2006 Research Publications

GCP Project Publications

1) Books
Ribaut J-M (2006). Drought adaptation in cereals. Haworth's Food Products Press, New York, USA, 642 pp. Abstract.

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2) Book chapters
Cooper M, van Eeuwijk F, Chapman SC, Podlich DW and Löffler C (2006). Genotype-by-environment interactions under water limited conditions. In: Drought adaptation in cereals (Ribaut J-M, ed.). Haworth's Food Products Press, New York, USA, pp. 51-96.

Davidson R,Manosalva  P, Vera Cruz C, Leung H, Leach J* (2006). Expression patterns of oxalate oxidase-like genes associated with blast resistance QTL on chromosome 8 of Oryza sativa. In: Biology of Plant-Microbe Interactions, Volume 5 (Proceedings of the 12th International Congress on Molecular Plant-Microbe Interactions, 14-19 December 2005, Yucatan, Mexico) (Sanchez F, Quiton C, Lopez-Lara I and Geiger O, eds).  IS-MPMI Press, Minneapolis, USA, pp 148-152.

Lafitte R, Bennett J and Kathiresan A (2006). Drought adaptation in rice. In: Drought adaptation in cereals (Ribaut J-M, ed). Haworth Food Products Press, New York, USA, pp 301-333.

Malosetti M, Ribaut J-M, Vargas M, Crossa J, Boer MP and van Eeuwijk FA (2006). Multi-trait multi-environment QTL modelling for drought stress adaptation in maize. In: Scale and Complexity in Plant Systems Research: Gene-Plant-Crop Relations (Spiertz JHJ, Struik PC, and van Laar HH, eds). Springer, Dordrecht, The Netherlands, pp 25-36. PDF

Tardieu F (2006). Leaf growth under water-limited conditions. In: Drought adaptation in cereals (Ribaut JM, ed). Haworth Food Products Press, New York, USA.

van Eeuwijk FA, Malosetti M and Boer MP (2006). Modelling the genetic basis of response curves underlying genotype x environment interaction. In: Scale and complexity in plant systems research: gene-plant-crop relations (Spiertz JHJ, Struik PC, and van Laar HH, eds). Springer, Dordrecht, The Netherlands, pp 115-126. PDF

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3) Journal articles 
Open Access

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). PDF

Franco J, Crossa J, Warburton M and Taba S (2006). Sampling strategies for conserving diversity when forming core subsets using genetic markers. Crop Science 46:854-864. Abstract

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). PDF

Islam MR, Gregorio GB , Collard BCY , Tumimbang-Raiz E, Adorada DL and Mendoza RD, Salam MA  and Hassan L (2006). Application to rice breeding population and haplotype diversity of molecular markers for salinity tolerance in chromosome 1. The Philippine Journal of Crop Science 31:17.

Islam MR, Faruquei MAB and Salam MA (2006). Genetic diversity in salt tolerant rice (O. sativa). Bangladesh Journal of Plant Breeding Genetics 19(1): 35-40. Article

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  Article. 

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 141:26-31. Article

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. PDF
 

Not Open Access
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 113:100–109.

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 10 (2):215-219.  PDF

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. PDF

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 114:43-54. 

Dwivedi, SL, Upadhyaya HD, Balaji  J, Buhariwalla HK, Blair MW, Ortiz R, Crouch JH and Serraj R (2006). Using genomics to exploit grain legume biodiversity in plant breeding.  Plant Breeding Reviews 26: 171-357.

Fregene M, Morante N, Sanchez T, Marin J, Ospina C, Barrera E, Gutierrez J, Guerrero J, Bellotti A, Santos L, Alzate A, Moreno S, and Ceballos H (2006). Molecular Markers for the Introgression of Useful Traits from Wild Manihot Relatives of Cassava; Marker-Assisted Selection of Disease and Root Quality Traits.  Journal of Root Crops 32 (1):1-31. - PDF

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 11:587-593.


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 97:101-110 (DOI: 10.1016/j.fcr.2005.08.021).

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. 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.

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 97:87-100. 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. Abstract

Miklas PN, Kelly JD, Beebe SE, Blair MW (2006). Common bean breeding for resistance against biotic and abiotic stresses: from classical to MAS breeding. Invited review paper for special issue on ‘Legume resistance breeding’. Euphytica 147:105-131. 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 34:1239-1246.

Monneveux P, Quillerou E, Sanchez C and Lopez-Cesati L (2006). Effect of zero tillage and residues conservation on continuous maize cropping in a subtropical environment (Mexico). Plant and Soil 279:95–105 (DOI: 10.1007/s11104-005-0436-3). 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 192:352-362 (DOI: 10.1111/j.1439-037X.2006.00225.x). Abstract

Singh M, Chabane K, Valkoun J and Blake T (2006). Optimum sample size for estimating gene diversity in wild wheat using AFLP markers. Genetic Resources and Crop Evolution 53 (1):23-33 (DOI: 10.1007/s10722-004-0597-6). 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 4:13-19. 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 112:1009-1023. 

