The Experts below are selected from a list of 1740 Experts worldwide ranked by ideXlab platform
David J Mackill - One of the best experts on this subject based on the ideXlab platform.
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mapping additional qtls from fr13a to increase submergence tolerance in rice beyond SUB1
Euphytica, 2016Co-Authors: Zennia Jean C. Gonzaga, David J Mackill, Endang M Septiningsih, Darlene L Sanchez, Jerome CarandangAbstract:Submergence is a common naturally occurring disaster in rice production in South and Southeast Asia. The development of mega-varieties with tolerance conferred by the SUB1 gene on chromosome 9 derived from FR13A that can withstand up to 2 weeks of complete submergence has been one of the best solutions. However, the recent severe conditions of flooding because of climate change, which has been predicted to become worse in the near future, calls for the development of an improved variety with superior tolerance of submergence. To search for novel quantitative trait loci (QTLs) that can complement the SUB1 gene, recombinant inbred lines (RILs) derived from an IR42/FR13A mapping population were explored. Five QTLs were detected on chromosomes 1, 4, 8, 9, and 10, four of which were from FR13A and one was from IR42. The study confirms the SUB1 QTL on chromosome 9 with a maximum LOD score of 19.51 and R2 of 53.60 %. Additional novel QTLs coming from FR13A on chromosomes 1, 8, and 10 were identified with LOD scores of 5.16, 3.56, and 3.85 and R2 of 23.33, 14.98, and 15.80 %, respectively. Interestingly, lines without SUB1 were still tolerant, with a maximum survival rate up to 95 % because of the presence of these additional QTLs. The non-SUB1 QTLs identified have great potential to enhance tolerance as evidenced by the superior tolerance of FR13A compared with that of the developed SUB1 lines. By transferring selected potential QTLs that are mostly additive to SUB1, it is hoped that crop damage from severe flooding can be significantly decreased.
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accelerating the development of new submergence tolerant rice varieties the case of ciherang SUB1 and psb rc18 SUB1
Euphytica, 2015Co-Authors: Endang M Septiningsih, A M Ismail, David J Mackill, Alvaro M Pamplona, Darlene L Sanchez, Jerome Carandang, Bertrand C. Y. Collard, Yudhistira Nugraha, Nurul HidayatunAbstract:Submergence is an escalating problem in many rice producing areas. A submergence tolerance gene, SUB1, derived from FR13A was previously introduced into six mega varieties through marker assisted backcrossing (MABC) with the final product selected at the BC2 or BC3 generation. Their phenotype was similar to the original varieties, but they could withstand complete inundation for up to 2 or 3 weeks. Several of these varieties have been released in South and Southeast Asia; nonetheless the development of additional submergence tolerant varieties is indispensable to provide farmers with diverse choices of varieties that are preferable for the local needs and to avoid ecological vulnerability due to planting only one variety across vast areas. To accelerate this effort, the SUB1 gene has now been introgressed into two new popular varieties from Indonesia and the Philippines, i.e. Ciherang and PSB Rc18, respectively, through MABC using only one backcross (BC1) with the previously developed IR64-SUB1 as the donor. Since this new donor is closely related to both recurrent parents, a more rapid MABC approach can be pursued due to the similarity of genetic backgrounds. Using this strategy, new submergence tolerant varieties Ciherang-SUB1 and PSB Rc18-SUB1 were developed in less than 2 years, presenting a promising approach to convert additional popular varieties in the future.
