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Laurentius A C J Voesenek - One of the best experts on this subject based on the ideXlab platform.
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root transcript profiling of two rorippa species reveals gene clusters associated with extreme Submergence tolerance
Plant Physiology, 2013Co-Authors: Rashmi Sasidharan, Alex Boonman, Melis Akman, A M H Ammerlaan, M. Eric Schranz, Angelika Mustroph, Timo M Breit, Laurentius A C J Voesenek, Peter H Van TienderenAbstract:Complete Submergence represses photosynthesis and aerobic respiration, causing rapid mortality in most terrestrial plants. However, some plants have evolved traits allowing them to survive prolonged flooding, such as species of the genus Rorippa, close relatives of Arabidopsis (Arabidopsis thaliana). We studied plant survival, changes in carbohydrate and metabolite concentrations, and transcriptome responses to Submergence of two species, Rorippa sylvestris and Rorippa amphibia. We exploited the close relationship between Rorippa species and the model species Arabidopsis by using Arabidopsis GeneChip microarrays for whole-genome transcript profiling of roots of young plants exposed to a 24-h Submergence treatment or air. A probe mask was used based on hybridization of genomic DNA of both species to the arrays, so that weak probe signals due to Rorippa species/Arabidopsis mismatches were removed. Furthermore, we compared Rorippa species microarray results with those obtained for roots of submerged Arabidopsis plants. Both Rorippa species could tolerate deep Submergence, with R. sylvestris surviving much longer than R. amphibia. Submergence resulted in the induction of genes involved in glycolysis and fermentation and the repression of many energy-consuming pathways, similar to the low-oxygen and Submergence response of Arabidopsis and rice (Oryza sativa). The qualitative responses of both Rorippa species to Submergence appeared roughly similar but differed quantitatively. Notably, glycolysis and fermentation genes and a gene encoding sucrose synthase were more strongly induced in the less tolerant R. amphibia than in R. sylvestris. A comparison with Arabidopsis microarray studies on submerged roots revealed some interesting differences and potential tolerance-related genes in Rorippa species.
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plasticity as a plastic response how Submergence induced leaf elongation in rumex palustris depends on light and nutrient availability in its early life stage
New Phytologist, 2012Co-Authors: Heidrun Huber, Laurentius A C J Voesenek, Xin Chen, Marloes Hendriks, Danny Keijsers, Ronald Pierik, Hendrik Poorter, Hans De KroonAbstract:Summary •Plants may experience different environmental cues throughout their development which interact in determining their phenotype. This paper tests the hypothesis that environmental conditions experienced early during ontogeny affect the phenotypic response to subsequent environmental cues. •This hypothesis was tested by exposing different accessions of Rumex palustris to different light and nutrient conditions, followed by subsequent complete Submergence. •Final leaf length and Submergence-induced plasticity were affected by the environmental conditions experienced at early developmental stages. In developmentally older leaves, Submergence-induced elongation was lower in plants previously subjected to high-light conditions. Submergence-induced elongation of developmentally younger leaves, however, was larger when pregrown in high light. High-light and low-nutrient conditions led to an increase of nonstructural carbohydrates in the plants. There was a positive correlation between Submergence-induced leaf elongation and carbohydrate concentration and content in roots and shoots, but not with root and shoot biomass before Submergence. •These results show that conditions experienced by young plants modulate the responses to subsequent environmental conditions, in both magnitude and direction. Internal resource status interacts with cues perceived at different developmental stages in determining plastic responses to the environment.
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molecular characterization of the Submergence response of the arabidopsis thaliana ecotype columbia
New Phytologist, 2011Co-Authors: Seung Cho Lee, Rashmi Sasidharan, Angelika Mustroph, Ole Pedersen, Laurentius A C J Voesenek, Divya Vashisht, Teruko Oosumi, Julia BaileyserresAbstract:Summary •A detailed description of the molecular response of Arabidopsis thaliana to Submergence can aid the identification of genes that are critical to flooding survival. •Rosette-stage plants were fully submerged in complete darkness and shoot and root tissue was harvested separately after the O2 partial pressure of the petiole and root had stabilized at c. 6 and 0.1 kPa, respectively. As controls, plants were untreated or exposed to darkness. Following quantitative profiling of cellular mRNAs with the Affymetrix ATH1 platform, changes in the transcriptome in response to Submergence, early darkness, and O2-deprivation were evaluated by fuzzy k-means clustering. This identified genes co-regulated at the conditional, developmental or organ-specific level. Mutants for 10 differentially expressed HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes were screened for altered Submergence tolerance. •The analysis identified 34 genes that were ubiquitously co-regulated by Submergence and O2 deprivation. The biological functions of these include signaling, transcription, and anaerobic energy metabolism. HUPs comprised 40% of the co-regulated transcripts and mutants of seven of these genes were significantly altered in Submergence tolerance. •The results define transcriptomic adjustments in response to Submergence in the dark and demonstrate that the manipulation of HUPs can alter Submergence tolerance.