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4) Workshop proceedings and published workshop papers
Alves A, Ceballos H, Fregene M, Ferguson M, and Setter T (2006). Identifying the physiological and genetic traits that make cassava one of the most drought tolerant crops. In: Proceedings of the GCP 2006 Annual Research Meeting: Generation Challenge Programme Competitive and Commisioned Research Project Mid-Year Reports. Mexico D.F.:Generation Challenge Programme. pp.9-10. - PDF

Alves AAC, Mendes RA, Fregene M,  Bellotti A (2006). Experiências em pré-melhoramento de mandioca: Utilização do potencial de espécies silvestres de mandioca como fonte de resistência a estresses bióticos e abióticos (Experiences in cassava pre-breeding: Potential utilization of cassava wild species as source for resistance to biotic and abiotic estresses). Curso Internacional de Pré-melhoramento de Plantas: Anais. Brasília: Embrapa Recursos Genéticos e Biotecnologia, 2006, pp.143-146. (184p. - Documentos / Embrapa Recursos Genéticos e Biotecnologia, 185). - PDF

Ambrus H, Soós V, Juhász A, Light ME, van Staden J, Balázs E, Barnabás B (2006): Effects of smoke compounds on in vitro germination of maize pollen. Paper presented at XIX International Congress on Sexual Plant Reproduction: from gametes to genes, 11-15 July 2006, Budapest, Hungary. Book of Abstracts. pp 112-113.

Bellotti A, Fregene M, and Alves A (2006). Development of low-cost technologies for pyramiding useful genes from wild relatives of cassava into elite progeniors. In: Proceedings of the GCP 2006 Annual Research Meeting:Generation Challenge Programme Competitive and Commisioned Research Project Mid-Year Reports. Mexico D.F.:Generation Challenge Programme. pp.24-28 - PDF

Gatdula KAI, Wissuwa M, Yano M, Lu X, Delhaize M, Schunmann P, Heuer S, and Ismail AM  (2006). Identification of candidate genes for phosphorus deficiency tolerance in rice. Proceedings of the 36th Crop Science Society of the Philippines Scientific Conference, 8-12 May 2006, Puerto Princesa, Palawan, Philippines.  The Philippines J. Crop Sci. 31(Supl. 1): p 44. PDF

Hribova, E., Macas, J., Dolezelova, M., Dolezel, J. (2006) The use of C0t analysis to characterize repeated part of the banana genome. – In: Abstracts of the Scientific Conference “Methods in Plant Sciences IV”. Bull. Czech. Soc. Exptl. Plant Biol. 6: 67, 2006.
Hribova, E., Macas, J., Dolezelova, M., Dolezel, J. (2006) Characterization of the highly repeated part of the banana genome. – In: Abstracts of the 5th Plant Genomics European Meetings. P. 205. The Italian Plant Genomics Network, Venice, 2006. 

Hurtado P, Marin J, Ospina C, Buitrago C, De Vicente C, Hearne S, Ferguson M, Alves A, Ferreira C, Wongtiem P, Killian A, and Fregene (2006).  Progress In Cassava Work And Delivery Plan. Proceedings of the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil.

Hurtado P, Rosero A, Buitrago C, and Fregene M (2006). Population structure, phenotypic information and association studies in long-generation crops: cassava update.  Proceedings of a workshop on Data Analysis, 16-20 October 2006, Zaragoza, Spain.

Islam MR, Salam MA, Hassan L, Collard BCY, Singh RK  and Gregorio GB (2006). QTL mapping for salinity tolerance of rice at seedling stage. In: Abstracts, 26th International Rice Research Conference and 2nd International Rice Congress held on October 9-13, 2006, New Delhi, India. p 171.

Islam MR, Gregorio GB, Salam MA , Collard BCY, Mohammadi-Nejad G,  Singh RK  and Hassan L (2006). Validation of SSR markers and haplotype diversity at the SalTol locus on chromosome 1 of rice. In: Abstracts, 26th International Rice Research Conference and 2nd International Rice Congress held on October 9-13, 2006, New Delhi, India. p 172.

Islam MR, Singh RK, Mohammadi-Nejad G, Salam MA, Hassan L and Gregorio GB (2006). Molecular diversity of stress tolerant rice genotypes using SSR markers. In: Abstracts, 26th International Rice Research Conference and 2nd International Rice Congress held on October 9-13, 2006, New Delhi, India. p 174.


Ismail AM, Gatdula KA, Heuer S, Lu X, and Wissuwa M (2006). Phosphorus deficiency tolerance in rice: genetic and molecular bases and implications for breeding. Paper presented at the Third International Symposium on Phosphorus dynamics in the Soil-Plant Continuum. pp. 121-122. 14-19 May 2006, Uberlândia, Minas Gerais, Brazil. pdf

Ismail AM, Gregorio G, Thomson M, Tumimbang E, Walia H, Blumwald E, Wilson C, Close T (2006). Salinity tolerance in rice: integration of QTL, expression analysis, and breeding. Proceedings of the Plant and Animal Genome Conference XIV, 14-18 Jan.uary 2006, San Diego, CA, USA. Abstract no. W262, http://www.intlpag.org/14/abstracts/PAG14_W262.html

Ismail AM, Wissuwa M, Gregorio G, Thomson M, Singh RK, Heuer S, and Mackill DJ (2006). Salinity, submergence and nutrient deficiency in rice: bases of tolerance and progress through breeding. Paper presented at Proc. 2st International Rice Congress, 9-13 October, 2006, New Delhi, India, p 15. PDF

