Journal articles 2006
Documents
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.
Full article (
Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers
Díaz LM, Blair MW (2006). Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers. Theoretical and Applied Genetics 114(1):143–154. (DOI: 10.1007/s00122-006-0417-9). Not open access: view abstract
Díaz LM, Blair MW (2006). Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers. Theoretical and Applied Genetics 114(1):143–154. (DOI: 10.1007/s00122-006-0417-9). Not open access: view abstract
Models for navigating biological complexity in breeding improved crop plants
Hammer GL, Cooper M, Tardieu F, Welch S, Walsh B, van Eeuwijk F, Chapman SC, and Podlich D (2006). Models for navigating biological complexity in breeding improved crop plants. Trends in Plant Science 11(12):587–593. (DOI: 10.1016/j.tplants.2006.10.006). Not open access: view abstract
Hammer GL, Cooper M, Tardieu F, Welch S, Walsh B, van Eeuwijk F, Chapman SC, and Podlich D (2006). Models for navigating biological complexity in breeding improved crop plants. Trends in Plant Science 11(12):587–593. (DOI: 10.1016/j.tplants.2006.10.006). Not open access: view abstract
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
In silico insight into two rice chromosomal regions associated with submergence tolerance and resistance to bacterial leaf blight and gall midge
Kottapalli RK, Sarla N, Kikuchi S (2006). In silico insight into two rice chromosomal regions associated with submergence tolerance and resistance to bacterial leaf blight and gall midge. Biotechnology Advances 24(6):561–589. (http://dx.doi.org/10.1016/j.biotechadv.2006.05.003). Not open access: view abstract
Kottapalli RK, Sarla N, Kikuchi S (2006). In silico insight into two rice chromosomal regions associated with submergence tolerance and resistance to bacterial leaf blight and gall midge. Biotechnology Advances 24(6):561–589. (http://dx.doi.org/10.1016/j.biotechadv.2006.05.003). Not open access: view abstract
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
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.
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.
Microsatellite marker diversity in common bean (Phaseolus vulgaris L.)
Blair MW, Giraldo MC, Buendia HF, Tovar E, Duque MC, Beebe SE (2006). Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics 113(1):100–109. (DOI: 10.1007/s00122-006-0276-4). Not open access: view abstract
Blair MW, Giraldo MC, Buendia HF, Tovar E, Duque MC, Beebe SE (2006). Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics 113(1):100–109. (DOI: 10.1007/s00122-006-0276-4). Not open access: view abstract