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long term Submergence induced elongation in rumex palustris requires abscisic acid dependent biosynthesis of gibberellin1
Plant Physiology, 2006Co-Authors: Joris J Benschop, Anton J M Peeters, Jordi Bou, Niels Wagemaker, Kerstin Guhl, D A Ward, Peter Hedden, Thomas Moritz, Laurentius A C J VoesenekAbstract:Rumex palustris (polygonceae) responds to complete Submergence with enhanced elongation of its youngest petioles. This process requires the presence of gibberellin (GA) and is associated with an increase in the concentration of GA1 in elongating petioles. We have examined how GA biosynthesis was regulated in submerged plants. Therefore, cDNAs encoding GA-biosynthetic enzymes GA 20-oxidase and GA 3-oxidase, and the GA-deactivating enzyme GA 2-oxidase were cloned from R. palustris and the kinetics of transcription of the corresponding genes was determined during a 24 h Submergence period. The Submergence-induced elongation response could be separated into several phases: (1) during the first phase of 4 h, petiole elongation was insensitive to GA; (2) from 4 to 6 h onward growth was limited by GA; and (3) from 15 h onward underwater elongation was dependent, but not limited by GA. Submergence induced an increase of GA1 concentration, as well as enhanced transcript levels of RpGA3ox1. Exogenous abscisic acid repressed the transcript levels of RpGA20ox1 and RpGA3ox1 and thus inhibited the Submergence-induced increase in GA1. Abscisic acid had no effect on the tissue responsiveness to GA.
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plant movement Submergence induced petiole elongation in rumex palustris depends on hyponastic growth
Plant Physiology, 2003Co-Authors: Marjolein C H Cox, Frank F Millenaar, Yvonne E M De Jong Van Berkel, Anton J M Peeters, Laurentius A C J VoesenekAbstract:The Submergence-tolerant species Rumex palustris (Sm.) responds to complete Submergence by an increase in petiole angle with the horizontal. This hyponastic growth, in combination with stimulated elongation of the petiole, can bring the leaf tips above the water surface, thus restoring gas exchange and enabling survival. Using a computerized digital camera set-up the kinetics of this hyponastic petiole movement and stimulated petiole elongation were studied. The hyponastic growth is a relatively rapid process that starts after a lag phase of 1.5 to 3 h and is completed after 6 to 7 h. The kinetics of hyponastic growth depend on the initial angle of the petiole at the time of Submergence, a factor showing considerable seasonal variation. For example, lower petiole angles at the time of Submergence result in a shorter lag phase for hyponastic growth. This dependency of the hyponastic growth kinetics can be mimicked by experimentally manipulating the petiole angle at the time of Submergence. Stimulated petiole elongation in response to complete Submergence also shows kinetics that are dependent on the petiole angle at the time of Submergence, with lower initial petiole angles resulting in a longer lag phase for petiole elongation. Angle manipulation experiments show that stimulated petiole elongation can only start when the petiole has reached an angle of 40° to 50°. The petiole can reach this “critical angle” for stimulated petiole elongation by the process of hyponastic growth. This research shows a functional dependency of one response to Submergence in R . palustris (stimulated petiole elongation) on another response (hyponastic petiole growth), because petiole elongation can only contribute to the leaf reaching the water surface when the petiole has a more or less upright position.
Julia Baileyserres - One of the best experts on this subject based on the ideXlab platform.
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molecular characterization of the Submergence response of the arabidopsis thaliana ecotype columbia
New Phytologist, 2011Co-Authors: Seung Cho Lee, Rashmi Sasidharan, Angelika Mustroph, Ole Pedersen, Laurentius A C J Voesenek, Divya Vashisht, Teruko Oosumi, Julia BaileyserresAbstract:Summary •A detailed description of the molecular response of Arabidopsis thaliana to Submergence can aid the identification of genes that are critical to flooding survival. •Rosette-stage plants were fully submerged in complete darkness and shoot and root tissue was harvested separately after the O2 partial pressure of the petiole and root had stabilized at c. 6 and 0.1 kPa, respectively. As controls, plants were untreated or exposed to darkness. Following quantitative profiling of cellular mRNAs with the Affymetrix ATH1 platform, changes in the transcriptome in response to Submergence, early darkness, and O2-deprivation were evaluated by fuzzy k-means clustering. This identified genes co-regulated at the conditional, developmental or organ-specific level. Mutants for 10 differentially expressed HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes were screened for altered Submergence tolerance. •The analysis identified 34 genes that were ubiquitously co-regulated by Submergence and O2 deprivation. The biological functions of these include signaling, transcription, and anaerobic energy metabolism. HUPs comprised 40% of the co-regulated transcripts and mutants of seven of these genes were significantly altered in Submergence tolerance. •The results define transcriptomic adjustments in response to Submergence in the dark and demonstrate that the manipulation of HUPs can alter Submergence tolerance.
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Submergence tolerant rice sub1 s journey from landrace to modern cultivar
Rice, 2010Co-Authors: Julia Baileyserres, A. M. Ismail, Takeshi Fukao, Sigrid Heuer, Pamela C Ronald, David J. MackillAbstract:Rice landraces tolerant of up to 2 weeks of complete Submergence were collected from farmers’ fields in the 1950s. Success in fine mapping of Submergence 1 (SUB1), a robust quantitative trait locus from the Submergence tolerant FR13A landrace, has enabled marker-assisted breeding of high-yielding rice capable of enduring transient complete Submergence. At the molecular level, SUB1 is a variable polygenic locus encoding two or three ethylene responsive factor (ERF) DNA binding proteins. All Oryza sativa accessions encode SUB1B and SUB1C at this locus. An additional ERF, SUB1A, is present at SUB1 in FR13A and other tolerant accessions. The induction of SUB1A expression by ethylene during Submergence disrupts the elongation escape strategy typical of lowland and deepwater rice, by limiting ethylene-induced gibberellic acid-promoted elongation. Microarray and metabolite studies confirm that SUB1A orchestrates its effects on metabolism and growth in a Submergence-dependent manner. Due to the conditional activity of SUB1A, new “Sub1” mega-varieties effectively provide Submergence tolerance without apparent ill effect on development, productivity, or grain quality.