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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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the contribution of submergence tolerant SUB1 rice varieties to food security in flood prone rainfed lowland areas in asia
Field Crops Research, 2013Co-Authors: A M Ismail, David J Mackill, Sudhanshu Singh, U S SinghAbstract:Abstract Transient complete submergence reduces survival and yield on more than 20 million ha of rice in rainfed lowlands and flood-prone areas in Asia. Poverty and food insecurity are concomitant problems in these heavily populated areas, because of the high risks and the lack of high-yielding, flood-tolerant varieties. Rice landraces that can withstand over 2 weeks of complete submergence were identified and the gene (named SUB1) that controls most of the tolerance phenotype was cloned and characterized. This enabled the use of marker-assisted backcrossing (MABC) to transfer this gene into numerous varieties that are popular among farmers, five of which were recently released for commercial use in five countries in South and Southeast Asia. Varieties carrying the SUB1 gene developed through this process had the same agronomic, yield and quality traits as their non-SUB1 counterparts when grown under non-flooded conditions, but showed yield advantages of 1 to more than 3 t ha−1 after complete submergence for various durations in naturally flooded fields. Furthermore, SUB1 was found to be effective at all growth stages from early seedling stage to about a week before flowering. SUB1 varieties have been spreading fast in several countries over the last few years, and are currently grown by more than 4 million farmers in Asia. This success is attributed to several factors, including the choice of varieties that are popular among rainfed lowland farmers for deploying SUB1 and its consistent effectiveness in different genetic backgrounds and environments. Other factors are a far-reaching network of partners along the research to adoption continuum, an effective awareness programme targeting appropriate partners, policymakers and farmers, and the additional resources made available by international donors and national programmes primarily to support the production and distribution of good-quality seeds and for strengthening seed systems. Further work is ongoing to incorporate SUB1 into more varieties and to strengthen the tolerance conferred by SUB1. Breeding varieties with multiple stresses is being accomplished by combining SUB1 with other tolerance traits/genes for wider adaptation in the less favourable rice ecosystems.
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response of SUB1 introgression lines of rice to various flooding conditions
Indonesian Journal of Agricultural Science, 2013Co-Authors: Yudhistira Nugraha, David J Mackill, Georgiana V Vergara, 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.
Michael J Blackman - One of the best experts on this subject based on the ideXlab platform.
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a malaria parasite subtilisin propeptide like protein is a potent inhibitor of the egress protease SUB1
Biochemical Journal, 2020Co-Authors: Sarah J Tarr, Chrislaine Withersmartinez, Helen R Flynn, Ambrosius P Snijders, Laura Masino, Konstantinos Koussis, David J Conway, Michael J BlackmanAbstract:Subtilisin-like serine peptidases (subtilases) play important roles in the life cycle of many organisms, including the protozoan parasites that are the causative agent of malaria, Plasmodium spp. As with other peptidases, subtilase proteolytic activity has to be tightly regulated in order to prevent potentially deleterious uncontrolled protein degradation. Maturation of most subtilases requires the presence of an N-terminal propeptide that facilitates folding of the catalytic domain. Following its proteolytic cleavage, the propeptide acts as a transient, tightly bound inhibitor until its eventual complete removal to generate active protease. Here we report the identification of a stand-alone malaria parasite propeptide-like protein, called SUB1-ProM, encoded by a conserved gene that lies in a highly syntenic locus adjacent to three of the four subtilisin-like genes in the Plasmodium genome. Template-based modelling and ab initio structure prediction showed that the SUB1-ProM core structure is most similar to the X-ray crystal structure of the propeptide of SUB1, an essential parasite subtilase that is discharged into the parasitophorous vacuole (PV) to trigger parasite release (egress) from infected host cells. Recombinant Plasmodium falciparum SUB1-ProM was found to be a fast-binding, potent inhibitor of P. falciparum SUB1, but not of the only other essential blood-stage parasite subtilase, SUB2, or of other proteases examined. Mass-spectrometry and immunofluorescence showed that SUB1-ProM is expressed in the PV of blood stage P. falciparum, where it may act as an endogenous inhibitor to regulate SUB1 activity in the parasite.
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The malaria parasite egress protease SUB1 is a calcium-dependent redox switch subtilisin.
