Journal articles 2006
Documents
Relationship between carbon isotope discrimination, ash content and grain yield in wheat in the Peninsular Zone of India
Misra SC, Randive R, Rao VS, Sheshshayee MS, Serraj R and Monneveux P (2006). Relationship between carbon isotope discrimination, ash content and grain yield in wheat in the Peninsular Zone of India. Journal of Agronomy and Crop Science 192(5):352–362. (DOI: 10.1111/j.1439-037X.2006.00225.x). Not open access: view abstract
Misra SC, Randive R, Rao VS, Sheshshayee MS, Serraj R and Monneveux P (2006). Relationship between carbon isotope discrimination, ash content and grain yield in wheat in the Peninsular Zone of India. Journal of Agronomy and Crop Science 192(5):352–362. (DOI: 10.1111/j.1439-037X.2006.00225.x). Not open access: view abstract
The Generation Challenge Programme (GCP): Standards for crop data
Bruskiewich R, Davenport G, Hazekamp T, Metz T, Ruiz M, Simon R, Takeya M, Lee J, Senger M, McLaren G, and van Hintum T (2006). The Generation Challenge Programme (GCP): Standards for crop data. OMICS: A Journal of Integrative Biology. 10(2):215–219.
The Generation Challenge Programme (GCP) is an international research consortium striving to apply molecular biological advances to crop improvement for developing countries. Central to its activities is the creation of a next generation global crop information platform and network to share genetic resources, genomics, and crop improvement information. This system is being designed based on a comprehensive scientific domain object model and associated shared ontology. This model covers germplasm, genotype, phenotype, functional genomics, and geographical information data types needed in GCP research. This paper provides an overview of this modelling effort.
Bruskiewich R, Davenport G, Hazekamp T, Metz T, Ruiz M, Simon R, Takeya M, Lee J, Senger M, McLaren G, and van Hintum T (2006). The Generation Challenge Programme (GCP): Standards for crop data. OMICS: A Journal of Integrative Biology. 10(2):215–219.
The Generation Challenge Programme (GCP) is an international research consortium striving to apply molecular biological advances to crop improvement for developing countries. Central to its activities is the creation of a next generation global crop information platform and network to share genetic resources, genomics, and crop improvement information. This system is being designed based on a comprehensive scientific domain object model and associated shared ontology. This model covers germplasm, genotype, phenotype, functional genomics, and geographical information data types needed in GCP research. This paper provides an overview of this modelling effort.
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SSR analysis of near isogenic lines (NILs) for P deficiency tolerance
Collard BCY, Thomson M, Penarubia M, Lu X, Heuer S, Wissuwa M, Mackill DJ and Ismail AM (2006). SSR analysis of near isogenic lines (NILs) for P deficiency tolerance. SABRAO Journal of Breeding and Genetics 38:131–138. Not open access: view journal website
Collard BCY, Thomson M, Penarubia M, Lu X, Heuer S, Wissuwa M, Mackill DJ and Ismail AM (2006). SSR analysis of near isogenic lines (NILs) for P deficiency tolerance. SABRAO Journal of Breeding and Genetics 38:131–138. Not open access: view journal website
Phylogenetic analysis based on ITS sequences and conditions affecting the type of conidial germination of Bipolaris oryzae
Dela Paz MAG, Goodwin PH, Raymundo AK, Ardales EY, Vera Cruz CM (2006). Phylogenetic analysis based on ITS sequences and conditions affecting the type of conidial germination of Bipolaris oryzae. Plant Pathology 55(6):756–765. (DOI: 10.1111/j.1365-3059.2006.01439.x).
One taxonomic characteristic of Bipolaris species is the bipolar germination of conidia, but conidia of Bipolaris oryzae, the causal pathogen of brown spot in rice, are regularly observed to show intercalary germination, a characteristic of Drechslera species. The effect of selection, culture media and culture age on type of conidial germination was determined for three brown spot isolates from Cavinti, San Pablo and Palawan in the Philippines, obtained from infected leaves showing typical disease symptoms. Based on the analyses of their ITS1, ITS2 and 5·8S rDNA nucleotide sequences, the local isolates were clearly identified as B. oryzae. Selection for colonies of the three isolates derived from single conidia with either bipolar or intercalary germination had no effect on the number of spores showing bipolar germination in subsequent cultures. Germination on seven different culture media was tested; of these, rabbit food agar and water agar increased the percentage of bipolar germination of conidia, although this varied between isolates. Incubation of the cultures of all three isolates for longer periods prior to harvesting conidia increased the percentage of bipolar-germinating conidia from c. 40 to c. 90% with 5-day-old and 30-day-old cultures, respectively.