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Submergence tolerance conferred by sub1a is mediated by slr1 and slrl1 restriction of gibberellin responses in rice
Proceedings of the National Academy of Sciences of the United States of America, 2008Co-Authors: Takeshi Fukao, Julia BaileyserresAbstract:Submergence-tolerant rice maintains viability during complete Submergence by limiting underwater elongation until floodwaters recede. Acclimation responses to Submergence are coordinated by the Submergence-inducible Sub1A, which encodes an ethylene-responsive factor-type transcription factor (ERF). Sub1A is limited to tolerant genotypes and sufficient to confer Submergence tolerance to intolerant accessions. Here we evaluated the role of Sub1A in the integration of ethylene, abscisic acid (ABA), and gibberellin (GA) signaling during Submergence. The Submergence-stimulated decrease in ABA content was Sub1A-independent, whereas GA-mediated underwater elongation was significantly restricted by Sub1A. Transgenics that ectopically express Sub1A displayed classical GA-insensitive phenotypes, leading to the hypothesis that Sub1A limits the response to GA. Notably Sub1A increased the accumulation of the GA signaling repressors Slender Rice-1 (SLR1) and SLR1 Like-1 (SLRL1) and concomitantly diminished GA-inducible gene expression under submerged conditions. In the Sub1A overexpression line, SLR1 protein levels declined under prolonged Submergence but were accompanied by an increase in accumulation of SLRL1, which lacks the DELLA domain. In the presence of Sub1A, the increase in these GA signaling repressors and decrease in GA responsiveness were stimulated by ethylene, which promotes Sub1A expression. Conversely, ethylene promoted GA responsiveness and shoot elongation in Submergence-intolerant lines. Together, these results demonstrate that Sub1A limits ethylene-promoted GA responsiveness during Submergence by augmenting accumulation of the GA signaling repressors SLR1 and SLRL1.
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sub1a is an ethylene response factor like gene that confers Submergence tolerance to rice
Nature, 2006Co-Authors: Kenong Xu, Julia Baileyserres, A. M. Ismail, Takeshi Fukao, Sigrid Heuer, Pamela C Ronald, Xia Xu, Patrick E Canlas, Reycel Maghirangrodriguez, David J. MackillAbstract:In many Asian countries, rice crops are prone to destruction by flooding. Most cultivars of rice, Oryza sativa, die after a week of complete Submergence, but a few strains can survive a couple of weeks under water due to a major quantitative trait locus called Submergence 1 (Sub1). A detailed study of the Sub1 genes has now identified one, Sub1A, as the primary determinant of tolerance to Submergence. The introduction of Sub1A into a widely grown Asian rice cultivar increases its survival rate in flood conditions without sacrificing its high yield and other good properties. A gene that enables some strains of rice to survive under water for a period of time is identified. Furthermore, this gene confers its Submergence tolerance when transferred into a strain of rice that normally dies when submerged under water. Most Oryza sativa cultivars die within a week of complete Submergence—a major constraint to rice production in south and southeast Asia that causes annual losses of over US$1 billion and affects disproportionately the poorest farmers in the world1,2. A few cultivars, such as the O. sativa ssp. indica cultivar FR13A, are highly tolerant and survive up to two weeks of complete Submergence owing to a major quantitative trait locus designated Submergence 1 (Sub1) near the centromere of chromosome 9 (refs 3, 4, 5–6). Here we describe the identification of a cluster of three genes at the Sub1 locus, encoding putative ethylene response factors. Two of these genes, Sub1B and Sub1C, are invariably present in the Sub1 region of all rice accessions analysed. In contrast, the presence of Sub1A is variable. A survey identified two alleles within those indica varieties that possess this gene: a tolerance-specific allele named Sub1A-1 and an intolerance-specific allele named Sub1A-2. Overexpression of Sub1A-1 in a Submergence-intolerant O. sativa ssp. japonica conferred enhanced tolerance to the plants, downregulation of Sub1C and upregulation of Alcohol dehydrogenase 1 (Adh1), indicating that Sub1A-1 is a primary determinant of Submergence tolerance. The FR13A Sub1 locus was introgressed into a widely grown Asian rice cultivar using marker-assisted selection. The new variety maintains the high yield and other agronomic properties of the recurrent parent and is tolerant to Submergence. Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers.
