Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A
The major rice quantitative-trait locus Submergence 1 (Sub1) confers tolerance of submergence for about 2 weeks. To identify novel sources of tolerance, we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C, two of the three transcription-factor genes within the...
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| creator | Singh, Namrata Dang, Trang T. M Vergara, Georgina V Pandey, Dev Mani Sanchez, Darlene Neeraja, C. N Septiningsih, Endang M Mendioro, Merlyn Tecson-Mendoza, Evelyn Mae Ismail, Abdelbagi M Mackill, David J Heuer, Sigrid |
| description | The major rice quantitative-trait locus Submergence 1 (Sub1) confers tolerance of submergence for about 2 weeks. To identify novel sources of tolerance, we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C, two of the three transcription-factor genes within the Sub1 locus. The objective was to identify tolerant genotypes without the SUB1A gene or with the intolerant SUB1A-2 allele. The survey revealed that all tolerant genotypes possessed the tolerant Sub1 haplotype (SUB1A-1/SUB1C-1), whereas all accessions without the SUB1A gene were intolerant. Only the variety James Wee with the SUB1A-2 allele was moderately tolerant. However, some intolerant genotypes with the SUB1A-1 allele were identified and RT-PCR analyses were conducted to compare gene expression in tolerant and intolerant accessions. Initial analyses of leaf samples failed to reveal a clear association of SUB1A transcript abundance and tolerance. Temporal and spatial gene expression analyses subsequently showed that SUB1A expression in nodes and internodes associated best with tolerance across representative genotypes. In James Wee, transcript abundance was high in all tissues, suggesting that some level of tolerance might be conferred by high expression of the SUB1A-2 allele. To further assess tissue-specific expression, we have expressed the GUS reporter gene under the control of the SUB1A-1 promoter. The data revealed highly specific GUS expression at the base of the leaf sheath and in the leaf collar region. Specific expression in the growing part of rice leaves is well in agreement with the role of SUB1A in suppressing leaf elongation under submergence. |
| doi_str_mv | 10.1007/s00122-010-1400-z |
| format | Article |
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M ; Vergara, Georgina V ; Pandey, Dev Mani ; Sanchez, Darlene ; Neeraja, C. N ; Septiningsih, Endang M ; Mendioro, Merlyn ; Tecson-Mendoza, Evelyn Mae ; Ismail, Abdelbagi M ; Mackill, David J ; Heuer, Sigrid</creator><creatorcontrib>Singh, Namrata ; Dang, Trang T. M ; Vergara, Georgina V ; Pandey, Dev Mani ; Sanchez, Darlene ; Neeraja, C. N ; Septiningsih, Endang M ; Mendioro, Merlyn ; Tecson-Mendoza, Evelyn Mae ; Ismail, Abdelbagi M ; Mackill, David J ; Heuer, Sigrid</creatorcontrib><description>The major rice quantitative-trait locus Submergence 1 (Sub1) confers tolerance of submergence for about 2 weeks. To identify novel sources of tolerance, we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C, two of the three transcription-factor genes within the Sub1 locus. The objective was to identify tolerant genotypes without the SUB1A gene or with the intolerant SUB1A-2 allele. The survey revealed that all tolerant genotypes possessed the tolerant Sub1 haplotype (SUB1A-1/SUB1C-1), whereas all accessions without the SUB1A gene were intolerant. Only the variety James Wee with the SUB1A-2 allele was moderately tolerant. However, some intolerant genotypes with the SUB1A-1 allele were identified and RT-PCR analyses were conducted to compare gene expression in tolerant and intolerant accessions. Initial analyses of leaf samples failed to reveal a clear association of SUB1A transcript abundance and tolerance. Temporal and spatial gene expression analyses subsequently showed that SUB1A expression in nodes and internodes associated best with tolerance across representative genotypes. In James Wee, transcript abundance was high in all tissues, suggesting that some level of tolerance might be conferred by high expression of the SUB1A-2 allele. To further assess tissue-specific expression, we have expressed the GUS reporter gene under the control of the SUB1A-1 promoter. The data revealed highly specific GUS expression at the base of the leaf sheath and in the leaf collar region. Specific expression in the growing part of rice leaves is well in agreement with the role of SUB1A in suppressing leaf elongation under submergence.