during RTYV infection. These phenomena correlate with the severity of the syndromes induced by the virus infections. Most of the genes in the NAC subgroups NAC22, SND, ONAC2, ANAC34, and ONAC3 were down-regulated for all virus infections. These OsNAC genes might be related to the health stage maintenance of the host plants. Interestingly, most of the genes in the subgroups TIP and SNAC were more highly expressed during RBSDV and RGSV infections. These results suggested that OsNAC genes might be related to the responses induced by the virus infection. All of the genes assigned to the TIP subgroups were highly expressed during RGSV infection when compared with the control. For RDV infection, the number of activated genes was greatest during infection with the S-strain, followed by the D84-strain and the O-strain, with seven OsNAC genes up-regulated during infection by all three strains. The Os12g03050 and Os11g05614 genes showed higher expression during infection with four of the five viruses, and Os11g03310, Os11g03370, and Os07g37920 genes showed high expression during at least three viral infections. We identified some duplicate genes that are classified as neofunctional and subfunctional according to their expression levels in different viral infections. A number of putative cis-elements were identified, which may help to clarify the function of these key genes in network pathways.

No MeSH data available.


Related in: MedlinePlus