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sub1a is an ethylene response factor like gene that confers Submergence tolerance to rice
Nature, 2006Co-Authors: Takeshi Fukao, Julia Baileyserres, Sigrid Heuer, Pamela C Ronald, Patrick E Canlas, Reycel Maghirangrodriguez, Abdelbagi M Ismail, David J. MackillAbstract:Most Oryza sativa cultivars die within a week of complete Submergence--a major constraint to rice production in south and southeast Asia that causes annual losses of over US 1 billion dollars and affects disproportionately the poorest farmers in the world. A few cultivars, such as the O. sativa ssp. indica cultivar FR13A, are highly tolerant and survive up to two weeks of complete Submergence owing to a major quantitative trait locus designated Submergence 1 (Sub1) near the centromere of chromosome 9 (refs 3, 4, 5-6). Here we describe the identification of a cluster of three genes at the Sub1 locus, encoding putative ethylene response factors. Two of these genes, Sub1B and Sub1C, are invariably present in the Sub1 region of all rice accessions analysed. In contrast, the presence of Sub1A is variable. A survey identified two alleles within those indica varieties that possess this gene: a tolerance-specific allele named Sub1A-1 and an intolerance-specific allele named Sub1A-2. Overexpression of Sub1A-1 in a Submergence-intolerant O. sativa ssp. japonica conferred enhanced tolerance to the plants, downregulation of Sub1C and upregulation of Alcohol dehydrogenase 1 (Adh1), indicating that Sub1A-1 is a primary determinant of Submergence tolerance. The FR13A Sub1 locus was introgressed into a widely grown Asian rice cultivar using marker-assisted selection. The new variety maintains the high yield and other agronomic properties of the recurrent parent and is tolerant to Submergence. Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers.
David J. Mackill - One of the best experts on this subject based on the ideXlab platform.
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physiological basis of tolerance to complete Submergence in rice involves genetic factors in addition to the sub1 gene
Aob Plants, 2014Co-Authors: Sudhanshu Singh, David J. Mackill, A. M. IsmailAbstract:Recurring floods in Asia cause poor crop establishment. Yields decline drastically when plants are com- pletely submerged for a few days. Traditional rice cultivars predominate because they have acquired moderate toler- ance to flooding but they carry the penalty of inherently lower grain yields. In contrast, modern high-yielding varieties are highly susceptible to flooding. Cultivars with tolerance to complete Submergence were recently developed in the background of popular varieties by transferring the Submergence tolerance gene Submergence1 (SUB1 )f rom the highly tolerant Indian landrace FR13A. The present study evaluated three pairs of Sub1 near-isogenic lines (NILs) to- gether with FR13A and two of its Submergence-tolerant derivatives under field conditions to assess the survival and growth processes occurring during Submergence and recovery that are associated with SUB1. Under control condi- tions, the NILs showed similar growth and biomass accumulation, indicating that SUB1 had no apparent effects. Submergence substantially decreased biomass accumulation but with greater reduction in the genotypes lacking SUB1, particularly when Submergence was prolonged for 17 days. When submerged, the lines lacking SUB1 showed greater elongation and lower or negative biomass accumulation. Sub1 lines maintained higher chlorophyll concentra- tions during Submergence and lost less non-structural carbohydrates (NSC) after Submergence. This indicates that the introgression of SUB1 resulted in better regulation of NSC during Submergence and that high pre-Submergence NSC is not essential for the Submergence tolerance conferred by SUB1. During recovery, chlorophyll degradation was faster in genotypes lacking SUB1 and any surviving plants showed poorer and delayed emergence of tillers and leaves. Sub1 lines restored new leaf and tiller production faster. During Submergence, FR13A showed not only slower leaf elongation but also accumulated extra biomass and was able to recover faster than Sub1 lines. This suggests the possibility of further improvements in Submergence tolerance by incorporating additional traits present in FR13A or other similar landraces.
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response of sub1 introgression lines of rice to various flooding conditions
Indonesian Journal of Agricultural Science, 2013Co-Authors: Yudhistira Nugraha, Georgiana V Vergara, David J. Mackill, A. M. IsmailAbstract:Two types of floods can be happen in rice crops, i.e. flash floods and stagnant floods. Flash floods cause complete Submergence for up to 2 weeks, while stagnant floods (SF) could partially submerge part of rice plant. To overcome yield loss due to the floods, introgression of SUB1 gene, known as a gene suppressing cell elongation and carbohydrate metabolism, to rice genotype can increase plant tolerance to complete Submergence for 10 days or more. The study aimed to evaluate the response of 18 rice genotypes, including the recently developed sixth pair SUB1 near isogenic lines (NILs) of mega-rice varieties (Swarna, Sambha Mahsuri, IR64, TDK1, BR11, and CR1009), to various flooding conditions. The rice genotypes were planted at field ponds at Los Banos, Philippines, in the wet season (WS) of 2009. The treatments were 15 days Submergence, SF, SF follows Submergence and normal conditions. Each treatment was arranged in completely randomized block design with three replications. The results showed that the SUB1 introgression rice lines had higher survival compared to the non-SUB1 and did not much elongate their shoots during Submergence. Nevertheless, under SF the rice genotypes should elongates their shoots to allow restoring contact with the air. SF and SF follows Submergence decreased the panicle number, grain number per panicle and panicle fertility. Consequently, the yield declined. It suggests that sensitive genotypes are mostly sourcelimited during grain filling. The SUB1 introgression lines had higher chlorophyll concentration and less depletion in soluble sugar and starch after Submergence. Under SF, soluble sugar and starch contents between the SUB1 NILs and non-SUB1 lines were not significantly different. Introgression of the SUB1 into high-yielding varieties improved Submergence tolerance without affecting yield potential. The study indicates that introgression of the SUB1 into taller type rice varieties should be done to compensate the effect of suppressed elongation.