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-010-1400-z</identifier><identifier>PMID: 20652530</identifier><identifier>CODEN: THAGA6</identifier><language>eng</language><publisher>Berlin/Heidelberg: Berlin/Heidelberg : Springer-Verlag</publisher><subject>Adaptation, Physiological - genetics ; Agriculture ; Alleles ; Amino Acid Sequence ; Base Sequence ; Biochemistry ; Biological and medical sciences ; Biomedical and Life Sciences ; Biotechnology ; Classical genetics, quantitative genetics, hybrids ; Climate change ; Fundamental and applied biological sciences. Psychology ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes ; Genes, Plant - genetics ; Genetic Markers ; Genetic transcription ; Genetics of eukaryotes. Biological and molecular evolution ; Glucuronidase - metabolism ; Haplotypes - genetics ; Life Sciences ; Molecular Sequence Data ; Organ Specificity - genetics ; Original Paper ; Oryza - genetics ; Oryza - physiology ; Oryza sativa ; Plant Biochemistry ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Plant Proteins - chemistry ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Promoter Regions, Genetic - genetics ; Pteridophyta, spermatophyta ; Rice ; Seedlings - genetics ; Seeds - genetics ; Survival Analysis ; Time Factors ; Vegetals ; Water - physiology</subject><ispartof>Theoretical and applied genetics, 2010-11, Vol.121 (8), p.1441-1453</ispartof><rights>Springer-Verlag 2010</rights><rights>2015 INIST-CNRS</rights><rights>COPYRIGHT 2010 Springer</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c557t-27c684c06a25322a6380eaab56709ae1a008c0f7ed2ec8ab91db01b177e3c9003</citedby><cites>FETCH-LOGICAL-c557t-27c684c06a25322a6380eaab56709ae1a008c0f7ed2ec8ab91db01b177e3c9003</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00122-010-1400-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00122-010-1400-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23395373$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20652530$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Singh, Namrata</creatorcontrib><creatorcontrib>Dang, Trang T. M</creatorcontrib><creatorcontrib>Vergara, Georgina V</creatorcontrib><creatorcontrib>Pandey, Dev Mani</creatorcontrib><creatorcontrib>Sanchez, Darlene</creatorcontrib><creatorcontrib>Neeraja, C. N</creatorcontrib><creatorcontrib>Septiningsih, Endang M</creatorcontrib><creatorcontrib>Mendioro, Merlyn</creatorcontrib><creatorcontrib>Tecson-Mendoza, Evelyn Mae</creatorcontrib><creatorcontrib>Ismail, Abdelbagi M</creatorcontrib><creatorcontrib>Mackill, David J</creatorcontrib><creatorcontrib>Heuer, Sigrid</creatorcontrib><title>Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A</title><title>Theoretical and applied genetics</title><addtitle>Theor Appl Genet</addtitle><addtitle>Theor Appl Genet</addtitle><description>The major rice quantitative-trait locus Submergence 1 (Sub1) confers tolerance of submergence for about 2 weeks. To identify novel sources of tolerance, we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C, two of the three transcription-factor genes within the Sub1 locus. The objective was to identify tolerant genotypes without the SUB1A gene or with the intolerant SUB1A-2 allele. The survey revealed that all tolerant genotypes possessed the tolerant Sub1 haplotype (SUB1A-1/SUB1C-1), whereas all accessions without the SUB1A gene were intolerant. Only the variety James Wee with the SUB1A-2 allele was moderately tolerant. However, some intolerant genotypes with the SUB1A-1 allele were identified and RT-PCR analyses were conducted to compare gene expression in tolerant and intolerant accessions. Initial analyses of leaf samples failed to reveal a clear association of SUB1A transcript abundance and tolerance. Temporal and spatial gene expression analyses subsequently showed that SUB1A expression in nodes and internodes associated best with tolerance across representative genotypes. In James Wee, transcript abundance was high in all tissues, suggesting that some level of tolerance might be conferred by high expression of the SUB1A-2 allele. To further assess tissue-specific expression, we have expressed the GUS reporter gene under the control of the SUB1A-1 promoter. The data revealed highly specific GUS expression at the base of the leaf sheath and in the leaf collar region. Specific expression in the growing part of rice leaves is well in agreement with the role of SUB1A in suppressing leaf elongation under submergence.