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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

Number of differentially expressed genes (DEGs) in rice seedlings (A) infected with RDV (3-strain) (B) infected with RBSDV, RGSV, RRSV, and RTYV respectively. Y-axis represents the number of DEGs and different viruses are indicated on the X-axis. (C) Common or specific up- or down-regulated genes are mentioned among all the virus infections. Red color indicated the common up-regulated genes and blue color indicated the common down-regulated genes. These genes are specific up- or -down regulated to following virus infection: RDV-84, 01g64310, 03g21030, and 04g35660; RDV-O, 10g38834 and 11g45950; RDV-S, 06g04090 and 01g09550; RBSDV, 01g09550 and 01g59640; RGSV, 08g44820, 07g48550, 06g46270, 03g03540, 08g33910, 03g60080, 07g12340, 11g08210, 08g42400, 02g34970, 01g01470, 10g25620, and 07g31410; RRSV, 12g43530, 07g17180, and 11g31360; RTYV, 07g27330. Elaborations of virus infection are in Table 1.
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Figure 2: Number of differentially expressed genes (DEGs) in rice seedlings (A) infected with RDV (3-strain) (B) infected with RBSDV, RGSV, RRSV, and RTYV respectively. Y-axis represents the number of DEGs and different viruses are indicated on the X-axis. (C) Common or specific up- or down-regulated genes are mentioned among all the virus infections. Red color indicated the common up-regulated genes and blue color indicated the common down-regulated genes. These genes are specific up- or -down regulated to following virus infection: RDV-84, 01g64310, 03g21030, and 04g35660; RDV-O, 10g38834 and 11g45950; RDV-S, 06g04090 and 01g09550; RBSDV, 01g09550 and 01g59640; RGSV, 08g44820, 07g48550, 06g46270, 03g03540, 08g33910, 03g60080, 07g12340, 11g08210, 08g42400, 02g34970, 01g01470, 10g25620, and 07g31410; RRSV, 12g43530, 07g17180, and 11g31360; RTYV, 07g27330. Elaborations of virus infection are in Table 1.

Mentions: To gain insight into the comprehensive roles of the OsNAC gene family members in response to various infections caused by viruses (RDV, RBSDV, RGSV, RRSV, and RTYV), their expression patterns were investigated in infected rice seedlings “(Oryza sativa L. ssp. Japonica cv. “Nipponbare”) by microarray analysis (Figure 2). Any selection based solely on fold change is arbitrary and there is no right nor wrong threshold. We compared the DEGs between 1.5 and 2 cutoff value under all virus infections and there is no gene up-regulated under RTYV infection (Table S1). We found small number of NAC genes in our array data, so we pick the threshold we feel is best for our experiment. We showed the data analysis and P-value of RDV-O and RTYV infections (for an example) in the Table S2. Only the genes whose expression change was at least 1.5-fold (increased or decreased) were considered to have responded to the above infections. Out of 151 NAC genes, we identified 112 OsNAC genes in our 44K array data. Among these genes, 75 were differentially expressed (up- or down-regulated) in at least one of the five virus infections (Figure 2; Table 1). The number of DEGs was different among plants infected with three RDV strains. The number of DEGs during infections with RDV-D84, RDV-O, and RDV-S was 24, 16, and 25, respectively (Figure 2). The number of genes up-regulated (33) was highest at 28 dpi during RGSV infection, followed by 21 and 24 dpi (listed in decreasing order) during RBSDV, RDV, RRSV, and RTYV infections (Figure 2). During infection with RDV, RBSDV, RGSV, and RRSV, there were higher numbers of up-regulated than down-regulated OsNAC genes. These up-regulated genes might be associated with the severity of the syndromes induced by the virus infections. However, in the case of RTYV infection, a higher number of OsNAC genes were down-regulated compared with the number up-regulated (Figure 2). Moreover, most of the genes in the NAC subgroups NAC22, SND, ONAC2, ANAC34, and ONAC3 were down-regulated on all days tested, during all virus infections (Table 1). These results indicated that 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 under RBSDV and RGSV infections.