Ismail AM, Wissuwa M, Gregorio GB, Thomson MJ, Singh RK, Heuer S and Mackill DJ (2007). Salinity, submergence, and nutrient deficiency in rice: bases of tolerance and progress through breeding. In: Science, Technology, and Trade for Peace and Prosperity. Aggrawal RK, Ladha JK, Singh RK, Devakumar C, Hardy B. (Eds). Proceedings of the 26nd International Rice Research Conference, 9-12 Oct 2006, New Delhi, India, Los Banos, Philippines. Macmillan India Ltd. pp 209-221. PDF

Mackill DJ, Collard BCY, Neeraja CN, Rodriguez RM, Heuer S, and Ismail AM (2006). QTLs in rice breeding: examples for abiotic stresses. In: Brar DS, Mackill DJ, Hardy B (eds). Rice genetics V,  Los Baños, Philippines, convened by International Rice Research Institute and Toh Tuck Link (Singapore): World Scientific Publishing. p 155-167. Abstract  PDF 

Malosetti M, Boer MP, Bink MCAM, van Eeuwijk FA (2006). Multi-trait QTL analysis based on mixed models with parsimonious covariance matrices.  In: Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, 13-18 August 2006, Belo Horizonte, MG, Brazil. ISBN:85-60088-00-8  PDF 

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5) Papers presented at workshops and conferences
Alves AAC, Fregene M, Ceballos H, Setter T, Ferguson M, Mkamilo G and Osei C (2006). Identifying the physiological and genetic traits that make cassava one of the most drought tolerant crops. Paper presented at the Annual Research Meeting of the Generation Challenge Programme, 12-16 September 2006, Caesar Business Hotel, São Paulo, Brazil. 

Azhar Mohamad and J.S. Heslop-Harrison  (2006). DNA and Genome Diversity in Bananas and Plantains (Musa). OECD meeting on Plant Domestication, Tsukuba, Japan October 2006

Bakry F, Baurens FC, Heslop-Harrison  J.S, Hippolyte I,  Matsumoto M, Miller R.G,  Rouard M, Roux N, Souza M, Sasaki T (2006). Targeted Musa Genome Sequencing and Frame Map Construction. GCP Annual Research Meeting, Sao Paulo, Brazil

Bennett J, Ji XM, Shobbar ZS, Raveendran M, Liao DQ, Liu JX, Dolferus R, Tuberosa R, Satoh K, Mauleon R, Kikuchi S, Bruskiewich R, Chandra Babu R, Ma ZQ (2006). Identifying genes responsible for failure of grain formation in rice and wheat under drought. Paper presented at the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil.

Billot C, Hash CT, Ramu P, Folkerstema RT, Upadhyaya HD, Rami J-F, Gardes L, Rivallan R, Deu M, Li Y, Wang T, Lu P (2006). Diversity analysis of the GCP sorghum composite germplasm set based on allelic variation at 41 SSR loci. Paper presented in the Annual meeting of Animal and Plant Genomics, 14-18 January 2006, San Diego, CA, USA. Presentation

Carrillo G, Ona I, Goodwin PH, Variar M, Leach J, Leung H, Vera Cruz C.  (2006). Integrating molecular, phenotypic and in silico approaches for quantitative resistance to rice blast. Paper presented at 6th IE Melhus Graduate Student Symposium, convened by the American Phytopathological Society, 29 July – 2 August 2006, Quebec City, Canada. PDF

Davidson RM, Manosalva P, Vera Cruz C, Leung H, Leach JE (2006). Expression patterns of oxalate oxidase-like genes associated with blast resistance QTL on chromosome 8 of Oryza sativa. Biology of Plant-Microbe Interactions: Proceedings of the 12th International Congress on Molecular Plant-Microbe Interactions, 14-19 December 2005, Merida Yucatan, Mexico.

Ferguson ME, D. Kiambi D, Kawuki R, Salih S, Hash T, and Hoisington D (2007). Tapping Crop Diversity for the Resource Poor in Eastern, Central and Southern Africa. Presented at the Third General Meeting on Biotechnology, Breeding & Seed Systems for African Crops, Rockefeller Foundation, 26-29 March 2007, Joaquim Chissano International Conference Centre, Maputo, Mozambique.  

Fregene M, Okogbenin E, Egesi C, Hurtado P, Santos L, Barrera E, Gutierrez J, Guerrero J, Carabali A, Parkes E, Baguma Y, Kawuki R, and Ceballos H (2007). Recent Advances in Genetic Improvement of Cassava. Paper presented at the 2007 GCP Annual Research Meeting, Benoni, South Africa, 12-16 September  2007. PDF

Hamilton RS, Sie M, Valkoun J, Upadhyaya HD, Mahalkshmi V (2006). The need for allele mining: perspectives of the System-wide Genetic Resources Programme (SGRP). Pages 67-68 in de Vicente M-C, Glaszmann, J-C (eds.) Molecular Markers in Allele Mining. Proceedings of a workshop, 22-26 August 2006, MS Swaminathan Reseach Foundation, Chennai, India. International Plant Genetic Resources Institute, Rome, Italy.

Heinemann AB, Luquet D, Dingkuhn M, Chapman S (2007). Análise da Estratégia de Melhoramento do Milho Safra em Função dos Estresses Hídricos para Goiás. In: 4 Congresso Brasileiro de Melhoramento de Plantas, 2007, São Lourenço. 4 Congresso Brasileiro de Melhoramento de Plantas.

