Journal articles 2007
Documents
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray
Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K et al (2007). Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS ONE 2(11): e1235. (DOI: 10.1371/journal.pone.0001235).
Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly.
Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K et al (2007). Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS ONE 2(11): e1235. (DOI: 10.1371/journal.pone.0001235).
Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly.
Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene
Karaba A, Dixit S, Greco R, Aharoni A, Trijatmiko KR, Marsch-Martinez N, Krishnan A, Nataraja KN, Udayakumar M and Pereira A (2007). Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene. Proceedings of the National Academy of Sciences of the USA 104:15270–15275 (DOI: 10.1073/pnas.0707294104).
Freshwater is a limited and dwindling global resource; therefore, efficient water use is required for food crops that have high water demands, such as rice, or for the production of sustainable energy biomass. We show here that expression of the Arabidopsis HARDY (HRD) gene in rice improves water use efficiency, the ratio of biomass produced to the water used, by enhancing photosynthetic assimilation and reducing transpiration. These drought-tolerant, low-water-consuming rice plants exhibit increased shoot biomass under well irrigated conditions and an adaptive increase in root biomass under drought stress.
Karaba A, Dixit S, Greco R, Aharoni A, Trijatmiko KR, Marsch-Martinez N, Krishnan A, Nataraja KN, Udayakumar M and Pereira A (2007). Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene. Proceedings of the National Academy of Sciences of the USA 104:15270–15275 (DOI: 10.1073/pnas.0707294104).
Freshwater is a limited and dwindling global resource; therefore, efficient water use is required for food crops that have high water demands, such as rice, or for the production of sustainable energy biomass. We show here that expression of the Arabidopsis HARDY (HRD) gene in rice improves water use efficiency, the ratio of biomass produced to the water used, by enhancing photosynthetic assimilation and reducing transpiration. These drought-tolerant, low-water-consuming rice plants exhibit increased shoot biomass under well irrigated conditions and an adaptive increase in root biomass under drought stress.
The rice genome encodes two vacuolar invertases with fructan exohydrolase activity but lacks the related fructan biosynthesis genes of the Pooideae
Ji XM, Van den Ende W, Schroeven L, Clerens S, Geuten K, Cheng SH and Bennett J (2007). The rice genome encodes two vacuolar invertases with fructan exohydrolase activity but lacks the related fructan biosynthesis genes of the Pooideae. New Phytologist 173:50–62 (DOI: 10.1111/j.1469-8137.2006.01896.x).
Fructans are believed to contribute to cold and drought tolerance in several plant families (Poaceae, Asparagaceae and Asteraceae), but it is not clear why the ability to accumulate these polymers is found in some genera (e.g. Triticum) but not in others (e.g. Oryza). As fructan biosynthesis enzymes (FBEs) evolved from vacuolar invertases (VINs), we searched the rice genome sequence for genes related to both FBE and VIN genes of wheat and other members of the Pooideae. We compared them at the levels of exon–intron structure, protein sequence, and the enzymatic properties of recombinant proteins after expression in the yeast
Pichia pastoris.
Ji XM, Van den Ende W, Schroeven L, Clerens S, Geuten K, Cheng SH and Bennett J (2007). The rice genome encodes two vacuolar invertases with fructan exohydrolase activity but lacks the related fructan biosynthesis genes of the Pooideae. New Phytologist 173:50–62 (DOI: 10.1111/j.1469-8137.2006.01896.x).
Fructans are believed to contribute to cold and drought tolerance in several plant families (Poaceae, Asparagaceae and Asteraceae), but it is not clear why the ability to accumulate these polymers is found in some genera (e.g. Triticum) but not in others (e.g. Oryza). As fructan biosynthesis enzymes (FBEs) evolved from vacuolar invertases (VINs), we searched the rice genome sequence for genes related to both FBE and VIN genes of wheat and other members of the Pooideae. We compared them at the levels of exon–intron structure, protein sequence, and the enzymatic properties of recombinant proteins after expression in the yeast
Pichia pastoris.
Are source and sinks strengths genetically linked in maize plants subjected to water deficit? A QTL study of the responses of leaf growth and Anthesis-Silking Interval to water deficit.
Welcker C, Boussuge B, Bencivenni C, Ribaut J-M and Tardieu F (2007). Are source and sinks strengths genetically linked in maize plants subjected to water deficit? A QTL study of the responses of leaf growth and Anthesis-Silking Interval to water deficit. Journal of Experimental Botany 58(2):339–349. (DOI: 10.1093/jxb/erl227).
Leaf growth and Anthesis–Silking Interval (ASI) are the main determinants of source and sink strengths of maize via their relations with light interception and yield, respectively. They depend on the abilities of leaves and silks to expand under fluctuating environmental conditions, so the possibility is raised that they may have a partly common genetic determinism. This possibility was tested in a mapping population which segregates for ASI. Maximum leaf elongation rate per unit thermal time (parameter a) and the slopes of its responses to evaporative demand and soil water status (parameters b and c) were measured in greenhouse and growth chamber experiments, in two series of 120 recombinant inbred lines (RILs) studied in 2004 and 2005 with 33 RILs in common both years.
Welcker C, Boussuge B, Bencivenni C, Ribaut J-M and Tardieu F (2007). Are source and sinks strengths genetically linked in maize plants subjected to water deficit? A QTL study of the responses of leaf growth and Anthesis-Silking Interval to water deficit. Journal of Experimental Botany 58(2):339–349. (DOI: 10.1093/jxb/erl227).