Nature Communications, 2014Co-Authors: Chrislaine Withers-martinez, Fiona Hackett, Malcolm Strath, Lesley F. Haire, Steven Howell, Philip A. Walker, Evangelos Christodoulou, Guy G. Dodson, Michael J BlackmanAbstract:In the malarial parasitophorous vacuole, the serine protease SUB1 processes parasite proteins that are required for release from host cells and invasion. Here, the authors report the first crystallographic structure of SUB1 in complex with its cognate prodomain revealing its substrate interactions and providing insight into its regulation.
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the malaria parasite egress protease SUB1 is a calcium dependent redox switch subtilisin
Nature Communications, 2014Co-Authors: Chrislaine Withersmartinez, Fiona Hackett, Malcolm Strath, Lesley F. Haire, Steven Howell, Philip A. Walker, Evangelos Christodoulou, Guy G. Dodson, Michael J BlackmanAbstract:Malaria is caused by a protozoan parasite that replicates within an intraerythrocytic parasitophorous vacuole. Release (egress) of malaria merozoites from the host erythrocyte is a highly regulated and calcium-dependent event that is critical for disease progression. Minutes before egress, an essential parasite serine protease called SUB1 is discharged into the parasitophorous vacuole, where it proteolytically processes a subset of parasite proteins that play indispensable roles in egress and invasion. Here we report the first crystallographic structure of Plasmodium falciparum SUB1 at 2.25 A, in complex with its cognate prodomain. The structure highlights the basis of the calcium dependence of SUB1, as well as its unusual requirement for interactions with substrate residues on both prime and non-prime sides of the scissile bond. Importantly, the structure also reveals the presence of a solvent-exposed redox-sensitive disulphide bridge, unique among the subtilisin family, that likely acts as a regulator of protease activity in the parasite.
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the malarial serine protease SUB1 plays an essential role in parasite liver stage development
PLOS Pathogens, 2013Co-Authors: Catherine Suarez, Katrin Volkmann, Ana Rita Gomes, Oliver Billker, Michael J BlackmanAbstract:Transmission of the malaria parasite to its vertebrate host involves an obligatory exoerythrocytic stage in which extensive asexual replication of the parasite takes place in infected hepatocytes. The resulting liver schizont undergoes segmentation to produce thousands of daughter merozoites. These are released to initiate the blood stage life cycle, which causes all the pathology associated with the disease. Whilst elements of liver stage merozoite biology are similar to those in the much better-studied blood stage merozoites, little is known of the molecular players involved in liver stage merozoite production. To facilitate the study of liver stage biology we developed a strategy for the rapid production of complex conditional alleles by recombinase mediated engineering in Escherichia coli, which we used in combination with existing Plasmodium berghei deleter lines expressing Flp recombinase to study subtilisin-like protease 1 (SUB1), a conserved Plasmodium serine protease previously implicated in blood stage merozoite maturation and egress. We demonstrate that SUB1 is not required for the early stages of intrahepatic growth, but is essential for complete development of the liver stage schizont and for production of hepatic merozoites. Our results indicate that inhibitors of SUB1 could be used in prophylactic approaches to control or block the clinically silent pre-erythrocytic stage of the malaria parasite life cycle.
A M Ismail - One of the best experts on this subject based on the ideXlab platform.
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accelerating the development of new submergence tolerant rice varieties the case of ciherang SUB1 and psb rc18 SUB1
Euphytica, 2015Co-Authors: Endang M Septiningsih, A M Ismail, David J Mackill, Alvaro M Pamplona, Darlene L Sanchez, Jerome Carandang, Bertrand C. Y. Collard, Yudhistira Nugraha, Nurul HidayatunAbstract:Submergence is an escalating problem in many rice producing areas. A submergence tolerance gene, SUB1, derived from FR13A was previously introduced into six mega varieties through marker assisted backcrossing (MABC) with the final product selected at the BC2 or BC3 generation. Their phenotype was similar to the original varieties, but they could withstand complete inundation for up to 2 or 3 weeks. Several of these varieties have been released in South and Southeast Asia; nonetheless the development of additional submergence tolerant varieties is indispensable to provide farmers with diverse choices of varieties that are preferable for the local needs and to avoid ecological vulnerability due to planting only one variety across vast areas. To accelerate this effort, the SUB1 gene has now been introgressed into two new popular varieties from Indonesia and the Philippines, i.e. Ciherang and PSB Rc18, respectively, through MABC using only one backcross (BC1) with the previously developed IR64-SUB1 as the donor. Since this new donor is closely related to both recurrent parents, a more rapid MABC approach can be pursued due to the similarity of genetic backgrounds. Using this strategy, new submergence tolerant varieties Ciherang-SUB1 and PSB Rc18-SUB1 were developed in less than 2 years, presenting a promising approach to convert additional popular varieties in the future.