Heinemann AB, Luquet D, Dingkuhn M, Chapman S (2007). Análise da Estratégia de Melhoramento do Arroz Ciclo em Função dos Estresses Hídricos para Goiás. In: 4 Congresso Brasileiro de Melhoramento de Plantas, 2007, São Lourenço. 4 Congresso Brasileiro de Melhoramento de Plantas.

Heinemann AB, Andrade CLT, Gomide, Albuquerque PEP, da Silva S C (2007). Determinação de padrões de estresse hídrico para a cultura do milho safra e safrinha no estado de Goiás. In: XV Congresso Brasileiro de Agrometeorologia, 2007, Aracaju. XV Congresso Brasileiro de Agrometeorologia. 

Hoekenga OE, Magalhaes JV and Kochian LV (2006). Interdisciplinary analysis of aluminum tolerance in maize. Root Genomics Workshop, Plant and Animal Genome XIV Meeting, January 18, 2006, San Diego, CA., USA.

Kikuchi S (2006). Outline and future plans of KOME & RED databases: Plant Ontology Workshop 30 May – 1 June 1 2006, Cornell University, Ithaca, New York, USA. PDF

Kochian LV and Magalhaes JV (2006) Physiological and molecular mechanisms of aluminum resistance in crops. Plenary talk at the CIAT-Embrapa sponsored workshop Advances in improving acid soil adaptation of tropical crops and forages, and management of acid soils, October 18-21, 2005, Brasilia, Brazil.

Kochian LV and Magalhaes, JV (2006). Isolation and Characterization of Aluminum Tolerance Genes in the Cereals: An Integrated Functional Genomic, Molecular Genetic and Physiological Analysis. Paper presented at 2006 Annual Research Meeting of the Generation Challenge Program, Sept 12-17, 2006, Sao Paolo, Brazil.

Kochian LV and Magalhaes, JV (2006). Using Genomic and Genetic Approaches to Elucidate Aluminum Resistance Genes and Mechanisms in Crop Plants. Plenary speaker at the International Symposium on Plant Nutrition meets Plant Breeding, Hohenheim University, Sept 25-28, 2006, Stuttgart, Germany.

Kochian LV and Magalhaes JV (2006). Molecular, genetic and physiological analysis of AltSB – A major aluminum tolerance gene recently identified in sorghum. Invited paper at the International Symposium in Memory of Vincent R. Francheschi, Washington State University, June 7-12, 2006, Pullman WA., USA.

Kochian LV and Magalhaes JV (2006). Molecular, genetic, and physiological analysis of Altsb - a major aluminum tolerance gene recently identified in sorghum. Invited paper at the 23rd Annual Missouri Symposium: Plant Roots: From Genes to Form and Function, at the University of Missouri, May 24-26, 2006, Columbia, MO., USA.

Kochian LV and Magalhaes JV (2006) High resolution mapping, cloning and characterization of a major aluminum tolerance gene using sorghum as a model system. Invited seminar to the Plant Biology Graduate Program Seminar Series, University of Massachusetts,. May 4, 2006, Amherst, MA., USA.

Kochian LV and Magalhaes JV (2006). Map-based cloning and characterization of Altsb, a major aluminum tolerance gene in sorghum. Abiotic Stress Workshp, Plant and Animal Genome XIV Meeting, January 18, 2006, San Diego, CA, USA.

Kumar A, Chamamerk V,  Haefele S, and Atlin G (2006). Germplasm development for drought-prone environments: Progress and implications for CNRM. Paper presented in the Natural Resource management workshop, 8-9 March 2006, organised by International Rice Research Institute, Philippines, Dhaka, Bangladesh. Paper

Leung H, Liu B, Mauleon R, Qiu F, Carrillo G, Vera Cruz C, Han SS, Roh J, Manosalva, P, Davidson R, Leach J, Satoh K, Kikuchi S (2006). Identifying favorable alleles in host defense genes for broad-spectrum resistance in rice. Paper presented at the International Rice Congress, 9-13 October 2006, New Delhi, India. PDF

Malosetti M, Ribaut J-M, Vargas M, Crossa J, Boer MP and van Eeuwijk FA (2006). Multi-trait multi-environment QTL modelling for drought stress adaptation in maize. Paper presented at workshop Scale and Complexity in Plant Systems Research: Gene-Plant-Crop Relations, 23-26 April 2006, convened by Frontis, Wageningen, The Netherlands. Paper

Malosetti M, Ribaut J-M, Vargas M, Crossa J and van Eeuwijk FA (2006). Multi-trait QTL mixed modelling with an application to drought stress in maize. Paper presented at XIII Meeting of the Biometrics in Plant Breeding Section of Eucarpia, 30 August – 1 September 2006, Zagreb, Croatia. Proceedings

Mathews KL, van Eeuwijk FA, Reynolds M, McIntyre L, Shorter R and Chapman SC (2006). Multi-environment QTL mixed models for drought stress adaptation in wheat. Paper presented at Australasian Genstat/StatGen Conference, 5-8 December 2006, Victor Harbor, Australia. 
Senthilvel S, Baskaran K, Hoisington D, Upadhyaya HD, Hash CT (2006). SSRs and sampling strategy for genotyping heterogeneous pearl millet germplasm accessions. Paper presented in the Annual meeting of Animal and Plant Genomics, 14-18 January 2006, San Diego, CA, USA

Satoh K, Doi K, Nagata T, Hosaka A, Suzuki K, Ji X, Raveendran M, Leung H, Bennett J, Kikuchi S (2006). Gene expression analysis and data mining from the microarray analysis applied to the drought stress in rice. Drought Frontier Project Planning Workshop, 2-6 October 2006, IRRI,  Los Baños, Philippines. PDF

Takeya M, Suzuki K, Doi K, Kikuchi S, and Bruskiewich R (2006). Development of a platform for functional genomics under the Generation Challenge Program (GCP) The Seventeenth International Conference on Genome Informatics 2006 ():P095-1-2.

