Journal articles 2006
Documents
Sequencing multiple and diverse rice varieties: Connecting whole-genome variation with phenotypes
McNally KL, Bruskiewich R, Mackill D, Leach JE, Buell CR, Leung H (2006). Sequencing multiple and diverse rice varieties: Connecting whole-genome variation with phenotypes. Plant Physiology 141(1):26–31. (DOI: 10.1104/pp.106.077313).
The International Rice Functional Genomics Consortium (IRFGC) has initiated a project to provide the rice research community with access to extensive information on genetic variation present within and between diverse rice cultivars and landraces, as well as the genetic resources to exploit that information. Among crop plants, rice is uniquely positioned to achieve this goal due to the release of a high-quality, whole-genome sequence; advances in the use of high-density arrays to compare complex genomes; and the availability of large collections of genetic materials rich in trait variation. In this project, the international rice research community will collaborate with Perlegen Sciences to identify a large fraction of the single nucleotide polymorphisms (SNPs) present in cultivated rice through whole-genome comparisons of 21 rice genomes, including cultivars, germplasm lines, and landraces.
McNally KL, Bruskiewich R, Mackill D, Leach JE, Buell CR, Leung H (2006). Sequencing multiple and diverse rice varieties: Connecting whole-genome variation with phenotypes. Plant Physiology 141(1):26–31. (DOI: 10.1104/pp.106.077313).
The International Rice Functional Genomics Consortium (IRFGC) has initiated a project to provide the rice research community with access to extensive information on genetic variation present within and between diverse rice cultivars and landraces, as well as the genetic resources to exploit that information. Among crop plants, rice is uniquely positioned to achieve this goal due to the release of a high-quality, whole-genome sequence; advances in the use of high-density arrays to compare complex genomes; and the availability of large collections of genetic materials rich in trait variation. In this project, the international rice research community will collaborate with Perlegen Sciences to identify a large fraction of the single nucleotide polymorphisms (SNPs) present in cultivated rice through whole-genome comparisons of 21 rice genomes, including cultivars, germplasm lines, and landraces.
Full article (
Gene expression microarrays and their application in drought stress research
Kathiresan A, Lafitte HR, Chen J, Mansueto L, Bruskiewich R, Bennett J (2006). Gene expression microarrays and their application in drought stress research. Field Crops Research 97(1):101–110. (DOI: 10.1016/j.fcr.2005.08.021). Not open access: view abstract
Kathiresan A, Lafitte HR, Chen J, Mansueto L, Bruskiewich R, Bennett J (2006). Gene expression microarrays and their application in drought stress research. Field Crops Research 97(1):101–110. (DOI: 10.1016/j.fcr.2005.08.021). Not open access: view abstract
Genetic variation in the sensitivity of anther dehiscence to drought stress in rice
Liu JX, Liao, DQ, Oane R, Estenor L, Yang XE, Li ZC and Bennett J (2006). Genetic variation in the sensitivity of anther dehiscence to drought stress in rice. Field Crops Research 97(1):87–100. (DOI: http://dx.doi.org/10.1016/j.fcr.2005.08.019). Not open access: view abstract
Liu JX, Liao, DQ, Oane R, Estenor L, Yang XE, Li ZC and Bennett J (2006). Genetic variation in the sensitivity of anther dehiscence to drought stress in rice. Field Crops Research 97(1):87–100. (DOI: http://dx.doi.org/10.1016/j.fcr.2005.08.019). Not open access: view abstract
Fenotipagem para tolerância à seca visando o melhoramento genético do trigo no cerrado
Ribeiro Júnior WQ, Ramos MLG, Vasconcelos U, Trindade MG, Ferreira FM, Siqueira MMH, da Silva HLM, Rodrigues GC, Guerra AF, Rocha OC, Amábile RF, Albuquerque AC, Só e Silva M, Albrecht JC and Durães FOM (2006). Fenotipagem para tolerância à seca visando o melhoramento genético do trigo no cerrado. Circular Técnica Online Embrapa Trigo 21. In Portuguese. Available online.