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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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the contribution of submergence tolerant SUB1 rice varieties to food security in flood prone rainfed lowland areas in asia
Field Crops Research, 2013Co-Authors: A M Ismail, David J Mackill, Sudhanshu Singh, U S SinghAbstract:Abstract Transient complete submergence reduces survival and yield on more than 20 million ha of rice in rainfed lowlands and flood-prone areas in Asia. Poverty and food insecurity are concomitant problems in these heavily populated areas, because of the high risks and the lack of high-yielding, flood-tolerant varieties. Rice landraces that can withstand over 2 weeks of complete submergence were identified and the gene (named SUB1) that controls most of the tolerance phenotype was cloned and characterized. This enabled the use of marker-assisted backcrossing (MABC) to transfer this gene into numerous varieties that are popular among farmers, five of which were recently released for commercial use in five countries in South and Southeast Asia. Varieties carrying the SUB1 gene developed through this process had the same agronomic, yield and quality traits as their non-SUB1 counterparts when grown under non-flooded conditions, but showed yield advantages of 1 to more than 3 t ha−1 after complete submergence for various durations in naturally flooded fields. Furthermore, SUB1 was found to be effective at all growth stages from early seedling stage to about a week before flowering. SUB1 varieties have been spreading fast in several countries over the last few years, and are currently grown by more than 4 million farmers in Asia. This success is attributed to several factors, including the choice of varieties that are popular among rainfed lowland farmers for deploying SUB1 and its consistent effectiveness in different genetic backgrounds and environments. Other factors are a far-reaching network of partners along the research to adoption continuum, an effective awareness programme targeting appropriate partners, policymakers and farmers, and the additional resources made available by international donors and national programmes primarily to support the production and distribution of good-quality seeds and for strengthening seed systems. Further work is ongoing to incorporate SUB1 into more varieties and to strengthen the tolerance conferred by SUB1. Breeding varieties with multiple stresses is being accomplished by combining SUB1 with other tolerance traits/genes for wider adaptation in the less favourable rice ecosystems.
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response of SUB1 introgression lines of rice to various flooding conditions
Indonesian Journal of Agricultural Science, 2013Co-Authors: Yudhistira Nugraha, David J Mackill, Georgiana V Vergara, 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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application of marker assisted backcrossing to introgress the submergence tolerance qtl SUB1 into the vietnam elite rice variety as996
American Journal of Plant Sciences, 2012Co-Authors: Luu T N Huyen, Pham T M Hien, Vu T T Hang, Vu D Quang, A M IsmailAbstract:The result of the study contributes to enhancing and sustaining future livelihoods and food security in Vietnam vis-a-vis climate change. An innovative strategy based on marker-assisted backcrossing (MABC) was used to transform popular rice variety AS996 into the one can tolerate submergence while maintaining its original characteristics preferred by farmers and consumers. The submergence tolerance QTL SUB1 counts for up to 70% of the submergence tolerant and provides a marked improvement of submergence tolerance in all genetic backgrounds and environments tested so far. Parental diversity was carried out with 460 markers. Of which, 53 polymorphic markers were used for assessment on BC1F1, BC2F1 and BC3F1 generations. The best BC1F1 plant was P422 with highest recipient allele was 87.5%, while the additional chosen plants were P412, P428, P215 and P39 (81% - 84%). All these plants were used to develop BC2F1 generation. The six BC2F1 plants were used to develop BC3F1 and BC2F2 were the plants number P422-11 and P422-14 having 93.75% recipient alleles and P422-12, P422-3, P39-17, P39-25 having 92.25% recipient alleles. Total of 445 BC3F1 plants were confirmed the introgresion of SUB1 using ART5 and SC3. After three generations of backcrossing, application of MABC resulted in the best BC3F1 individual P422-14-177 with 100% of recipient alleles based on the number of 53 markers used with only the introgression size of SUB1 was 0.3Mb between ART5 and SC3. Phenotyping was carried out on BC3F1 and BC2F2 of the selected lines. The survival ratio of these selected lines and IR64SUB1 were the same. It convinced the successfully introgress SUB1 into AS996 rice variety. The breeding line BC4F1 having 100% genetic background of donor variety is ready for develop new submergence tolerant rice variety ASS996-SUB1 to cope with climate change.