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Submergence tolerant rice sub1 s journey from landrace to modern cultivar
Rice, 2010Co-Authors: Julia Baileyserres, A. M. Ismail, Takeshi Fukao, Sigrid Heuer, Pamela C Ronald, David J. MackillAbstract:Rice landraces tolerant of up to 2 weeks of complete Submergence were collected from farmers’ fields in the 1950s. Success in fine mapping of Submergence 1 (SUB1), a robust quantitative trait locus from the Submergence tolerant FR13A landrace, has enabled marker-assisted breeding of high-yielding rice capable of enduring transient complete Submergence. At the molecular level, SUB1 is a variable polygenic locus encoding two or three ethylene responsive factor (ERF) DNA binding proteins. All Oryza sativa accessions encode SUB1B and SUB1C at this locus. An additional ERF, SUB1A, is present at SUB1 in FR13A and other tolerant accessions. The induction of SUB1A expression by ethylene during Submergence disrupts the elongation escape strategy typical of lowland and deepwater rice, by limiting ethylene-induced gibberellic acid-promoted elongation. Microarray and metabolite studies confirm that SUB1A orchestrates its effects on metabolism and growth in a Submergence-dependent manner. Due to the conditional activity of SUB1A, new “Sub1” mega-varieties effectively provide Submergence tolerance without apparent ill effect on development, productivity, or grain quality.
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responses of sub1 rice introgression lines to Submergence in the field yield and grain quality
Field Crops Research, 2009Co-Authors: Sudhanshu Singh, David J. Mackill, A. M. IsmailAbstract:Abstract Prolonged Submergence is a major constraint to rice production, affecting over 15 million ha in South and Southeast Asia and causing an annual yield loss of over US$ 600 million. This is because all the modern high-yielding rice varieties are sensitive to complete Submergence. A major quantitative trait locus (QTL), SUB1, associated with Submergence tolerance, was mapped on chromosome 9 and recently bred into popular rainfed lowland rice varieties sensitive of complete Submergence, using marker-assisted backcrossing (MABC). Here, we assessed the impact of introgressing SUB1 into three rice varieties popular in farmers’ fields of South and Southeast Asia, Swarna, Sambha Mahsuri, and IR64, under control conditions as well as following Submergence in the field. Under control conditions, no differences were observed between Sub1 introgression lines and their recurrent parents in grain yield or quality aspects. Submergence substantially delayed flowering and maturity, and reduced grain yield, shoot biomass, harvest index, and yield components across cultivars. The reduction in yield was more drastic in the sensitive varieties, particularly when submerged for longer duration (17 d). The significant decline in grain yield was mainly attributed to reductions in grain filling, number of grains per panicle, and grain weight. The SUB1 QTL is effective in conferring tolerance of Submergence for about 12–17 d, depending on floodwater conditions. Sub1 introgression lines showed a yield advantage of up to 3.8 t ha −1 and slightly better grain quality after Submergence compared with their parents. Apparently, the introgression of SUB1 into popular varieties did not have any negative impact on their performance under control conditions but considerably enhanced their yield and grain quality following short-term Submergence.
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sub1a is an ethylene response factor like gene that confers Submergence tolerance to rice
Nature, 2006Co-Authors: Kenong Xu, Julia Baileyserres, A. M. Ismail, Takeshi Fukao, Sigrid Heuer, Pamela C Ronald, Xia Xu, Patrick E Canlas, Reycel Maghirangrodriguez, David J. MackillAbstract:In many Asian countries, rice crops are prone to destruction by flooding. Most cultivars of rice, Oryza sativa, die after a week of complete Submergence, but a few strains can survive a couple of weeks under water due to a major quantitative trait locus called Submergence 1 (Sub1). A detailed study of the Sub1 genes has now identified one, Sub1A, as the primary determinant of tolerance to Submergence. The introduction of Sub1A into a widely grown Asian rice cultivar increases its survival rate in flood conditions without sacrificing its high yield and other good properties. A gene that enables some strains of rice to survive under water for a period of time is identified. Furthermore, this gene confers its Submergence tolerance when transferred into a strain of rice that normally dies when submerged under water. Most Oryza sativa cultivars die within a week of complete Submergence—a major constraint to rice production in south and southeast Asia that causes annual losses of over US$1 billion and affects disproportionately the poorest farmers in the world1,2. A few cultivars, such as the O. sativa ssp. indica cultivar FR13A, are highly tolerant and survive up to two weeks of complete Submergence owing to a major quantitative trait locus designated Submergence 1 (Sub1) near the centromere of chromosome 9 (refs 3, 4, 5–6). Here we describe the identification of a cluster of three genes at the Sub1 locus, encoding putative ethylene response factors. Two of these genes, Sub1B and Sub1C, are invariably present in the Sub1 region of all rice accessions analysed. In contrast, the presence of Sub1A is variable. A survey identified two alleles within those indica varieties that possess this gene: a tolerance-specific allele named Sub1A-1 and an intolerance-specific allele named Sub1A-2. Overexpression of Sub1A-1 in a Submergence-intolerant O. sativa ssp. japonica conferred enhanced tolerance to the plants, downregulation of Sub1C and upregulation of Alcohol dehydrogenase 1 (Adh1), indicating that Sub1A-1 is a primary determinant of Submergence tolerance. The FR13A Sub1 locus was introgressed into a widely grown Asian rice cultivar using marker-assisted selection. The new variety maintains the high yield and other agronomic properties of the recurrent parent and is tolerant to Submergence. Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers.