Upadhyaya HD, Baum M, Buhariwalla HK, Udupa SM, Furman BJ, Dwivedi SL, Hoisington DH, Gaur PM, Chandra S, Gowda CLL, Crouch JH, Valkoun J (2006). Mining Chickpea Composite Collection for Allelic Variation. Page 25 in de Vicente, M-C, Glaszmann J-C (eds.) Molecular Markers in Allele Mining. Proceedings of a workshop, 22-26 August 2006, MS Swaminathan Reseach Foundation, Chennai, India. International Plant Genetic Resources Institute, Rome, Italy.

van Eeuwijk FA, Malosetti M and Boer MP (2006) Modelling the genetic basis of response curves underlying genotype x environment Interaction. Paper presented at workshop Scale and Complexity in Plant Systems Research: Gene-Plant-Crop Relations, convened by Frontis, 23-26 April 2006, Wageningen, The Netherlands.   Presentation  Paper

van Eeuwijk FA (2006). An eco-physiological – statistical framework for the analysis of GxE and QTLxE as occurring in abiotic stress trials, with applications to the CIMMYT drought stress programs in tropical maize and bread wheat. Paper presented at the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil. 

Vera Cruz CM, Cho YC,  Kim BR,  Hong YK,  Kim YH, Yoon DW, Jung KH., Lee JY, Lee SW, Manosalva P, Davidson R, Leach JE, Leung H (2006). Functional genomics approach to identification of broad-spectrum resistance genes against rice blast. Paper presented at the RDA-IRRI Biennial Meeting, 26-27 April 2006, Suwon, Korea.  

Vera Cruz CM, Mercado EFL, Reveche MYV, Chen J, Skinner DJ, Carrillo MGC, Collard BCY, Bernardo M, William M, and Xu Y (2006). Development of low-cost gene-based trait assay technologies in cereals. Paper presented at the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paolo, Brazil.

Warburton M, Dreisigacker S, Crossa J, Franco J, and Taba S (2006). Determination of population structure of the CIMMYT maize collection. Paper presented during the ‘Closing the Circle on Plant Genetic Resources Conservation and Utilization: I’ Symposium at the ASA–CSSA–SSA Annual Meetings, 12–16 November 2006, Indianapolis, USA.
 http://a-c-s.confex.com/crops/2006am/techprogram/P23305.HTM


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6) Working Papers and discussion papers
Warburton M (2006). Invited Speaker, “Closing the Circle” symposium on the use of germplasm collections, ASA-CSSA-SSA Annual Meetings, November 12 – 16, 2006, Indianapolis, USA

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7) Briefs, booklets and brochures  

There were no briefs, booklets or brochures in 2006.
 
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8). Learning materials and other resources

There were no learning materials or related resources in 2006.


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9). Posters
Alves AAC, Fregene M, Ceballos H, Setter, T, Duque L, Silva A, Ferguson M, Mkamilo G, Osei C (2006). Identifying the physiological and genetic traits related to drought tolerance in cassava. Poster presentation at the 2006 GCP Annual Research Meeting, Sao Paulo, Brazil, 12-16 September 2006. - PDF

Balint-Kurti P, Zwonitzer J, and Baesman R (2006).  Analysis of Disease Resistance Loci in Maize.  Presented at the Maize Genetics meeting, March 9-12, 2006, Pacific Grove, CA, USA. - PDF

Banu SP, Miah B, Ali A, Brar D, and Vera Cruz CM (2006). New sources identified for resistance to brown spot disease in rice. Poster presented at the International Rice Congress, October 2006, New Delhi, India. - PDF

Bennett J, Ishitani M, Vadez V (2006). Evaluation and deployment of transgenic drought-tolerant varieties (SP3-19). Poster presented at the 2005 GCP Annual Research Meeting 29 September - 1 October 2005, Rome, Italy.

Bennett J, Ishitani M, Vadez V, Reynolds M (2006). Evaluation and deployment of transgenic drought-tolerant varieties (SP3-19). Poster presented at the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil.

Bennett J, Shobbar ZS, Raveendran M, Ji XM (2006). Identifying Genes Responsible for Failure of Grain Formation in Rice and Wheat under Drought (SP2-1). Poster presented at the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil.