Dela Paz MAG, Goodwin PH, Raymundo AK, Ardales EY, Vera Cruz CM (2006). Phylogenetic analysis based on ITS sequences and conditions affecting the type of conidial germination of Bipolaris oryzae. Plant Pathology 55(6):756–765. (DOI: 10.1111/j.1365-3059.2006.01439.x).
One taxonomic characteristic of Bipolaris species is the bipolar germination of conidia, but conidia of Bipolaris oryzae, the causal pathogen of brown spot in rice, are regularly observed to show intercalary germination, a characteristic of Drechslera species. The effect of selection, culture media and culture age on type of conidial germination was determined for three brown spot isolates from Cavinti, San Pablo and Palawan in the Philippines, obtained from infected leaves showing typical disease symptoms. Based on the analyses of their ITS1, ITS2 and 5·8S rDNA nucleotide sequences, the local isolates were clearly identified as B. oryzae. Selection for colonies of the three isolates derived from single conidia with either bipolar or intercalary germination had no effect on the number of spores showing bipolar germination in subsequent cultures. Germination on seven different culture media was tested; of these, rabbit food agar and water agar increased the percentage of bipolar germination of conidia, although this varied between isolates. Incubation of the cultures of all three isolates for longer periods prior to harvesting conidia increased the percentage of bipolar-germinating conidia from c. 40 to c. 90% with 5-day-old and 30-day-old cultures, respectively.
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.
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.
Development of a wheat fingerprinting database and assembling an SSR reference kit for wheat genetic diversity analysis
Li GY, Dreisigacker S, Warburton ML, Xianchun X, Zhonghu H and Qixin S (2006). Development of a wheat fingerprinting database and assembling an SSR reference kit for wheat genetic diversity analysis. Acta Agronomica Sinica 32(12):1771–1778. (URL: http://211.155.251.148:8080/zwxb/EN/Y2006/V32/I12/1771). Not open access: viewe abstract
Li GY, Dreisigacker S, Warburton ML, Xianchun X, Zhonghu H and Qixin S (2006). Development of a wheat fingerprinting database and assembling an SSR reference kit for wheat genetic diversity analysis. Acta Agronomica Sinica 32(12):1771–1778. (URL: http://211.155.251.148:8080/zwxb/EN/Y2006/V32/I12/1771). Not open access: viewe abstract
Low nitrogen tolerance in tropical quality protein maize (Zea mays L.): value of predictive traits
Monneveux P, Cabon G and Sanchez C (2006). Low nitrogen tolerance in tropical quality protein maize (Zea mays L.): value of predictive traits. Cereal Research Communications 34(4):1239–1246. (DOI: 10.1556/CRC.34.2006.4.264). Not open access: view abstract
Monneveux P, Cabon G and Sanchez C (2006). Low nitrogen tolerance in tropical quality protein maize (Zea mays L.): value of predictive traits. Cereal Research Communications 34(4):1239–1246. (DOI: 10.1556/CRC.34.2006.4.264). Not open access: view abstract
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.
Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping
Jayashree B, Reddy PT, Leeladevi Y, Crouch JH, Mahalakshmi V, Hutokshi, K Buhariwalla, Eshwar KE, Mace E, Folkertsma R, Senthilvel S, Varshney RK, Seetha K, Rajalakshmi R, Prasanth VP, Chandra S, Swarupa L, Srikalyani P and Hoisington DA (2006). Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping. BMC Bioinformatics 7:383. (DOI: 10.1186/1471-2105-7-383).
A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics.
Jayashree B, Reddy PT, Leeladevi Y, Crouch JH, Mahalakshmi V, Hutokshi, K Buhariwalla, Eshwar KE, Mace E, Folkertsma R, Senthilvel S, Varshney RK, Seetha K, Rajalakshmi R, Prasanth VP, Chandra S, Swarupa L, Srikalyani P and Hoisington DA (2006). Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping. BMC Bioinformatics 7:383. (DOI: 10.1186/1471-2105-7-383).
A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics.