A. M. Ismail - One of the best experts on this subject based on the ideXlab platform.
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physiological basis of tolerance to complete Submergence in rice involves genetic factors in addition to the sub1 gene
Aob Plants, 2014Co-Authors: Sudhanshu Singh, David J. Mackill, A. M. IsmailAbstract:Recurring floods in Asia cause poor crop establishment. Yields decline drastically when plants are com- pletely submerged for a few days. Traditional rice cultivars predominate because they have acquired moderate toler- ance to flooding but they carry the penalty of inherently lower grain yields. In contrast, modern high-yielding varieties are highly susceptible to flooding. Cultivars with tolerance to complete Submergence were recently developed in the background of popular varieties by transferring the Submergence tolerance gene Submergence1 (SUB1 )f rom the highly tolerant Indian landrace FR13A. The present study evaluated three pairs of Sub1 near-isogenic lines (NILs) to- gether with FR13A and two of its Submergence-tolerant derivatives under field conditions to assess the survival and growth processes occurring during Submergence and recovery that are associated with SUB1. Under control condi- tions, the NILs showed similar growth and biomass accumulation, indicating that SUB1 had no apparent effects. Submergence substantially decreased biomass accumulation but with greater reduction in the genotypes lacking SUB1, particularly when Submergence was prolonged for 17 days. When submerged, the lines lacking SUB1 showed greater elongation and lower or negative biomass accumulation. Sub1 lines maintained higher chlorophyll concentra- tions during Submergence and lost less non-structural carbohydrates (NSC) after Submergence. This indicates that the introgression of SUB1 resulted in better regulation of NSC during Submergence and that high pre-Submergence NSC is not essential for the Submergence tolerance conferred by SUB1. During recovery, chlorophyll degradation was faster in genotypes lacking SUB1 and any surviving plants showed poorer and delayed emergence of tillers and leaves. Sub1 lines restored new leaf and tiller production faster. During Submergence, FR13A showed not only slower leaf elongation but also accumulated extra biomass and was able to recover faster than Sub1 lines. This suggests the possibility of further improvements in Submergence tolerance by incorporating additional traits present in FR13A or other similar landraces.
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response of sub1 introgression lines of rice to various flooding conditions
Indonesian Journal of Agricultural Science, 2013Co-Authors: Yudhistira Nugraha, Georgiana V Vergara, David J. Mackill, A. M. IsmailAbstract:Two types of floods can be happen in rice crops, i.e. flash floods and stagnant floods. Flash floods cause complete Submergence for up to 2 weeks, while stagnant floods (SF) could partially submerge part of rice plant. To overcome yield loss due to the floods, introgression of SUB1 gene, known as a gene suppressing cell elongation and carbohydrate metabolism, to rice genotype can increase plant tolerance to complete Submergence for 10 days or more. The study aimed to evaluate the response of 18 rice genotypes, including the recently developed sixth pair SUB1 near isogenic lines (NILs) of mega-rice varieties (Swarna, Sambha Mahsuri, IR64, TDK1, BR11, and CR1009), to various flooding conditions. The rice genotypes were planted at field ponds at Los Banos, Philippines, in the wet season (WS) of 2009. The treatments were 15 days Submergence, SF, SF follows Submergence and normal conditions. Each treatment was arranged in completely randomized block design with three replications. The results showed that the SUB1 introgression rice lines had higher survival compared to the non-SUB1 and did not much elongate their shoots during Submergence. Nevertheless, under SF the rice genotypes should elongates their shoots to allow restoring contact with the air. SF and SF follows Submergence decreased the panicle number, grain number per panicle and panicle fertility. Consequently, the yield declined. It suggests that sensitive genotypes are mostly sourcelimited during grain filling. The SUB1 introgression lines had higher chlorophyll concentration and less depletion in soluble sugar and starch after Submergence. Under SF, soluble sugar and starch contents between the SUB1 NILs and non-SUB1 lines were not significantly different. Introgression of the SUB1 into high-yielding varieties improved Submergence tolerance without affecting yield potential. The study indicates that introgression of the SUB1 into taller type rice varieties should be done to compensate the effect of suppressed elongation.
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Submergence tolerant rice sub1 s journey from landrace to modern cultivar
Rice, 2010Co-Authors: Julia Baileyserres, A. M. Ismail, Takeshi Fukao, Sigrid Heuer, Pamela C Ronald, David J. MackillAbstract:Rice landraces tolerant of up to 2 weeks of complete Submergence were collected from farmers’ fields in the 1950s. Success in fine mapping of Submergence 1 (SUB1), a robust quantitative trait locus from the Submergence tolerant FR13A landrace, has enabled marker-assisted breeding of high-yielding rice capable of enduring transient complete Submergence. At the molecular level, SUB1 is a variable polygenic locus encoding two or three ethylene responsive factor (ERF) DNA binding proteins. All Oryza sativa accessions encode SUB1B and SUB1C at this locus. An additional ERF, SUB1A, is present at SUB1 in FR13A and other tolerant accessions. The induction of SUB1A expression by ethylene during Submergence disrupts the elongation escape strategy typical of lowland and deepwater rice, by limiting ethylene-induced gibberellic acid-promoted elongation. Microarray and metabolite studies confirm that SUB1A orchestrates its effects on metabolism and growth in a Submergence-dependent manner. Due to the conditional activity of SUB1A, new “Sub1” mega-varieties effectively provide Submergence tolerance without apparent ill effect on development, productivity, or grain quality.