Sudhanshu Singh - One of the best experts on this subject based on the ideXlab platform.
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improved early season management of SUB1 rice varieties enhances post submergence recovery and yield
Experimental Agriculture, 2018Co-Authors: Nino P M C Banayo, Sudhanshu Singh, Ranee C Mabesatelosa, Yoichiro KatoAbstract:More than 10 SUB1 rice varieties carrying the submergence-tolerance gene have been released for flood-prone environments in tropical Asia. Improved management practices have been shown to enhance yields of these varieties. The objective of this study was to dissect the growth response of IR64-SUB1 to integrated crop management in a flash flood at the late vegetative stage. Field experiments were conducted at the International Rice Research Institute, Philippines in the dry and wet seasons of 2013. Complete submergence was imposed for 14 days starting at 37 days after transplanting. Integrated management practice (IMP) consisting of: (i) application of fertilizer (compared with no fertilizer use in conventional practice), (ii) use of lower seeding rate (400 vs. 800 kg ha −1 ) in the nursery bed, (iii) use of slightly older seedling for transplanting (30 vs. 18 day-old), and (iv) higher planting density (33.3 vs. 25.0 hills m −2 ) gave yields higher by 8–87% compared with the conventional practice (1.3–2.4 t ha −1 ) in both seasons. This was attributable to higher shoot biomass after water recession, more tillers m −2 , greater leaf area expansion and shoot biomass accumulation during the recovery period, and higher filled-grain percentage at maturity. The improved management had no positive effect on panicle formation, spikelets panicle −1 , and harvest index since stress was imposed at the transition period between vegetative and reproductive phases. Our results suggest the appropriate nursery management, for submergence-resilient seedlings to further alleviate damage caused by flash floods and increase the yield of SUB1 varieties in flood-prone rainfed lowlands.
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improved management options for submergence tolerant SUB1 rice genotype in flood prone rainfed lowlands of west bengal
American Journal of Plant Sciences, 2014Co-Authors: Malay K Bhowmick, Sudhanshu Singh, Madhab C Dhara, U S SinghAbstract:Flash flood or submergence is a common phenomenon in rice growing rainfed lowland areas that seriously affects crop establishment leading to severe yield losses. A few submergence-tolerant rice varieties have been developed by introgressing SUB1 gene into mega rice varieties of South Asia. Two of these, Swarna-SUB1 and Sambha Mahsuri-SUB1, are already released in India for the commercial cultivation. Performance of these varieties can be further enhanced through adoption of appropriate management practices both in nursery and in main field. Two on-station field experiments were conducted using Swarna-SUB1 during the wet season (kharif) of 2011 at Rice Research Station, Chinsurah, Hooghly, West Bengal (India). Results of these experiments revealed that the use of lower seeding density (25 g m-2), application of balanced doses of N-P2O5-K2O @ 80-40-40 kg ha-1 in nursery and transplanting of aged seedlings (44 days) significantly improved plant survival, yield attributing traits and grain yield. An additional N-dose of 20 kg ha-1 at 7 days after receding of flood water resulted in better post-submergence recovery and maximum grain yield. In the on-farm trials conducted at three different locations in West Bengal, nursery raising of seedlings with the application of N-P2O5-K2O @ 80-40-40 kg ha-1, transplanting them at an optimum age (35 days) and application of 20 kg·N ha-1 after 7 days of de-submergence produced maximum grain yield of Swarna-SUB1.
