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Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background.

Zhang F, Huang L, Wang W, Zhao X, Zhu L, Fu B, Li Z - BMC Genomics (2012)

Bottom Line: K354-specific cold-induced genes were functionally related to stimulus response, cellular cell wall organization, and microtubule-based movement processes that may contribute to increase CT.A set of genes encoding membrane fluidity and defensive proteins were highly enriched only in K354, suggesting that they contribute to the inherent CT of K354.In K354, a number of DEGs were co-localized onto introgressed segments associated with CT QTLs, providing a basis for gene cloning and elucidation of molecular mechanisms responsible for CT in rice.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage, resulting in poor growth and yield loss. Although japonica rice is generally more cold tolerant (CT) than indica rice, there are several favorable alleles for CT exist in indica that can be used to enhance CT in rice with a japonica background. Genome-wide gene expression profiling is an efficient way to decipher the molecular genetic mechanisms of CT enhancement and to provide valuable information for CT improvement in rice molecular breeding. In this study, the transcriptome of the CT introgression line (IL) K354 and its recurrent parent C418 under cold stress were comparatively analyzed to explore the possible CT enhancement mechanisms of K354.

Results: A total of 3184 differentially expressed genes (DEGs), including 195 transcription factors, were identified in both lines under cold stress. About half of these DEGs were commonly regulated and involved in major cold responsive pathways associated with OsDREB1 and OsMyb4 regulons. K354-specific cold-induced genes were functionally related to stimulus response, cellular cell wall organization, and microtubule-based movement processes that may contribute to increase CT. A set of genes encoding membrane fluidity and defensive proteins were highly enriched only in K354, suggesting that they contribute to the inherent CT of K354. Candidate gene prediction based on introgressed regions in K354 revealed genotype-dependent CT enhancement mechanisms, associated with Sir2, OsFAD7, OsWAK112d, and programmed cell death (PCD) related genes, present in CT IL K354 but absent in its recurrent parent C418. In K354, a number of DEGs were co-localized onto introgressed segments associated with CT QTLs, providing a basis for gene cloning and elucidation of molecular mechanisms responsible for CT in rice.

Conclusions: Genome-wide gene expression analysis revealed that genotype-specific cold induced genes and genes with higher basal expression in the CT genotype contribute jointly to CT improvement. The molecular genetic pathways of cold stress tolerance uncovered in this study, as well as the DEGs co-localized with CT-related QTLs, will serve as useful resources for further functional dissection of the molecular mechanisms of cold stress response in rice.

No MeSH data available.


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Expression patterns of OsDREB1 and OsDREB1 regulon cold-responsive DEGs in K354 and C418. Gene expression values during control conditions to 48 h after cold stress were log-transformed and median-normalized. (A) OsDREB1 regulon; (B) OsDREB1C-specific regulon. Black, green, blue and red lines indicate the OsDREB1 regulon, OsDREB1A, OsDREB1B, and OsDREB1C, respectively.
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Figure 4: Expression patterns of OsDREB1 and OsDREB1 regulon cold-responsive DEGs in K354 and C418. Gene expression values during control conditions to 48 h after cold stress were log-transformed and median-normalized. (A) OsDREB1 regulon; (B) OsDREB1C-specific regulon. Black, green, blue and red lines indicate the OsDREB1 regulon, OsDREB1A, OsDREB1B, and OsDREB1C, respectively.

Mentions: The OsDREB1 regulon has been shown to play an important role in conferring cold stress response in rice [28]. OsDREB1s belong to a sub-family of AP2/EREBP proteins unique to plants and sharing a highly conserved AP2 domain. To identify commonly cold-induced genes within the OsDREB1 regulon, we examined cis-regulatory elements in the 1-kb upstream regions of 991 commonly induced genes in both genotypes using the DRE core motif A/GCCGAC [29]. Of these genes, 298 (30.1%) contained at least one DRE core motif in the 1-kb upstream region (Additional file 15). As shown in Figure 4A, expression patterns of the OsDREB1 regulon (298 genes in Additional file 15) were roughly consistent with that of three OsDREB1 genes (OsDREB1A, OsDREB1B, and OsDREB1C). Of these 298 genes, 108 had been previously shown to be co-expressed with OsDREB1 in other rice microarray experiments using a positive correlation coefficient of 0.9 as the cutoff on the TIGR website [30] (Additional file 15). OsDREB1A and OsDREB1B were induced by cold with a similar expression pattern but OsDREB1C was expressed differentially during phase I (2–6 h) between the two genotypes (Figure 4). Interestingly, analysis of gene expression profiles revealed the existence of an OsDREB1C-specific regulon, which included 22 genes exclusively regulated by OsDREB1C, (Figure 4B and Table 4) accounting for the main difference in the OsDREB1 regulon between two genotypes. These results indicate that the DREB1 regulon plays an important role in cold stress response in both genotypes, even though there are a few genes, such as the OsDREB1C regulon, whose regulation is unique to genotype-specific pathways.


Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background.