Billot C, Deu M , Rami J-F Rivallan, Hash CT, Ramu P, Folkertsma RT, Bantte K, Upadhyaya HD, Li Y, Fonceka D (2006). Insight into genetic diversity analysis of sorghum biocolor- use of SSR markers. Poster presented in the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil - PDF

Bruskiewich R, Davenport G, Hazekamp T, Metz T, Ruiz M, Simon R, Takeya M, Lee J, Senger M, and McLaren G (2006). Development and Application of Generation Challenge Programme Domain Models, Plant & Animal Genome XIV Conference, 14–18 January 2006, San Diego, California, USA - Abstract   Full Poster (PDF)

Carrillo G, Ona I, Lestari P, Qui F, Goodwin P, Variar M, Bustamam M, Leach J, Nelson R, Leung H, Vera Cruz C (2006). QTLs meet genomics: targeting superior disease QTL alleles in the rice genome. Poster presented at the 2006 GCP-Annual Research Meeting, 12-16 September 2006, Sao Paolo, Brazil. - PDF

Choumane W, Zhag J, Valkoun J, Hang C, Baum M  (2006). Assessment of genetic Diversity in a composite germplasm set of barley and the development of a core collection.  Presented at the 2006 GCP Annual Research Meeting, 12-16 September, Sao Paulo, Brazil. Abstract

Conte M, Gaillard S, Périn C (2006). GREENPHYL: An optimized phylogenomic pipeline for Ortholog prediction between two model plant species Arabidopsis thaliana and Oryza sativa. 14th Annual International Conference on Intelligent Systems in Molecular Biology (ISMB), 6-10 August, Fortaleza, Brazil – PDF

Crossa Franco JJ, Dreisigacker S, Li Yu, Menkir A, Hearne S, Mahalakshmi V,. Charcosset A, and Warburton M (2006). Developing a Useful Subset of the Maize GCP Composite Genotype Set.  GCP Annual Research Meeting 2006, 12-16 September 2006, Sao Paulo, Brazil. Poster

Doi K, Nagata T, Satoh K, Suzuki K, Iizumi S, Kimura S, Hosaka A, Kikuchi S (2006). Analysis of relationship between upstream element of genes and expression data profile from microarray analysis: An attempt to find cis-elements by combining method of motif searching and data mining. The 8th International Congress of Plant Molecular Biology, 20-25 August 2006, Adelaide, Australia - PDF

Doi K, Nagata T, Satoh K, Suzuki K, Iizumi S, Kimura S, Hosaka A, Kikuchi S (2006). Development of a data mining tool to find cis-elements concerning in gene expression detectable by microarray analysis. 20th IUBMB International Congress of biochemistry and molecular biology and 11th FAOBMB Congress, 18-23 July 2006, Kyoto, Japan -  PDF

Dreisigacker S, Kishii M, Lage J, and Warburton M (2006).  Use of synthetic hexaploid wheat to increase diversity for CIMMYT bread wheat improvement.  1st Synthetic Wheat Symposium, Brisbane, Australia.

Egesi C, Okogbenin E, Ekpe E, Uyovbisere E, Oselebe H, Aduramigba-Modupe V,  Osunde A, Fregene M (2006). A partnership with improved cassava germplasm comes to the aid of poor farmers in Nigeria. Poster presented at CGIAR Annual Research Meetimg, 3-5 December 2006, Innovationa Marketplace, Washington D.C, USA. PDF

Egesi C, Sanchez T, Morante N, Ospina C, Ceballos H and Fregene M (2006). Identification of delayed PPD in an inter-specific hybrid of cassava and a wild relative Manihot walkerae. Poster presented at the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil. PDF

Ferguson M, Dumet D, Hurtado P, Duque MC, Mkumbira J, and Fregene M (2006). Cassava Reference Set Selection and Preparation for Cassava Mapping. GCP SP1: 2006 (Commissioned Research Project. Poster presented at the 2006 GCP Annual Research Meeting, 12 - 16 September 2006, Sao Paulo, Brazil - PDF

Furman BJ, Baum M, Hamwieh A, and Jung C (2006). Developmnet of a composite collection of lentil and its molecular characterisation. Presented at the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil. Abstract

Furman BJ, Baum M, Hamwieh A, Suso MJ, and Duc G (2006). Development of a composite collection and the genotyping of a tier 2 (orphan) crop: Faba bean. Presented at the 2006 GCP Annual Research Meeting,  12-16 September 2006, Sao Paulo, Brazil.

Gatdula KA, Lu X, Yano M, Wissuwa M, Chua T, Ismail AM. Candidate genes in the Pup1 locus for tolerance to phosphorus deficiency. The 8th international Congress of Plant Molecular Biology, August 20-25, 2006, Adelaide, Australia. Abstract No. POS-TH-236. p 135 Abstract

Hazekamp T, Bink M, Chandra S, Davenport G, Endresen D, Gaiji S, Simon R, Sood R and Skofic M (2006). Management of the GCP Central Registry, 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paolo, Brazil. - PDF 

Heinemann AB, Dingkuhn M, Chapman SC, Luquet D, Combres JC, De Raissac M, and Lafarge T (2006). Determination of drought critical periods for upland rice in Brazilian savannahs. International Rice Research Congress, India October 2006 – PDF

Hoisington DA, Jayashree B, Ferguson M, and Hearne S, de Villiers E,  de Villiers S,  and Kiambi D (2006). Installation and implementation of ICRISAT LIMS at Biosciences Eastern and Central Africa (BecA) facility and IITA-Ibadan. SP4, Commissioned Resarch Project No. 1d 34. Poster presented at Generation Challenge Program Annual Research Meeting, Sao Paulo, Brazil, 12– 16 September 2006. - PDF 