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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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improved management options for submergence tolerant SUB1 rice genotype in flood prone rainfed lowlands of
2014Co-Authors: West Bengal, Sudhanshu Singh, Malay K Bhowmick, Madhab C Dhara, U S SinghAbstract:Flash flood or submergence is a common phenomenon in rice growing rainfed lowland areas that seriously af- fects crop establishment leading to severe yield losses. A few submergence-tolerant rice varieties have been de- veloped by introgressing SUB1 gene into mega rice varieties of South Asia. Two of these, Swarna-SUB1 and Sambha Mahsuri-SUB1, are already released in India for the commercial cultivation. Performance of these va- rieties can be further enhanced through adoption of appropriate management practices both in nursery and in main field. Two on-station field experiments were conducted using Swarna-SUB1 during the wet season (kharif) of 2011 at Rice Research Station, Chinsurah, Hooghly, West Bengal (India). Results of these experiments re- vealed that the use of lower seeding density (25 g m −2 ), application of balanced doses of N-P2O5-K2O @ 80-40-40 kg ha −1 in nursery and transplanting of aged seedlings (44 days) significantly improved plant survival, yield attributing traits and grain yield. An additional N-dose of 20 kg ha −1 at 7 days after receding of flood water re- sulted in better post-submergence recovery and maximum grain yield. In the on-farm trials conducted at three different locations in West Bengal, nursery raising of seedlings with the application of N-P2O5-K2O @ 80-40-40 kg ha −1 , transplanting them at an optimum age (35 days) and application of 20 kg·N ha −1 after 7 days of de-submergence produced maximum grain yield of Swarna-SUB1.
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the contribution of submergence tolerant SUB1 rice varieties to food security in flood prone rainfed lowland areas in asia
Field Crops Research, 2013Co-Authors: A M Ismail, David J Mackill, Sudhanshu Singh, U S SinghAbstract:Abstract Transient complete submergence reduces survival and yield on more than 20 million ha of rice in rainfed lowlands and flood-prone areas in Asia. Poverty and food insecurity are concomitant problems in these heavily populated areas, because of the high risks and the lack of high-yielding, flood-tolerant varieties. Rice landraces that can withstand over 2 weeks of complete submergence were identified and the gene (named SUB1) that controls most of the tolerance phenotype was cloned and characterized. This enabled the use of marker-assisted backcrossing (MABC) to transfer this gene into numerous varieties that are popular among farmers, five of which were recently released for commercial use in five countries in South and Southeast Asia. Varieties carrying the SUB1 gene developed through this process had the same agronomic, yield and quality traits as their non-SUB1 counterparts when grown under non-flooded conditions, but showed yield advantages of 1 to more than 3 t ha−1 after complete submergence for various durations in naturally flooded fields. Furthermore, SUB1 was found to be effective at all growth stages from early seedling stage to about a week before flowering. SUB1 varieties have been spreading fast in several countries over the last few years, and are currently grown by more than 4 million farmers in Asia. This success is attributed to several factors, including the choice of varieties that are popular among rainfed lowland farmers for deploying SUB1 and its consistent effectiveness in different genetic backgrounds and environments. Other factors are a far-reaching network of partners along the research to adoption continuum, an effective awareness programme targeting appropriate partners, policymakers and farmers, and the additional resources made available by international donors and national programmes primarily to support the production and distribution of good-quality seeds and for strengthening seed systems. Further work is ongoing to incorporate SUB1 into more varieties and to strengthen the tolerance conferred by SUB1. Breeding varieties with multiple stresses is being accomplished by combining SUB1 with other tolerance traits/genes for wider adaptation in the less favourable rice ecosystems.