</description><subject>Adaptation, Physiological - genetics</subject><subject>Agriculture</subject><subject>Alleles</subject><subject>Amino Acid Sequence</subject><subject>Base Sequence</subject><subject>Biochemistry</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Classical genetics, quantitative genetics, hybrids</subject><subject>Climate change</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes</subject><subject>Genes, Plant - genetics</subject><subject>Genetic Markers</subject><subject>Genetic transcription</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Glucuronidase - metabolism</subject><subject>Haplotypes - genetics</subject><subject>Life Sciences</subject><subject>Molecular Sequence Data</subject><subject>Organ Specificity - genetics</subject><subject>Original Paper</subject><subject>Oryza - genetics</subject><subject>Oryza - physiology</subject><subject>Oryza sativa</subject><subject>Plant Biochemistry</subject><subject>Plant Breeding/Biotechnology</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Proteins - chemistry</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Promoter Regions, Genetic - genetics</subject><subject>Pteridophyta, spermatophyta</subject><subject>Rice</subject><subject>Seedlings - genetics</subject><subject>Seeds - genetics</subject><subject>Survival Analysis</subject><subject>Time Factors</subject><subject>Vegetals</subject><subject>Water - physiology</subject><issn>0040-5752</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkt-L1DAQx4Mo3rr6B_iiRRHxoeckaZr2cT38cXAiuO6bEKbptPbstntJK7f315vS1WNFlDwkk3y-3yQzw9hjDqccQL_2AFyIGDjEPAGIb-6wBU-kiIVIxF22AEggVlqJE_bA-0sAEArkfXYiIFVCSViwrx_7luzYoou26L6Ti_zoftA-wq6M6HrnyPum70KI7d6Tj_oqGr5R5BpLAS225GrqLMVD8HEYVlGIKVpv3vDVQ3avwtbTo8O8ZJt3b7-cfYgvPr0_P1tdxFYpPcRC2zRLLKQY3iQEpjIDQixUqiFH4giQWag0lYJshkXOywJ4wbUmaXMAuWQvZ9-d669G8oPZNt5S22JH_ehNDkKmqeL5f0mdBlRLmQXy2R_kZT-6kAVvMpVyUKB0gJ7PUI0tmaar-sGhnSzNSqZcKh4-FKjTv1BhlLRtbN9R1YT9I8GrI0FgBroeahy9N-frz8csn1nreu8dVWbnmlDKveFgpi4xc5cYmOLQJeYmaJ4c_jYVsPyt-NUWAXhxANBbbKupsI2_5aTM1ZSmJRMz58NRV5O7TdK_bn86iyrsDdYuGG_WArgEnkOS5Vz-BGII2cw</recordid><startdate>20101101</startdate><enddate>20101101</enddate><creator>Singh, Namrata</creator><creator>Dang, Trang T. 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M ; Vergara, Georgina V ; Pandey, Dev Mani ; Sanchez, Darlene ; Neeraja, C. N ; Septiningsih, Endang M ; Mendioro, Merlyn ; Tecson-Mendoza, Evelyn Mae ; Ismail, Abdelbagi M ; Mackill, David J ; Heuer, Sigrid</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c557t-27c684c06a25322a6380eaab56709ae1a008c0f7ed2ec8ab91db01b177e3c9003</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Adaptation, Physiological - genetics</topic><topic>Agriculture</topic><topic>Alleles</topic><topic>Amino Acid Sequence</topic><topic>Base Sequence</topic><topic>Biochemistry</topic><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>Classical genetics, quantitative genetics, hybrids</topic><topic>Climate change</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Plant</topic><topic>Genes</topic><topic>Genes, Plant - genetics</topic><topic>Genetic Markers</topic><topic>Genetic transcription</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Glucuronidase - metabolism</topic><topic>Haplotypes - genetics</topic><topic>Life Sciences</topic><topic>Molecular Sequence Data</topic><topic>Organ Specificity - genetics</topic><topic>Original Paper</topic><topic>Oryza - genetics</topic><topic>Oryza - physiology</topic><topic>Oryza sativa</topic><topic>Plant Biochemistry</topic><topic>Plant Breeding/Biotechnology</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Proteins - chemistry</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Promoter Regions, Genetic - genetics</topic><topic>Pteridophyta, spermatophyta</topic><topic>Rice</topic><topic>Seedlings - genetics</topic><topic>Seeds - genetics</topic><topic>Survival Analysis</topic><topic>Time Factors</topic><topic>Vegetals</topic><topic>Water - physiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Singh, Namrata</creatorcontrib><creatorcontrib>Dang, Trang T. 