Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice
Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A,...
| Autores principales: | , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2018
|
| Acceso en línea: | https://hdl.handle.net/10568/164916 |
| _version_ | 1855534298604503040 |
|---|---|
| author | Sharma, Niharika Dang, Trang Minh Singh, Namrata Ruzicic, Slobodan Mueller-Roeber, Bernd Baumann, Ute Heuer, Sigrid |
| author_browse | Baumann, Ute Dang, Trang Minh Heuer, Sigrid Mueller-Roeber, Bernd Ruzicic, Slobodan Sharma, Niharika Singh, Namrata |
| author_facet | Sharma, Niharika Dang, Trang Minh Singh, Namrata Ruzicic, Slobodan Mueller-Roeber, Bernd Baumann, Ute Heuer, Sigrid |
| author_sort | Sharma, Niharika |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression This study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance |
| format | Journal Article |
| id | CGSpace164916 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1649162024-12-19T14:13:12Z Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice Sharma, Niharika Dang, Trang Minh Singh, Namrata Ruzicic, Slobodan Mueller-Roeber, Bernd Baumann, Ute Heuer, Sigrid Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression This study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance 2018-12 2024-12-19T12:54:28Z 2024-12-19T12:54:28Z Journal Article https://hdl.handle.net/10568/164916 en Open Access Springer Sharma, Niharika; Dang, Trang Minh; Singh, Namrata; Ruzicic, Slobodan; Mueller-Roeber, Bernd; Baumann, Ute and Heuer, Sigrid. 2018. Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice. Rice, Volume 11, no. 1 |
| spellingShingle | Sharma, Niharika Dang, Trang Minh Singh, Namrata Ruzicic, Slobodan Mueller-Roeber, Bernd Baumann, Ute Heuer, Sigrid Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice |
| title | Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice |
| title_full | Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice |
| title_fullStr | Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice |
| title_full_unstemmed | Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice |
| title_short | Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice |
| title_sort | allelic variants of ossub1a cause differential expression of transcription factor genes in response to submergence in rice |
| url | https://hdl.handle.net/10568/164916 |
| work_keys_str_mv | AT sharmaniharika allelicvariantsofossub1acausedifferentialexpressionoftranscriptionfactorgenesinresponsetosubmergenceinrice AT dangtrangminh allelicvariantsofossub1acausedifferentialexpressionoftranscriptionfactorgenesinresponsetosubmergenceinrice AT singhnamrata allelicvariantsofossub1acausedifferentialexpressionoftranscriptionfactorgenesinresponsetosubmergenceinrice AT ruzicicslobodan allelicvariantsofossub1acausedifferentialexpressionoftranscriptionfactorgenesinresponsetosubmergenceinrice AT muellerroeberbernd allelicvariantsofossub1acausedifferentialexpressionoftranscriptionfactorgenesinresponsetosubmergenceinrice AT baumannute allelicvariantsofossub1acausedifferentialexpressionoftranscriptionfactorgenesinresponsetosubmergenceinrice AT heuersigrid allelicvariantsofossub1acausedifferentialexpressionoftranscriptionfactorgenesinresponsetosubmergenceinrice |