Ribeiro Júnior WQ, Ramos MLG, Vasconcelos U, Trindade MG, Ferreira FM, Siqueira MMH, da Silva HLM, Rodrigues GC, Guerra AF, Rocha OC, Amábile RF, Albuquerque AC, Só e Silva M, Albrecht JC and Durães FOM (2006). Fenotipagem para tolerância à seca visando o melhoramento genético do trigo no cerrado. Circular Técnica Online Embrapa Trigo 21. In Portuguese. Available online.
Access to plant genetic resources for genomic research for the poor: from global policies to target-oriented rules
Louwaars NP, Thörn E, Esquinas-Alcazar J, Wang S, Demissie A and Stannard C (2006). Access to plant genetic resources for genomic research for the poor: from global policies to target-oriented rules. Plant Genetic Resources 4(1):54–63. (DOI: http://dx.doi.org/10.1079/PGR2006112). Not open access: view abstract
Louwaars NP, Thörn E, Esquinas-Alcazar J, Wang S, Demissie A and Stannard C (2006). Access to plant genetic resources for genomic research for the poor: from global policies to target-oriented rules. Plant Genetic Resources 4(1):54–63. (DOI: http://dx.doi.org/10.1079/PGR2006112). Not open access: view abstract
Development of a composite collection for mining germplasm possessing allelic variation for beneficial traits in chickpea
Upadhyaya HD, Furman BJ, Dwivedi SL, Udupa SM, Gowda CLL, Baum M, Crouch JH, Buhariwalla HK, and Sube Singh (2006). Development of a composite collection for mining germplasm possessing allelic variation for beneficial traits in chickpea. Plant Genetic Resources 4(1):13–19. (DOI: http://dx.doi.org/10.1079/PGR2005101). Not open access: view abstract
Upadhyaya HD, Furman BJ, Dwivedi SL, Udupa SM, Gowda CLL, Baum M, Crouch JH, Buhariwalla HK, and Sube Singh (2006). Development of a composite collection for mining germplasm possessing allelic variation for beneficial traits in chickpea. Plant Genetic Resources 4(1):13–19. (DOI: http://dx.doi.org/10.1079/PGR2005101). Not open access: view abstract
Mapping QTLs and QTL-environment interaction for CIMMYT maize drought stress program using factorial regression and partial least squares methods
Vargas M, van Eeuwijk F, Crossa J and Ribaut J-M (2006). Mapping QTLs and QTL-environment interaction for CIMMYT maize drought stress program using factorial regression and partial least squares methods. Theoretical and Applied Genetics 112(6):1009–1023. (DOI: 10.1007/s00122-005-0204-z). Not open access: view abstract
Vargas M, van Eeuwijk F, Crossa J and Ribaut J-M (2006). Mapping QTLs and QTL-environment interaction for CIMMYT maize drought stress program using factorial regression and partial least squares methods. Theoretical and Applied Genetics 112(6):1009–1023. (DOI: 10.1007/s00122-005-0204-z). Not open access: view abstract
Sampling strategies for conserving diversity when forming core subsets using genetic marker
Franco J, Crossa J, Warburton M and Taba S (2006). Sampling strategies for conserving diversity when forming core subsets using genetic markers. Crop Science 46(2):854–864. (DOI: 10.2135/cropsci2005.07-0201). Not open access: view abstract
Franco J, Crossa J, Warburton M and Taba S (2006). Sampling strategies for conserving diversity when forming core subsets using genetic markers. Crop Science 46(2):854–864. (DOI: 10.2135/cropsci2005.07-0201). Not open access: view abstract
Identification of quantitative trait loci for resistance to Southern Leaf Blight and days to anthesis in a maize recombinant inbred line population
Balint-Kurti PJ, Krakowsky MD, Jines MP, Robertson LA, Molnár TL, Goodman MM and Holland JB (2006). Identification of quantitative trait loci for resistance to Southern Leaf Blight and days to anthesis in a maize recombinant inbred line population. Phytopathology 96:1067–1071. (DOI: 10.1094/PHYTO-96-1067).