Hoisington D, Ferguson M, Kiambi D, Hash T, de Villiers S, Kawuki R, and Salih S (2006). Tapping Crop Diversity for the Resource Poor in Eastern, Central and Southern Africa. GCP SP1: 2005 (Commissioned Research Project (2005-2008). Poster presented at the 2006 GCP Annual Research Meeting, Sao Paulo, Brazil. - PDF

Hoisington D, Upadhyaya HD, Dwivedi SL, Baum M, Udupa SM, Furman BJ, Chandra S, Eswar K, Gowda CLL, Singh S, Prasanth VP (2006). Genotypic and phenotypic variation in the global collection of chickpea (Cicer aritinum L.). Paper presented in the 3rd International Conference on Legume Genomics & Genetics, 9-13 April 2006, Brisbane, Queensland, Australia. PDF  Abstract

Hurtado P, de Vicente C, and Fregene M (2006). Validation of Diversity Arrays Technology (DArT) as a Platform for Whole Genome Profiling in Orphan Crops. Poster presentation at the 2006 GCP Annual Research Meeting,   Annual General Meeting, 12-16 September 2006 Sao Paulo, Brazil.

Malosetti M, Mathews KL, Ribaut J-M, Reynolds MP, Crossa J, Chapman SC and van Eeuwijk FA (2006). Multi-environment (multi-trait) QTL mapping using mixed models. Applications to drought stress trials in maize and wheat. Presented at the 2006 GCP Annual Research Meeting, 12-16 September, 2006, São Paulo, Brazil submitted by van Eeuwijk FA – PDF

Manzano R, Macatangay M, Redondo M, Lacorte V, Zaidem M, Detras J, Barile M, Pabale D, Hamilton NRS, Benoit L, Rivallan R, Courtois B, Billot C, Garavito A, Lorieux M, Martinez CP, Borba T, Brondani RV, Brondani C, Cissoko M, Ndjiondjop MN, Famoso A, McCouch SR, Zhang YY, Han LZ, and McNally KL (2006). Population structure of the rice composite set. Poster presented at 9th National Genetics Symposium, 25-28 October 2006, Benguet State University, La Trinidad, Benguet, Philippines – PDF

Mercado EFL, Reveche MYV, Chen J, Skinner DJ, Carrillo MGC, Collard BCY, Bernardo M, William M, Xu Y, and Vera Cruz CM (2006). Development of gene-based marker technologies for high throughput genotyping. Poster presented at the 2006 GCP Annual Research Meeting, Sao Paolo, 12-16 September 2006, Brazil. - PDF

Metz T, Bruskiewich R, Mendoza MJ, Davenport G, Simon R (2006). GCP Software Engineering and Collaboration Platform. Poster presented in the Generation Challenge Program Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil - PDF

Nakhoda B, Leung H, Egdane J, Ismail AM (2006).  Isolation and characterization of rice mutant lines with altered responses to salt stress. The 36th Crop Science Conference of the Philippines, 8-12 May 2006, Puerto Princesa City, Palawan, Philippines. PDF

Nakhoda B, Leung H, Egdane J, Ismail AM (2006).  Morphological, physiological and biochemical evaluation of IR64 mutant lines under saline and normal conditions. The 2nd International Rice Congress, 9-13 October 2006, New Delhi, India. PDF

Naredo MEB, Gamalinda MB, Atienza GA, Melgar RJA, and McNally KL (2006). EcoTILLING: a technique for detecting natural variation and a diagnostic tool for biosystematic studies in Oryza. Poster presented at 9th National Genetics Symposium, 25-28 October 2006, Benguet State University, La Trinidad, Benguet, Philippines –  PDF

Philippe R, Courtois B, Billot C, Rami JF, Brunel D, Mournet P, This D (2006). ADOC : allelic diversity of orthologous candidate genes for drought tolerance in crops : example of the ASR gene family. Poster presentation at Plant Gems, 18-21 october 2006,Venize, Italy. PDF

Poland JA, Wisser RJ, Kresovich S, and Nelson RJ (2006). Recurrent Selection Mapping in Two Maize Populations Suggests that Some Common Loci are Associated with Northern Leaf Blight Selection.  Maize Genetics Conference, Pacific Grove, CA; March 9-12, 2006. - PDF

Poland JA, Wisser RJ, and Nelson RJ (2006). Selection Mapping in Two Maize Populations Improved for Northern Leaf Blight Resistance. International Plant Breeding Symposium, 20-25 August, 2006, Mexico City, Mexico. - PDF

Raghavan C, Liu B , Leach JE , Nelson RJ, McNally K, Leung H (2006). Application of a simple SNP detection method for mapping and association studies. Poster (abstract P186) presented at the Plant & Animal Genome XIV Conference, 14-18 January 2006, San Diego, CA, USA – PDF

Ramírez S, Dreisigacker S, Taba S, Charcosset A, Warburton M (2006).  Genetic Characterization of Maize Landraces from Central and South America.  GCP Annual Research Meeting 2006, 12-16 September 2006, Sao Paulo, Brazil,