Leaf growth and Anthesis–Silking Interval (ASI) are the main determinants of source and sink strengths of maize via their relations with light interception and yield, respectively. They depend on the abilities of leaves and silks to expand under fluctuating environmental conditions, so the possibility is raised that they may have a partly common genetic determinism. This possibility was tested in a mapping population which segregates for ASI. Maximum leaf elongation rate per unit thermal time (parameter a) and the slopes of its responses to evaporative demand and soil water status (parameters b and c) were measured in greenhouse and growth chamber experiments, in two series of 120 recombinant inbred lines (RILs) studied in 2004 and 2005 with 33 RILs in common both years.
A Ds-insertion mutant of OSH6 (Oryza sativa Homeobox 6) exhibits outgrowth of vestigial leaf-like structures, bracts, in rice
Park SH, Kim CM, Je BI, Park SH, Park SJ, Piao HL, Xuan YH, Choe MS, Satoh K, Kikuchi S, Lee KH, Cha YS, Ahn BO, Ji HS, Yun DW, Lee MC, Suh SC, Eun MY and Han CD (2007). A Ds-insertion mutant of OSH6 (Oryza sativa Homeobox 6) exhibits outgrowth of vestigial leaf-like structures, bracts, in rice. Planta 227(1):1–12. (DOI: 10.1007/s00425-007-0576-1). Not open access: view abstract
Park SH, Kim CM, Je BI, Park SH, Park SJ, Piao HL, Xuan YH, Choe MS, Satoh K, Kikuchi S, Lee KH, Cha YS, Ahn BO, Ji HS, Yun DW, Lee MC, Suh SC, Eun MY and Han CD (2007). A Ds-insertion mutant of OSH6 (Oryza sativa Homeobox 6) exhibits outgrowth of vestigial leaf-like structures, bracts, in rice. Planta 227(1):1–12. (DOI: 10.1007/s00425-007-0576-1). Not open access: view abstract
Precise mapping of quantitative trait loci for resistance to southern leaf blight, caused by Cochliobolus heterostrophus race O, and flowering time using advanced intercross maize line
Balint-Kurti PJ, Zwonitzer JC, Wisser RJ, Carson ML, Oropeza-Rosas M, Holland JB and Szalma SJ (2007). Precise mapping of quantitative trait loci for resistance to southern leaf blight, caused by Cochliobolus heterostrophus race O, and flowering time using advanced intercross maize lines. Genetics 176(1):645–657. (DOI: 10.1534/genetics.106.067892). Not open access: view abstract
Balint-Kurti PJ, Zwonitzer JC, Wisser RJ, Carson ML, Oropeza-Rosas M, Holland JB and Szalma SJ (2007). Precise mapping of quantitative trait loci for resistance to southern leaf blight, caused by Cochliobolus heterostrophus race O, and flowering time using advanced intercross maize lines. Genetics 176(1):645–657. (DOI: 10.1534/genetics.106.067892). Not open access: view abstract
Stress-inducible expression of At DREB1A in transgenic peanut (Arachis hypogaea L.) increases transpiration efficiency under water-limiting condition
Bhatnagar-Mathur P, Devi MJ, Reddy DS, Lavanya M, Vadez V, Serraj R, Yamaguchi-Shinozaki K and Sharma KK (2007). Stress-inducible expression of At DREB1A in transgenic peanut (Arachis hypogaea L.) increases transpiration efficiency under water-limiting conditions. Plant Cell Reports 26(12):2071–2082. (DOI: 10.1007/s00299-007-0406-8). Not open access: view abstract
Bhatnagar-Mathur P, Devi MJ, Reddy DS, Lavanya M, Vadez V, Serraj R, Yamaguchi-Shinozaki K and Sharma KK (2007). Stress-inducible expression of At DREB1A in transgenic peanut (Arachis hypogaea L.) increases transpiration efficiency under water-limiting conditions. Plant Cell Reports 26(12):2071–2082. (DOI: 10.1007/s00299-007-0406-8). Not open access: view abstract
Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.)
Blair MW, Díaz JM, Hidalgo R, Díaz LM, Duque MC (2007). Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.). Theoretical Applied Genetics 116(1): 29–43. (DOI: 10.1007/s00122-007-0644-8). Not open access: view abstract
Blair MW, Díaz JM, Hidalgo R, Díaz LM, Duque MC (2007). Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.). Theoretical Applied Genetics 116(1): 29–43. (DOI: 10.1007/s00122-007-0644-8). Not open access: view abstract
Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification
Spooner DM, Nuñez J, Trujillo G, del Rosario Herrera M, Guzmán F and Ghislain M (2007). Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Proceedings of the National Academy of Sciences of the United States of America 104(49):19398–19403 (DOI: 10.1073/pnas.0709796104). View online
Spooner DM, Nuñez J, Trujillo G, del Rosario Herrera M, Guzmán F and Ghislain M (2007). Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Proceedings of the National Academy of Sciences of the United States of America 104(49):19398–19403 (DOI: 10.1073/pnas.0709796104). View online
Use of crop models to understand genotype by environment interactions for drought in real-world and simulated plant breeding trials
Chapman SC (2008). Use of crop models to understand genotype by environment interactions for drought in real-world and simulated plant breeding trials. Euphytica published online 4 December 2007. Also printed in 2008. (DOI: 10.1007/s10681-007-9623-z). Not open access: view abstract
Chapman SC (2008). Use of crop models to understand genotype by environment interactions for drought in real-world and simulated plant breeding trials. Euphytica published online 4 December 2007. Also printed in 2008. (DOI: 10.1007/s10681-007-9623-z). Not open access: view abstract