A recombinant inbred line population derived from a cross between the maize lines NC300 (resistant) and B104 (susceptible) was evaluated for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O and for days to anthesis in four environments (Clayton, NC, and Tifton, GA, in both 2004 and 2005). Entry mean and average genetic correlations between disease ratings in different environments were high (0.78 to 0.89 and 0.9, respectively) and the overall entry mean heritability for SLB resistance was 0.89. When weighted mean disease ratings were fitted to a model using multiple interval mapping, seven potential quantitative trait loci (QTL) were identified, the two strongest being on chromosomes 3 (bin 3.04) and 9 (bin 9.03-9.04). These QTL explained a combined 80% of the phenotypic variation for SLB resistance. Some time-point-specific SLB resistance QTL were also identified. There was no significant correlation between disease resistance and days to anthesis. Six putative QTL for time to anthesis were identified, none of which coincided with any SLB resistance QTL.
Balint-Kurti PJ, Krakowsky MD, Jines MP, Robertson LA, Molnár TL, Goodman MM and Holland JB (2006). Identification of quantitative trait loci for resistance to Southern Leaf Blight and days to anthesis in a maize recombinant inbred line population. Phytopathology 96:1067–1071. (DOI: 10.1094/PHYTO-96-1067).
A recombinant inbred line population derived from a cross between the maize lines NC300 (resistant) and B104 (susceptible) was evaluated for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O and for days to anthesis in four environments (Clayton, NC, and Tifton, GA, in both 2004 and 2005). Entry mean and average genetic correlations between disease ratings in different environments were high (0.78 to 0.89 and 0.9, respectively) and the overall entry mean heritability for SLB resistance was 0.89. When weighted mean disease ratings were fitted to a model using multiple interval mapping, seven potential quantitative trait loci (QTL) were identified, the two strongest being on chromosomes 3 (bin 3.04) and 9 (bin 9.03-9.04). These QTL explained a combined 80% of the phenotypic variation for SLB resistance. Some time-point-specific SLB resistance QTL were also identified. There was no significant correlation between disease resistance and days to anthesis. Six putative QTL for time to anthesis were identified, none of which coincided with any SLB resistance QTL.
The genetic architecture of disease resistance in maize: a synthesis of published studies
Wisser RJ, Balint-Kurti PJ and Nelson RJ (2006). The genetic architecture of disease resistance in maize: a synthesis of published studies. Phytopathology 96(2):120–129. (DOI: 10.1094/PHYTO-96-0120).
Fifty publications on the mapping of maize disease resistance loci were synthesized. These papers reported the locations of 437 quantitative trait loci (QTL) for disease (dQTL), 17 resistance genes (R-genes), and 25 R-gene analogs. A set of rules was devised to enable the placement of these loci on a single consensus map, permitting analysis of the distribution of resistance loci identified across a variety of maize germplasm for a number of different diseases. The confidence intervals of the dQTL were distributed over all 10 chromosomes and covered 89% of the genetic map to which the data were anchored. Visual inspection indicated the presence of clusters of dQTL for multiple diseases. Clustering of dQTL was supported by statistical tests that took into account genome-wide variations in gene density. Several novel clusters of resistance loci were identified. Evidence was also found for the association of dQTL with maturity-related QTL. It was evident from the distinct dQTL distributions for the different diseases that certain breeding schemes may be more suitable for certain diseases. This review provides an up-to-date synthesis of reports on the locations of resistance loci in maize.
Wisser RJ, Balint-Kurti PJ and Nelson RJ (2006). The genetic architecture of disease resistance in maize: a synthesis of published studies. Phytopathology 96(2):120–129. (DOI: 10.1094/PHYTO-96-0120).
Fifty publications on the mapping of maize disease resistance loci were synthesized. These papers reported the locations of 437 quantitative trait loci (QTL) for disease (dQTL), 17 resistance genes (R-genes), and 25 R-gene analogs. A set of rules was devised to enable the placement of these loci on a single consensus map, permitting analysis of the distribution of resistance loci identified across a variety of maize germplasm for a number of different diseases. The confidence intervals of the dQTL were distributed over all 10 chromosomes and covered 89% of the genetic map to which the data were anchored. Visual inspection indicated the presence of clusters of dQTL for multiple diseases. Clustering of dQTL was supported by statistical tests that took into account genome-wide variations in gene density. Several novel clusters of resistance loci were identified. Evidence was also found for the association of dQTL with maturity-related QTL. It was evident from the distinct dQTL distributions for the different diseases that certain breeding schemes may be more suitable for certain diseases. This review provides an up-to-date synthesis of reports on the locations of resistance loci in maize.
