Journal articles 2007
Documents
Characterization of AtALMT1 expression in aluminium inducible malate release and its role for rhizotoxic stress tolerance in Arabidopsis thaliana
Kobayasi Y, Hoekenga OA, Ito H, Nakashima M, Saito S, Shaff JE , Maron LG, Piñeros MA, Kochian LV, Koyama H. 2007. Characterization of AtALMT1 expression in aluminium inducible malate release and its role for rhizotoxic stress tolerance in Arabidopsis thaliana. Plant Physiology 145: 843–852 (DOI:10.1104/pp.107.102335).
Malate transporters play a critical role in aluminium (Al) tolerance responses for some plant species, such as Arabidopsis (Arabidopsis thaliana). Here, we further characterize AtALMT1, an Arabidopsis aluminum-activated malate transporter, to clarify its specific role in malate release and Al stress responses. Malate excretion from the roots of accession Columbia was sharply induced by Al, which is concomitant with the induction of AtALMT1 gene expression.
Kobayasi Y, Hoekenga OA, Ito H, Nakashima M, Saito S, Shaff JE , Maron LG, Piñeros MA, Kochian LV, Koyama H. 2007. Characterization of AtALMT1 expression in aluminium inducible malate release and its role for rhizotoxic stress tolerance in Arabidopsis thaliana. Plant Physiology 145: 843–852 (DOI:10.1104/pp.107.102335).
Malate transporters play a critical role in aluminium (Al) tolerance responses for some plant species, such as Arabidopsis (Arabidopsis thaliana). Here, we further characterize AtALMT1, an Arabidopsis aluminum-activated malate transporter, to clarify its specific role in malate release and Al stress responses. Malate excretion from the roots of accession Columbia was sharply induced by Al, which is concomitant with the induction of AtALMT1 gene expression.
CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences
Chen X, Laudeman TW, Rushton PJ, Spraggins TA and Timko MP (2007). CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC Bioinformatics 8:129. (DOI: 10.1186/1471-2105-8-129).
Chen X, Laudeman TW, Rushton PJ, Spraggins TA and Timko MP (2007). CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC Bioinformatics 8:129. (DOI: 10.1186/1471-2105-8-129).
Bacteriophage lambda genomic library construction of Oryza sativa L. var. Pokkali
Rahman S, Masa-aki Ohto, Seraj S and Blumwald E (2007). Bacteriophage lambda genomic library construction of Oryza sativa L. var. Pokkali. Plant Tissue Culture and Biotechnology 17(2):149–159. (DOI: 10.3329/ptcb.v17i2.3235).
A major QTL called ‘Saltol’ on rice chromosome 1 has been identified as linked to salinity tolerance traits of the landrace, Pokkali. A genomic library of Pokkali rice variety was constructed in bacteriophage Lamda Fix II with 20 kb inserts. Plaques containing genes implicated to salt tolerance have been identified using probes homologous to S-Ad methionine synthetase (SAM) and cation chloride co-transporter after two rounds of hybridization. Clearly demarcated plaques of the two clones of interest have been lifted out for DNA isolation and subsequent characterization to be followed by subcloning into TAC vectors for Agrobacterium-mediated transformation of large genomic fragments into sensitive rice.
Rahman S, Masa-aki Ohto, Seraj S and Blumwald E (2007). Bacteriophage lambda genomic library construction of Oryza sativa L. var. Pokkali. Plant Tissue Culture and Biotechnology 17(2):149–159. (DOI: 10.3329/ptcb.v17i2.3235).
A major QTL called ‘Saltol’ on rice chromosome 1 has been identified as linked to salinity tolerance traits of the landrace, Pokkali. A genomic library of Pokkali rice variety was constructed in bacteriophage Lamda Fix II with 20 kb inserts. Plaques containing genes implicated to salt tolerance have been identified using probes homologous to S-Ad methionine synthetase (SAM) and cation chloride co-transporter after two rounds of hybridization. Clearly demarcated plaques of the two clones of interest have been lifted out for DNA isolation and subsequent characterization to be followed by subcloning into TAC vectors for Agrobacterium-mediated transformation of large genomic fragments into sensitive rice.
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.
Application of population genetic theory and simulation models to efficiently pyramid multiple genes via marker-assisted selection
Wang J, Chapman SC, Bonnett DG, Rebetzke GJ and Crouch J (2007). Application of population genetic theory and simulation models to efficiently pyramid multiple genes via marker-assisted selection. Crop Science 47(2):582–588. (DOI: 10.2135/cropsci2006.05.0341). View online
Wang J, Chapman SC, Bonnett DG, Rebetzke GJ and Crouch J (2007). Application of population genetic theory and simulation models to efficiently pyramid multiple genes via marker-assisted selection. Crop Science 47(2):582–588. (DOI: 10.2135/cropsci2006.05.0341). View online
An integrated pipeline of open source software adapted for multi-CPU architectures: use in the large-scale identification of single nucleotide polymorphisms
Jayashree B, Hanspal MS, Srinivasan R, Vigneshwaran R, Varshney RK, Naya S, Eshwar K, Ramesh N, Chandra S and Hoisington DA (2007). An integrated pipeline of open source software adapted for multi-CPU architectures: use in the large-scale identification of single nucleotide polymorphisms. Comparative and Functional Genomics 2007, Article ID 35604 7 pp7. (DOI: 10.1155/2007/35604).