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responses of sub1 rice introgression lines to Submergence in the field yield and grain quality
Field Crops Research, 2009Co-Authors: Sudhanshu Singh, David J. Mackill, A. M. IsmailAbstract:Abstract Prolonged Submergence is a major constraint to rice production, affecting over 15 million ha in South and Southeast Asia and causing an annual yield loss of over US$ 600 million. This is because all the modern high-yielding rice varieties are sensitive to complete Submergence. A major quantitative trait locus (QTL), SUB1, associated with Submergence tolerance, was mapped on chromosome 9 and recently bred into popular rainfed lowland rice varieties sensitive of complete Submergence, using marker-assisted backcrossing (MABC). Here, we assessed the impact of introgressing SUB1 into three rice varieties popular in farmers’ fields of South and Southeast Asia, Swarna, Sambha Mahsuri, and IR64, under control conditions as well as following Submergence in the field. Under control conditions, no differences were observed between Sub1 introgression lines and their recurrent parents in grain yield or quality aspects. Submergence substantially delayed flowering and maturity, and reduced grain yield, shoot biomass, harvest index, and yield components across cultivars. The reduction in yield was more drastic in the sensitive varieties, particularly when submerged for longer duration (17 d). The significant decline in grain yield was mainly attributed to reductions in grain filling, number of grains per panicle, and grain weight. The SUB1 QTL is effective in conferring tolerance of Submergence for about 12–17 d, depending on floodwater conditions. Sub1 introgression lines showed a yield advantage of up to 3.8 t ha −1 and slightly better grain quality after Submergence compared with their parents. Apparently, the introgression of SUB1 into popular varieties did not have any negative impact on their performance under control conditions but considerably enhanced their yield and grain quality following short-term Submergence.
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sub1a is an ethylene response factor like gene that confers Submergence tolerance to rice
Nature, 2006Co-Authors: Kenong Xu, Julia Baileyserres, A. M. Ismail, Takeshi Fukao, Sigrid Heuer, Pamela C Ronald, Xia Xu, Patrick E Canlas, Reycel Maghirangrodriguez, David J. MackillAbstract:In many Asian countries, rice crops are prone to destruction by flooding. Most cultivars of rice, Oryza sativa, die after a week of complete Submergence, but a few strains can survive a couple of weeks under water due to a major quantitative trait locus called Submergence 1 (Sub1). A detailed study of the Sub1 genes has now identified one, Sub1A, as the primary determinant of tolerance to Submergence. The introduction of Sub1A into a widely grown Asian rice cultivar increases its survival rate in flood conditions without sacrificing its high yield and other good properties. A gene that enables some strains of rice to survive under water for a period of time is identified. Furthermore, this gene confers its Submergence tolerance when transferred into a strain of rice that normally dies when submerged under water. Most Oryza sativa cultivars die within a week of complete Submergence—a major constraint to rice production in south and southeast Asia that causes annual losses of over US$1 billion and affects disproportionately the poorest farmers in the world1,2. A few cultivars, such as the O. sativa ssp. indica cultivar FR13A, are highly tolerant and survive up to two weeks of complete Submergence owing to a major quantitative trait locus designated Submergence 1 (Sub1) near the centromere of chromosome 9 (refs 3, 4, 5–6). Here we describe the identification of a cluster of three genes at the Sub1 locus, encoding putative ethylene response factors. Two of these genes, Sub1B and Sub1C, are invariably present in the Sub1 region of all rice accessions analysed. In contrast, the presence of Sub1A is variable. A survey identified two alleles within those indica varieties that possess this gene: a tolerance-specific allele named Sub1A-1 and an intolerance-specific allele named Sub1A-2. Overexpression of Sub1A-1 in a Submergence-intolerant O. sativa ssp. japonica conferred enhanced tolerance to the plants, downregulation of Sub1C and upregulation of Alcohol dehydrogenase 1 (Adh1), indicating that Sub1A-1 is a primary determinant of Submergence tolerance. The FR13A Sub1 locus was introgressed into a widely grown Asian rice cultivar using marker-assisted selection. The new variety maintains the high yield and other agronomic properties of the recurrent parent and is tolerant to Submergence. Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers.
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can rice cultivar with Submergence tolerant quantitative trait locus sub1 manage Submergence stress better during reproductive stage
Archives of Agronomy and Soil Science, 2017Co-Authors: Debabrata Panda, R. K. SarkarAbstract:ABSTRACTCultivars with Submergence tolerant quantitative trait locus (SUB1) greatly enhance Submergence tolerance at vegetative stage. Whether such cultivar is better off or not at reproductive stage Submergence is not known. Due to uncertainties in rainfall pattern and delayed monsoon, flooding at later stages corresponding to reproductive stage is very much common now. Therefore, the main goal of the present investigation is to work out the effect of Submergence at reproductive stage on yield and yield attributes in three rice cultivars namely Swarna, Swarna-Sub1, and Baliadhan (a traditional rice cultivar showed similar reaction to SUB1). The present study envisages that Submergence at reproductive stage greatly decreased the grain yield even though there was no mortality of plants. Yield reduction was greater at flowering stage followed by booting and panicle initiation stage. Swarna-Sub1 performed significantly better compared to Swarna when Submergence was given at panicle initiation stage. Swarna-S...
