Oryza sativa
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ABSTRACT:
PROVIDER: PRJNA255318 | ENA |
REPOSITORIES: ENA
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Project description:Background: Weedy rice (Oryza sativa L.) is a worldwide problem in rice production, being highly tolerant to sub-optimal nutrient levels hence competitive in nutrient acquisition. To understand the function of genes that are potentially involved in the high nutrient acquisition ability of weedy rice, we compared the transcriptomes of strawhull weedy red rice (tolerant to N deficit) with the rice cultivar M-bM-^@M-^XWellsM-bM-^@M-^Y (intolerant to N deficit), by examining profiles in flag leaves at panicle initiation under low and optimum N levels. Strawhull weedy red rice and cultivar M-bM-^@M-^XWellsM-bM-^@M-^Y were grown in nutrient solution with NH4NO3 concentration manipulated to simulate optimum and deficient N conditions. Changes in gene expression in leaf tissues were analyzed at three conditions: N deficiency, and at 24- and 48-h NH4NO3 supplementation after N starvation. Differential gene expression on weedy red rice was evaluated using oligonucleotide arrays representing 44,974 rice gene models. Overall, comparative real-time PCR analysis of 21 candidate genes identified from the microarray data between weedy red rice and cultivar M-bM-^@M-^XWellsM-bM-^@M-^Y supported our hypothesis that key genes involved in N assimilation are expressed differentially at N- deficient conditions between the tolerant and intolerant strains. Results: Eight candidate genes showed significant differences in expression at one of the time points: N and starch metabolism-related [alanine aminotransferase (OsAlaAT) locus ID Os10g25140.1; soluble starch synthase 2-1(OsSSSII1), Os10g30156.1; and soluble starch synthase 2-3(OsSSSII3), Os06g12450.1]; cell structure-related [alpha-L-fucosidase 2 precursor (OsFUCA2), Os06g06250.1]; signal transduction [two-component response regulator-like(OsPRR1), Os02g40510.1 and EF hand family protein (OsPOLC2_JUNOX), Os02g50060.1]; and transcription factors [zinc finger, C2H2 type family protein(OsC2H2Znf), Os11g06840.1 and Myb-like DNA-binding domain (OsMYB), Os01g62660.1]. Genome-wide gene expression analysis of weedy rice showed that nitrite reductase (Os01g25484.1; Os01g25484.2; Os01g25484.3) was most highly induced at N starvation and was most deeply repressed at 24 h of N-stress recovery. A few other genes, namely SANT/MYB (Os01g47370.1), chaperonin (Os02g54060.1; Os02g54060.2), protein phosphatase (Os09g15670.1), polyamine transporter (Os01g61044.1), trehalose-6-phosphate synthase (Os02g54820.2), uracil phosphoribosyltransferase (Os05g38170.1), an MIKCc type-box transcription factor (Os02g52340.1), a cell homeostasis-related uncharacterized protein (Os02g16880.1), a protease inhibitor (Os07g18990.1), dehydrin (Os11g26760.1), and cytochrome P450 (Os11g05380.1) were also strong indicators of starvation and recovery. Conclusions: Weedy rice has N-stress adaptive mechanisms that are probably distinct to the mechanisms in most cultivars. This mechanism potentially contributes to its high vigor and competitive advantage over most rice cultivars under sub-optimal nutrient levels. Expression of key genes involved in nitrate assimilation, trehalose synthesis, and protein modification appeared to be critical for adaptation to N stress in weedy rice. N-stress tolerance of weedy red rice appeared to be due at least in part to the ability to sustain C fixation and starch synthesis during N starvation. Plants were subjected to four treatments: T1 M-bM-^@M-^S Full N; T2 M-bM-^@M-^S NH4NO3starvation until NSI <95%; T3 - 24-h NH4NO3 readdition post-starvation; and T4 M-bM-^@M-^S 48-h NH4NO3 readdition post-starvation. The 24- and 48-h time points for NH4NO3 supplementation were selected to assess both the early and late molecular responses. There were four replications, with three plants per replication per N treatment.
