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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.


Related in: MedlinePlus

Functional classification of all 2562 cold-responsive DEGs detected in C418 and K354. (A) Biological processes; (B) cellular components; (C) molecular functions; (D) Venn diagram showing the overlap among the three categories. Bars show numbers of cold-induced genes in the two genotypes. Only significantly overrepresented GO slim categories are shown (P ≤ 0.05).
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Figure 1: Functional classification of all 2562 cold-responsive DEGs detected in C418 and K354. (A) Biological processes; (B) cellular components; (C) molecular functions; (D) Venn diagram showing the overlap among the three categories. Bars show numbers of cold-induced genes in the two genotypes. Only significantly overrepresented GO slim categories are shown (P ≤ 0.05).

Mentions: Gene Ontology (GO) enrichment of all detected cold-responsive DEGs with known and putative functions is shown in Figure 1. The predominant DEGs were functionally involved in metabolism (23.5%, p = 5.85E-33), such as macromolecule metabolism, oxidation-reduction, and primary metabolism; cellular processes (18.6%, p = 6.71E-11), including microtubule-based processes; stimulus response (4.9%, p = 1.04E-8); binding activity (31.0%, p = 5.26E-43), including ion, tetrapyrrole, and nucleotide binding; and catalytic activity (27.4%, p = 1.76E-43), such as hydrolase, transferase, and oxidoreductase activity. GO enrichment analysis of the 710 genotype-specific DEGs, however, indicated that the most prevalent DEGs were involved in programmed cell death (PCD) (3.2%, p = 4.68E-7) and electron carrier activity (3.0%, p = 0.0002), revealing genotype-specific transcriptome changes in response to cold environmental stimuli.


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)

Functional classification of all 2562 cold-responsive DEGs detected in C418 and K354. (A) Biological processes; (B) cellular components; (C) molecular functions; (D) Venn diagram showing the overlap among the three categories. Bars show numbers of cold-induced genes in the two genotypes. Only significantly overrepresented GO slim categories are shown (P ≤ 0.05).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Functional classification of all 2562 cold-responsive DEGs detected in C418 and K354. (A) Biological processes; (B) cellular components; (C) molecular functions; (D) Venn diagram showing the overlap among the three categories. Bars show numbers of cold-induced genes in the two genotypes. Only significantly overrepresented GO slim categories are shown (P ≤ 0.05).
Mentions: Gene Ontology (GO) enrichment of all detected cold-responsive DEGs with known and putative functions is shown in Figure 1. The predominant DEGs were functionally involved in metabolism (23.5%, p = 5.85E-33), such as macromolecule metabolism, oxidation-reduction, and primary metabolism; cellular processes (18.6%, p = 6.71E-11), including microtubule-based processes; stimulus response (4.9%, p = 1.04E-8); binding activity (31.0%, p = 5.26E-43), including ion, tetrapyrrole, and nucleotide binding; and catalytic activity (27.4%, p = 1.76E-43), such as hydrolase, transferase, and oxidoreductase activity. GO enrichment analysis of the 710 genotype-specific DEGs, however, indicated that the most prevalent DEGs were involved in programmed cell death (PCD) (3.2%, p = 4.68E-7) and electron carrier activity (3.0%, p = 0.0002), revealing genotype-specific transcriptome changes in response to cold environmental stimuli.

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