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role of non structural carbohydrate and its catabolism associated with sub 1 qtl in rice subjected to complete Submergence
Experimental Agriculture, 2012Co-Authors: Debabrata Panda, R. K. SarkarAbstract:The present study is to characterise the non-structural carbohydrate (NSC) status and its catabolism along with elongation growth in rice cultivars either possessing or not possessing the Sub 1 quantitative trait locus (QTL), i.e. Swarna and Swarna Sub1 exposed to seven days of complete Submergence. During Submergence, Swarna accelerated the rate of stem and leaf elongation and rapidly consumed NSC. In contrast, Swarna Sub1 consumed energy resources more slowly and maintained similar growth rate to that of non-submerged plants. Swarna Sub1 showed better utilisation of carbohydrate than that of Swarna by progressive induction of alcohol dehydrogenase, starch phosphorylase and total and α-amylase enzyme activity during Submergence. Overall, Submergence tolerance conferred by the Swarna Sub1 QTL is correlated with better maintenance and utilisation of NSC than that of Swarna.
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leaf photosynthetic activity and antioxidant defense associated with sub1 qtl in rice subjected to Submergence and subsequent re aeration
Rice Science, 2012Co-Authors: Debabrata Panda, R. K. SarkarAbstract:The influence of Submergence on photosynthesis and antioxidant capacities in rice varieties Swarna and Swarna-Sub1 with or without Sub1 QTL were evaluated under control, simulated complete Submergence and subsequent re-aeration. The leaf photosynthetic rate and stomatal conductance decreased in the both varieties during the progression of Submergence as compared to the control plants, but significant varietal differences were observed after 1 d of Submergence. Submergence also altered the PSII activity, as reflected in a decrease in the values of Fo, Fm and Fv/Fm and degradation of chlorophyll, more in Swarna than in Swarna-Sub1. During early Submergence period, the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), glutathione reductase (GR) against reactive oxygen species were increased in the both varieties. However, with the progress of Submergence period (after 7 d), the activities of SOD, catalase (CAT), APX, guaiacol peroxidase (GPX), GR and DHAR declined, more in Swarna than in Swarna-Sub1. During re-aeration, Swarna-Sub1 showed significant increase of above antioxidant enzymes but not in Swarna. Swarna-Sub1 improves photosynthetic activity, showing higher photosynthetic rate compared to Swarna under Submergence and subsequent re-aeration because of less degradation of chlorophyll, higher stomatal conductance, and efficient PSII activity along with better antioxidant protection from oxidative damage.
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rice genotypes with sub1 qtl differ in Submergence tolerance elongation ability during Submergence and re generation growth at re emergence
Rice, 2011Co-Authors: R. K. Sarkar, Bijoya BhattacharjeeAbstract:Submergence tolerance is an important trait where short term flash flooding damages rice. Tolerant landraces that withstand Submergence for 1–2 weeks were identified. Due to the heterogeneity in flood-prone ecosystem many different types of traditional rice cultivars are being grown by the farmers. The local landraces adapted to extremes in water availability could be the sources of genetic variation are to be used to improve the adaptability of rice to excess water stress. Greater genotypic variability was observed for plant height, elongation and survival %, absolute growth rate, non-structural carbohydrate retention capacity, chlorophyll content, different chlorophyll fluorescence parameters (FPs) characteristics, and re-generation growth at re-emergence. Twenty days Submergence caused greater damage even in Submergence 1 (SUB1) introgressed cultivars compared to the 14 days of Submergence. The FPs, carbohydrate content and dry weight at the end of Submergence showed positive and highly significant association with re-generation growth. The presence of SUB1 associated primers, either SC3 or ART5, was noticed even in greater elongating types of rice genotypes. These genotypes possess one or more of the adaptive traits required for the flood-prone ecosystem, which range from temporary Submergence of 1–2 weeks to long period of stagnant water tolerance.
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improvement of photosynthesis by sub1 qtl in rice under Submergence probed by chlorophyll fluorescence ojip transients
Journal of Stress Physiology & Biochemistry, 2011Co-Authors: Debabrata Panda, R. K. SarkarAbstract:The influence of Submergence on the photosynthetic activity in rice plants either possessing or not possessing Sub1 QTL i.e. Swarna and Swarna Sub1 cultivars (cv.) were evaluated under simulated complete Submergence. The leaf photosynthetic rate and stomatal conductance decreased in both the cv. during the progression of Submergence as compared to control plant but significant varietal differences was observed after 1 day (d) of Submergence. Submergence also alters the photo-system (PS) II activity, as reflected in a decrease in the values of Fo, Fm and the Fv/Fm ratio and degradation of chlorophyll, more in Swarna than that of Swarna Sub1. Under complete Submergence the shape of the OJIP transient also changed in rice leaves with decrease in maximal fluorescence (P=Fm) intensity, resulted lowering of variable fluorescence levels. The decrease was more pronounced in Swarna compared to the Swarna Sub1 cv. Thus, Swarna Sub1 improves photosynthetic activity showing more photosynthetic rate compared to Swarna under Submergence because, of less degradation of chlorophyll, higher stomatal conductance, and efficient PS II activity.