2014-07-16 | E-GEOD-59438 | biostudies-arrayexpress
Project description:Background: Weedy rice (Oryza sativa L.) is a worldwide problem in rice production, being highly tolerant to sub-optimal nutrient levels hence competitive in nutrient acquisition. To understand the function of genes that are potentially involved in the high nutrient acquisition ability of weedy rice, we compared the transcriptomes of strawhull weedy red rice (tolerant to N deficit) with the rice cultivar ‘Wells’ (intolerant to N deficit), by examining profiles in flag leaves at panicle initiation under low and optimum N levels. Strawhull weedy red rice and cultivar ‘Wells’ were grown in nutrient solution with NH4NO3 concentration manipulated to simulate optimum and deficient N conditions. Changes in gene expression in leaf tissues were analyzed at three conditions: N deficiency, and at 24- and 48-h NH4NO3 supplementation after N starvation. Differential gene expression on weedy red rice was evaluated using oligonucleotide arrays representing 44,974 rice gene models. Overall, comparative real-time PCR analysis of 21 candidate genes identified from the microarray data between weedy red rice and cultivar ‘Wells’ supported our hypothesis that key genes involved in N assimilation are expressed differentially at N- deficient conditions between the tolerant and intolerant strains. Results: Eight candidate genes showed significant differences in expression at one of the time points: N and starch metabolism-related [alanine aminotransferase (OsAlaAT) locus ID Os10g25140.1; soluble starch synthase 2-1(OsSSSII1), Os10g30156.1; and soluble starch synthase 2-3(OsSSSII3), Os06g12450.1]; cell structure-related [alpha-L-fucosidase 2 precursor (OsFUCA2), Os06g06250.1]; signal transduction [two-component response regulator-like(OsPRR1), Os02g40510.1 and EF hand family protein (OsPOLC2_JUNOX), Os02g50060.1]; and transcription factors [zinc finger, C2H2 type family protein(OsC2H2Znf), Os11g06840.1 and Myb-like DNA-binding domain (OsMYB), Os01g62660.1]. Genome-wide gene expression analysis of weedy rice showed that nitrite reductase (Os01g25484.1; Os01g25484.2; Os01g25484.3) was most highly induced at N starvation and was most deeply repressed at 24 h of N-stress recovery. A few other genes, namely SANT/MYB (Os01g47370.1), chaperonin (Os02g54060.1; Os02g54060.2), protein phosphatase (Os09g15670.1), polyamine transporter (Os01g61044.1), trehalose-6-phosphate synthase (Os02g54820.2), uracil phosphoribosyltransferase (Os05g38170.1), an MIKCc type-box transcription factor (Os02g52340.1), a cell homeostasis-related uncharacterized protein (Os02g16880.1), a protease inhibitor (Os07g18990.1), dehydrin (Os11g26760.1), and cytochrome P450 (Os11g05380.1) were also strong indicators of starvation and recovery. Conclusions: Weedy rice has N-stress adaptive mechanisms that are probably distinct to the mechanisms in most cultivars. This mechanism potentially contributes to its high vigor and competitive advantage over most rice cultivars under sub-optimal nutrient levels. Expression of key genes involved in nitrate assimilation, trehalose synthesis, and protein modification appeared to be critical for adaptation to N stress in weedy rice. N-stress tolerance of weedy red rice appeared to be due at least in part to the ability to sustain C fixation and starch synthesis during N starvation.
2014-07-16 | GSE59438 | GEO
Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.
2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress
Project description:Weedy rice Genome resequencing to discover novel genes
| PRJNA851178 | ENA
Project description:To better understand the complex mechanisms regulating Pi homeostasis in rice (Oryza sativa L. cv. Nipponbare), a time course experiment was performed, where pre-germinated seedlings were grown hydroponically for two weeks on Pi-sufficient medium (0.32 mM Pi), before transferring half of the plants to Pi-deficient solution (0 mM Pi) for 21 days (d). After three weeks of Pi-starvation treatment, half of these plants where then re-supplied with Pi sufficient media for up to 24 hours (h). In total, nine time points were selected in order to cover short and long term responses to Pi starvation as well as the effects of Pi re-supply on Pi starved plants.
2013-11-25 | E-MTAB-4427 | biostudies-arrayexpress
Project description:5 leaves old rice plantlets were infected with Magnaporthe grisea spores and zero, two hours and twenty four houres after infection samples were collected
2014-01-31 | GSE50454 | GEO
Project description:Genetic Background and Evolutionary Pathways of Southeast Asian Weedy Rice
| PRJNA1057574 | ENA
Project description:A comprehensive time-course experiment of Pi-starved plants was undertaken, spanning medium (3 and 7 days), and long-term (21 days up to 52 days) Pi deprivation (âPi), as well as both short term (1 and 3 days) and long-term (31 days) recovery. The 52 days time point consisting of 21 days starvation +31 days recovery enabled investigation of the effects of long term resupply on Pi starved plants, and coincided with the emergence of the first panicles and grains. Pre-germinated rice seedlings were grown for 14 days in Pi sufficient conditions (0.32 mM Pi) before being transferred to either Pi sufficient (0.32 mM Pi) or Pi deficient (0 mM Pi) media for 21 days. After 21 days of Pi deficient treatment, half of the plants were either maintained under Pi deficient conditions or re-supplied with Pi (0.32 mM) for 1, 3 or 31 days. To confirm the effectiveness of the Pi starvation and resupply treatments, physiological and molecular analyses were performed.
2015-07-31 | E-MTAB-4334 | biostudies-arrayexpress