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a novel plasmodium specific prodomain fold regulates the malaria drug target SUB1 subtilase
Nature Communications, 2014Co-Authors: Lina Tawk, Anthony Bouillon, David Giganti, Fabienne Robert, Mariano MartinezAbstract:Subtilase SUB1, a proteolytic enzyme required for the exit of malarial parasites from host cells, represents a promising target for anti-malarial drugs. Here, Giganti et al. report the structure of Plasmodium SUB1 and identify an essential domain involved in calcium-dependent activation of the enzyme.
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in silico screening on the three dimensional model of the plasmodium vivax SUB1 protease leads to the validation of a novel anti parasite compound
Journal of Biological Chemistry, 2013Co-Authors: Olivier Gorgette, Anthony Bouillon, David Giganti, Christophe Benedet, Stéphane Petres, Elodie Crublet, Christine GirardblancAbstract:Widespread drug resistance calls for the urgent development of new antimalarials that target novel steps in the life cycle of Plasmodium falciparum and Plasmodium vivax. The essential subtilisin-like serine protease SUB1 of Plasmodium merozoites plays a dual role in egress from and invasion into host erythrocytes. It belongs to a new generation of attractive drug targets against which specific potent inhibitors are actively searched. We characterize here the P. vivax SUB1 enzyme and show that it displays a typical auto-processing pattern and apical localization in P. vivax merozoites. To search for small PvSUB1 inhibitors, we took advantage of the similarity of SUB1 with bacterial subtilisins and generated P. vivax SUB1 three-dimensional models. The structure-based virtual screening of a large commercial chemical compounds library identified 306 virtual best hits, of which 37 were experimentally confirmed inhibitors and 5 had Ki values of <50 μm for PvSUB1. Interestingly, they belong to different chemical families. The most promising competitive inhibitor of PvSUB1 (compound 2) was equally active on PfSUB1 and displayed anti-P. falciparum and Plasmodium berghei activity in vitro and in vivo, respectively. Compound 2 inhibited the endogenous PfSUB1 as illustrated by the inhibited maturation of its natural substrate PfSERA5 and inhibited parasite egress and subsequent erythrocyte invasion. These data indicate that the strategy of in silico screening of three-dimensional models to select for virtual inhibitors combined with stringent biological validation successfully identified several inhibitors of the PvSUB1 enzyme. The most promising hit proved to be a potent cross-inhibitor of PlasmodiumSUB1, laying the groundwork for the development of a globally active small compound antimalarial.
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In Silico Screening on the Three-dimensional Model of the Plasmodium vivax SUB1 Protease Leads to the Validation of a Novel Anti-parasite Compound
Journal of Biological Chemistry, 2013Co-Authors: Anthony Bouillon, Olivier Gorgette, David Giganti, Christophe Benedet, Stéphane Petres, Elodie Crublet, Christine Girard-blanc, Benoit Witkowski, Didier Ménard, Michael NilgesAbstract:Widespread drug resistance calls for the urgent development of new antimalarials that target novel steps in the life cycle of Plasmodium falciparum and Plasmodium vivax. The essential subtilisin-like serine protease SUB1 of Plasmodium merozoites plays a dual role in egress from and invasion into host erythrocytes. It belongs to a new generation of attractive drug targets against which specific potent inhibitors are actively searched. We characterize here the P. vivax SUB1 enzyme and show that it displays a typical auto-processing pattern and apical localization in P. vivax merozoites. To search for small PvSUB1 inhibitors, we took advantage of the similarity of SUB1 with bacterial subtilisins and generated P. vivax SUB1 three-dimensional models. The structure-based virtual screening of a large commercial chemical compounds library identified 306 virtual best hits, of which 37 were experimentally confirmed inhibitors and 5 had Ki values of