The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets.
Jayashree B, Hanspal MS, Srinivasan R, Vigneshwaran R, Varshney RK, Naya S, Eshwar K, Ramesh N, Chandra S and Hoisington DA (2007). An integrated pipeline of open source software adapted for multi-CPU architectures: use in the large-scale identification of single nucleotide polymorphisms. Comparative and Functional Genomics 2007, Article ID 35604 7 pp7. (DOI: 10.1155/2007/35604).
The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets.
Ability of chromosome 4H to compensate for 4D in response to drought stress in a newly developed and identified wheat-barley 4H(4D) disomic substitution line
Molnár I, Linc G, Dulai SD Nagy E and Molnár-Láng M (2007). Ability of chromosome 4H to compensate for 4D in response to drought stress in a newly developed and identified wheat-barley 4H(4D) disomic substitution line. Plant Breeding 126(4):369–374. (DOI: 10.1111/j.1439-0523.2007.01300.x).
A spontaneously developed wheat–barley 4H(4D) disomic substitution line was identified cytogenetically using genomic in situ hybridization (GISH), multicolour fluorescent in situ hybridization (FISH) and microsatellite markers. The ability of the barley 4H chromosome to compensate for wheat 4D in response to mild drought stress was also investigated. In the barley cv. ‘Betzes’ and the 4H(4D) substitution line, mild osmotic stress induced intensive stomatal closure, resulting in reduced water loss through transpiration and unchanged relative water content in the leaves.
Molnár I, Linc G, Dulai SD Nagy E and Molnár-Láng M (2007). Ability of chromosome 4H to compensate for 4D in response to drought stress in a newly developed and identified wheat-barley 4H(4D) disomic substitution line. Plant Breeding 126(4):369–374. (DOI: 10.1111/j.1439-0523.2007.01300.x).
A spontaneously developed wheat–barley 4H(4D) disomic substitution line was identified cytogenetically using genomic in situ hybridization (GISH), multicolour fluorescent in situ hybridization (FISH) and microsatellite markers. The ability of the barley 4H chromosome to compensate for wheat 4D in response to mild drought stress was also investigated. In the barley cv. ‘Betzes’ and the 4H(4D) substitution line, mild osmotic stress induced intensive stomatal closure, resulting in reduced water loss through transpiration and unchanged relative water content in the leaves.
A model of sorghum photoperiodism using the concept of threshold-lowering during prolonged appetence
Dingkuhn M, Kouressy M, Vaksmann M, Clerget B and Chantereau J (2007). A model of sorghum photoperiodism using the concept of threshold-lowering during prolonged appetence. European Journal of Agronomy published online 23 July 2007. Also printed in 2008. (DOI: 10.1016/j.eja.2007.05.005). Not open access: view abstract
Dingkuhn M, Kouressy M, Vaksmann M, Clerget B and Chantereau J (2007). A model of sorghum photoperiodism using the concept of threshold-lowering during prolonged appetence. European Journal of Agronomy published online 23 July 2007. Also printed in 2008. (DOI: 10.1016/j.eja.2007.05.005). Not open access: view abstract
A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice
Bernier J, Kumar A, Ramaiah V, Spaner D and Atlin G (2007). A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Crop Science 47(2):505–516 (DOI: 10.2135/cropsci2006.07.0495). Not open access: view abstract
Bernier J, Kumar A, Ramaiah V, Spaner D and Atlin G (2007). A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Crop Science 47(2):505–516 (DOI: 10.2135/cropsci2006.07.0495). Not open access: view abstract
A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminium tolerance in sorghum
Magalhães JV, Liu J, Guimarães CT, Lana UGP, Alves VMC, Wang YH, Schaffert RE, Hoekenga OA, Piñeros MA, Shaff JE, Klein PE, Carneiro NP, Coelho CM, Trick HN and Kochian LV (2007). A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminium tolerance in sorghum. Nature Genetics 39(9):1156–1161 (DOI: 10.1038/ng2074). Not open access: view abstract
Magalhães JV, Liu J, Guimarães CT, Lana UGP, Alves VMC, Wang YH, Schaffert RE, Hoekenga OA, Piñeros MA, Shaff JE, Klein PE, Carneiro NP, Coelho CM, Trick HN and Kochian LV (2007). A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminium tolerance in sorghum. Nature Genetics 39(9):1156–1161 (DOI: 10.1038/ng2074). Not open access: view abstract