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M</au><au>Vergara, Georgina V</au><au>Pandey, Dev Mani</au><au>Sanchez, Darlene</au><au>Neeraja, C. N</au><au>Septiningsih, Endang M</au><au>Mendioro, Merlyn</au><au>Tecson-Mendoza, Evelyn Mae</au><au>Ismail, Abdelbagi M</au><au>Mackill, David J</au><au>Heuer, Sigrid</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A</atitle><jtitle>Theoretical and applied genetics</jtitle><stitle>Theor Appl Genet</stitle><addtitle>Theor Appl Genet</addtitle><date>2010-11-01</date><risdate>2010</risdate><volume>121</volume><issue>8</issue><spage>1441</spage><epage>1453</epage><pages>1441-1453</pages><issn>0040-5752</issn><eissn>1432-2242</eissn><coden>THAGA6</coden><abstract>The major rice quantitative-trait locus Submergence 1 (Sub1) confers tolerance of submergence for about 2 weeks. To identify novel sources of tolerance, we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C, two of the three transcription-factor genes within the Sub1 locus. The objective was to identify tolerant genotypes without the SUB1A gene or with the intolerant SUB1A-2 allele. The survey revealed that all tolerant genotypes possessed the tolerant Sub1 haplotype (SUB1A-1/SUB1C-1), whereas all accessions without the SUB1A gene were intolerant. Only the variety James Wee with the SUB1A-2 allele was moderately tolerant. However, some intolerant genotypes with the SUB1A-1 allele were identified and RT-PCR analyses were conducted to compare gene expression in tolerant and intolerant accessions. Initial analyses of leaf samples failed to reveal a clear association of SUB1A transcript abundance and tolerance. Temporal and spatial gene expression analyses subsequently showed that SUB1A expression in nodes and internodes associated best with tolerance across representative genotypes. In James Wee, transcript abundance was high in all tissues, suggesting that some level of tolerance might be conferred by high expression of the SUB1A-2 allele. To further assess tissue-specific expression, we have expressed the GUS reporter gene under the control of the SUB1A-1 promoter. The data revealed highly specific GUS expression at the base of the leaf sheath and in the leaf collar region. Specific expression in the growing part of rice leaves is well in agreement with the role of SUB1A in suppressing leaf elongation under submergence.</abstract><cop>Berlin/Heidelberg</cop><pub>Berlin/Heidelberg : Springer-Verlag</pub><pmid>20652530</pmid><doi>10.1007/s00122-010-1400-z</doi><tpages>13</tpages></addata></record> |
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| subjects | Adaptation, Physiological - genetics Agriculture Alleles Amino Acid Sequence Base Sequence Biochemistry Biological and medical sciences Biomedical and Life Sciences Biotechnology Classical genetics, quantitative genetics, hybrids Climate change Fundamental and applied biological sciences. Psychology Gene expression Gene Expression Profiling Gene Expression Regulation, Plant Genes Genes, Plant - genetics Genetic Markers Genetic transcription Genetics of eukaryotes. Biological and molecular evolution Glucuronidase - metabolism Haplotypes - genetics Life Sciences Molecular Sequence Data Organ Specificity - genetics Original Paper Oryza - genetics Oryza - physiology Oryza sativa Plant Biochemistry Plant Breeding/Biotechnology Plant Genetics and Genomics Plant Proteins - chemistry Plant Proteins - genetics Plant Proteins - metabolism Promoter Regions, Genetic - genetics Pteridophyta, spermatophyta Rice Seedlings - genetics Seeds - genetics Survival Analysis Time Factors Vegetals Water - physiology |
| title | Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A |
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