Zhang F, Huang L, Wang W, Zhao X, Zhu L, Fu B, Li Z - BMC Genomics (2012)

Expression patterns of OsDREB1 and OsDREB1 regulon cold-responsive DEGs in K354 and C418. Gene expression values during control conditions to 48 h after cold stress were log-transformed and median-normalized. (A) OsDREB1 regulon; (B) OsDREB1C-specific regulon. Black, green, blue and red lines indicate the OsDREB1 regulon, OsDREB1A, OsDREB1B, and OsDREB1C, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3526417&req=5

Figure 4: Expression patterns of OsDREB1 and OsDREB1 regulon cold-responsive DEGs in K354 and C418. Gene expression values during control conditions to 48 h after cold stress were log-transformed and median-normalized. (A) OsDREB1 regulon; (B) OsDREB1C-specific regulon. Black, green, blue and red lines indicate the OsDREB1 regulon, OsDREB1A, OsDREB1B, and OsDREB1C, respectively.
Mentions: The OsDREB1 regulon has been shown to play an important role in conferring cold stress response in rice [28]. OsDREB1s belong to a sub-family of AP2/EREBP proteins unique to plants and sharing a highly conserved AP2 domain. To identify commonly cold-induced genes within the OsDREB1 regulon, we examined cis-regulatory elements in the 1-kb upstream regions of 991 commonly induced genes in both genotypes using the DRE core motif A/GCCGAC [29]. Of these genes, 298 (30.1%) contained at least one DRE core motif in the 1-kb upstream region (Additional file 15). As shown in Figure 4A, expression patterns of the OsDREB1 regulon (298 genes in Additional file 15) were roughly consistent with that of three OsDREB1 genes (OsDREB1A, OsDREB1B, and OsDREB1C). Of these 298 genes, 108 had been previously shown to be co-expressed with OsDREB1 in other rice microarray experiments using a positive correlation coefficient of 0.9 as the cutoff on the TIGR website [30] (Additional file 15). OsDREB1A and OsDREB1B were induced by cold with a similar expression pattern but OsDREB1C was expressed differentially during phase I (2–6 h) between the two genotypes (Figure 4). Interestingly, analysis of gene expression profiles revealed the existence of an OsDREB1C-specific regulon, which included 22 genes exclusively regulated by OsDREB1C, (Figure 4B and Table 4) accounting for the main difference in the OsDREB1 regulon between two genotypes. These results indicate that the DREB1 regulon plays an important role in cold stress response in both genotypes, even though there are a few genes, such as the OsDREB1C regulon, whose regulation is unique to genotype-specific pathways.

Bottom Line: K354-specific cold-induced genes were functionally related to stimulus response, cellular cell wall organization, and microtubule-based movement processes that may contribute to increase CT.A set of genes encoding membrane fluidity and defensive proteins were highly enriched only in K354, suggesting that they contribute to the inherent CT of K354.In K354, a number of DEGs were co-localized onto introgressed segments associated with CT QTLs, providing a basis for gene cloning and elucidation of molecular mechanisms responsible for CT in rice.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage, resulting in poor growth and yield loss. Although japonica rice is generally more cold tolerant (CT) than indica rice, there are several favorable alleles for CT exist in indica that can be used to enhance CT in rice with a japonica background. Genome-wide gene expression profiling is an efficient way to decipher the molecular genetic mechanisms of CT enhancement and to provide valuable information for CT improvement in rice molecular breeding. In this study, the transcriptome of the CT introgression line (IL) K354 and its recurrent parent C418 under cold stress were comparatively analyzed to explore the possible CT enhancement mechanisms of K354.

Results: A total of 3184 differentially expressed genes (DEGs), including 195 transcription factors, were identified in both lines under cold stress. About half of these DEGs were commonly regulated and involved in major cold responsive pathways associated with OsDREB1 and OsMyb4 regulons. K354-specific cold-induced genes were functionally related to stimulus response, cellular cell wall organization, and microtubule-based movement processes that may contribute to increase CT. A set of genes encoding membrane fluidity and defensive proteins were highly enriched only in K354, suggesting that they contribute to the inherent CT of K354. Candidate gene prediction based on introgressed regions in K354 revealed genotype-dependent CT enhancement mechanisms, associated with Sir2, OsFAD7, OsWAK112d, and programmed cell death (PCD) related genes, present in CT IL K354 but absent in its recurrent parent C418. In K354, a number of DEGs were co-localized onto introgressed segments associated with CT QTLs, providing a basis for gene cloning and elucidation of molecular mechanisms responsible for CT in rice.

Conclusions: Genome-wide gene expression analysis revealed that genotype-specific cold induced genes and genes with higher basal expression in the CT genotype contribute jointly to CT improvement. The molecular genetic pathways of cold stress tolerance uncovered in this study, as well as the DEGs co-localized with CT-related QTLs, will serve as useful resources for further functional dissection of the molecular mechanisms of cold stress response in rice.

No MeSH data available.


Related in: MedlinePlus