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)

Number of differentially expressed genes (DEGs) in rice seedlings (A) infected with RDV (3-strain) (B) infected with RBSDV, RGSV, RRSV, and RTYV respectively. Y-axis represents the number of DEGs and different viruses are indicated on the X-axis. (C) Common or specific up- or down-regulated genes are mentioned among all the virus infections. Red color indicated the common up-regulated genes and blue color indicated the common down-regulated genes. These genes are specific up- or -down regulated to following virus infection: RDV-84, 01g64310, 03g21030, and 04g35660; RDV-O, 10g38834 and 11g45950; RDV-S, 06g04090 and 01g09550; RBSDV, 01g09550 and 01g59640; RGSV, 08g44820, 07g48550, 06g46270, 03g03540, 08g33910, 03g60080, 07g12340, 11g08210, 08g42400, 02g34970, 01g01470, 10g25620, and 07g31410; RRSV, 12g43530, 07g17180, and 11g31360; RTYV, 07g27330. Elaborations of virus infection are in Table 1.
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Figure 2: Number of differentially expressed genes (DEGs) in rice seedlings (A) infected with RDV (3-strain) (B) infected with RBSDV, RGSV, RRSV, and RTYV respectively. Y-axis represents the number of DEGs and different viruses are indicated on the X-axis. (C) Common or specific up- or down-regulated genes are mentioned among all the virus infections. Red color indicated the common up-regulated genes and blue color indicated the common down-regulated genes. These genes are specific up- or -down regulated to following virus infection: RDV-84, 01g64310, 03g21030, and 04g35660; RDV-O, 10g38834 and 11g45950; RDV-S, 06g04090 and 01g09550; RBSDV, 01g09550 and 01g59640; RGSV, 08g44820, 07g48550, 06g46270, 03g03540, 08g33910, 03g60080, 07g12340, 11g08210, 08g42400, 02g34970, 01g01470, 10g25620, and 07g31410; RRSV, 12g43530, 07g17180, and 11g31360; RTYV, 07g27330. Elaborations of virus infection are in Table 1.
Mentions: To gain insight into the comprehensive roles of the OsNAC gene family members in response to various infections caused by viruses (RDV, RBSDV, RGSV, RRSV, and RTYV), their expression patterns were investigated in infected rice seedlings “(Oryza sativa L. ssp. Japonica cv. “Nipponbare”) by microarray analysis (Figure 2). Any selection based solely on fold change is arbitrary and there is no right nor wrong threshold. We compared the DEGs between 1.5 and 2 cutoff value under all virus infections and there is no gene up-regulated under RTYV infection (Table S1). We found small number of NAC genes in our array data, so we pick the threshold we feel is best for our experiment. We showed the data analysis and P-value of RDV-O and RTYV infections (for an example) in the Table S2. Only the genes whose expression change was at least 1.5-fold (increased or decreased) were considered to have responded to the above infections. Out of 151 NAC genes, we identified 112 OsNAC genes in our 44K array data. Among these genes, 75 were differentially expressed (up- or down-regulated) in at least one of the five virus infections (Figure 2; Table 1). The number of DEGs was different among plants infected with three RDV strains. The number of DEGs during infections with RDV-D84, RDV-O, and RDV-S was 24, 16, and 25, respectively (Figure 2). The number of genes up-regulated (33) was highest at 28 dpi during RGSV infection, followed by 21 and 24 dpi (listed in decreasing order) during RBSDV, RDV, RRSV, and RTYV infections (Figure 2). During infection with RDV, RBSDV, RGSV, and RRSV, there were higher numbers of up-regulated than down-regulated OsNAC genes. These up-regulated genes might be associated with the severity of the syndromes induced by the virus infections. However, in the case of RTYV infection, a higher number of OsNAC genes were down-regulated compared with the number up-regulated (Figure 2). Moreover, most of the genes in the NAC subgroups NAC22, SND, ONAC2, ANAC34, and ONAC3 were down-regulated on all days tested, during all virus infections (Table 1). These results indicated that 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 under RBSDV and RGSV infections.

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