Reveche MYV, Mercado EFL, Chen J, Collard BCY, Bernardo M, Skinner DJ, Wu J, Redoña E, Kadirvel P, Bustamam M, Verdier V, William M, Vera Cruz CM (2006). Development of non gel-based, high-throughput, and low-cost technologies for marker-assisted selection in rice. Poster presented during the 32nd Scientific Meeting of the Crop Science Society of the Philippines (CSSP), 8-12 May 2006 Palawan, Philippines-  PDF

Reveche  MYV, Mercado EFL, Skinner DJ, Carrillo  MGC, Collard BCY, William M, Xu Y, and Vera Cruz CM (2006). Dot blot assay technology: Low cost, non gel-based, high throughput technology for marker-assisted selection in cereals. Poster presented at the 2006 GCP Annual Research Meeting, 12-16 September, Sao Paolo, Brazil. - PDF

Simo H, von Korff M, Ghannam Z, Choumane W, Hamwieh A, Sayed H, Udupa S, Baum M, and Akintunde A (2006). ICARDA generation GLIMS and GeMS.  Presented at the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil.

Singh M, Guo P, and Baum M (2006). Estimating Confidence Limits for Differential Expression OF Genes Based on Control Experiments. Presented at GCP, ARM 2006, Sao Paulo. submitted by M. BAUM – Report (PDF)   Poster (PDF)

This D, Courtois B, Billot C, Rami JF, Philippe R, Bonierbale M, Simon R, Schaftleitner R, Brunel D, Mournet P, McNally P, Baum M, Coumane W, Hash CT, Varshney RK, Hoisington D, Nayak S, Blair T, Upadyaya H, Fregene M, Bennet J, Ji X, Dingkuhn M, Masle J, Zivy M, Falque M, Setter T (2006). ADOC : allelic diversity of orthologous candidate genes. Poster presentation at the Annual research meeting of the Generation Challenge Program, 12-16 september 2006, Sao Paulo, Brasil. Poster

Thomson MJ, Gregorio G, Singh RK, de Ocampo M, Egdane J, Katimbang M, Tumimbang E, Walia H, Blumwald E, Wilson C, Seraj Z, Close TJ, and Ismail AM (2006).  QTL Mapping, Candidate Gene Analysis, and Marker-assisted Backcrossing for Improved Salinity Tolerance in Rice.  Presented at the 2006 GCP Annual Research Meeting, 12-16 September 2006, Sao Paolo, Brazil. PDF

Upadhyaya HD, Bhattacharjee R, Hoisington DA, Chandra S, Varshney RK, Reddy KN, Saxena KB (2006). Molecular characterization of pigeonpea [Cajanus cajan (L.) Millspaugh] composite collection. Poster presented in the Generation Challenge Program Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil - PDF

Upadhyaya HD, Bhattacharjee R, Hoisington DA, Chandra S, Varshney RK, Singh S, Valls JFS, Moretzsohn ,  MC, Leal-Bertioli S, Patricia Guimarăes, David Bertioli (2006). Molecular characterization of groundnut (Arachis hypogaea L.) composite collection. Poster presented in the Generation Challenge Program Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil - PDF

Upadhyaya HD, Hash CT, Senthilvel S, Varshney RK, Hoisington DA, Rai KN, Reddy KN, Thakur RP, Chandra S (2006). Development of composite collection and genotyping of pearl millet  [Pennisetum glaucum (L.) R. Br.]. Poster presented in the Generation Challenge Program Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil - PDF

Upadhyaya HD, Hoisington DA, Dwivedi SL, Baum M, Udupa SM, Furman BJ, Chandra S,  Eshwar K, Gowda CLL, Singh S,. Prasanth V (2006). Genotypic and Phenotypic Variation in the Global Collection of Chickpea (Cicer arietinum L.). Poster presented in the Generation Challenge Program Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil - PDF

Upadhyaya  HD, Varshney RK, Hash CT, Hoisington DA, Gowda CLL, Reddy VG, Chandra S, Lalitha, N, Bharthi A. (2006). Development of composite collection and genotyping of foxtail millet  [Setaria italica (L.) Beauv.] composite collection. Poster presented in the Generation Challenge Program Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil - PDF

Upadhyaya  HD, Varshney RK, Hoisington DA, Gowda CLL, Hash CT, Reddy VG, Chandra S, Bharathi A, Lalitha N (2006). Genotyping composite collection of finger millet [Eleusine coracana (L.) Gaertn]. Poster presented in the Generation Challenge Program Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil - PDF

Vadez V., Jyotsna  Devi M., Bhatnagar-Mathur P., Serraj R., Sharma K.K.. Evaluation and Deployment of Transgenic Drought-Tolerant Groundnut at ICRISAT. Poster presented at the Annual Review Metting of the Generation CP, Sao Paulo, Brasil, 12-16 Sept 2006.

Vadez V., Krishnamurthy L., Varshney R.K., Serraj R., Jyotsna Devi M., Nigam S.N., Aruna R., Moss B., Seetha Kannan., Hoisington D., Rupa K., Sridevi.,  Chandra S.. Variation in transpiration efficiency in a groundnut (Arachis hypogaea L.) mapping population Poster presented at the Annual Review Metting of the Generation CP, Sao Paulo, Brasil, 12-16 Sept 2006.

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10). Media coverage and press releases
Press releases
Generation Challenge Programme (2006). GCP selects Philippe Monneveux as new SP3 Leader/Product Manager. 29 May 2006. View press release.

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11) Academic dissertations and theses

There were no reported academic dissertations/theses in 2006.

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