Molecular Tools for Quality Improvement in Vegetatively Propagated Crops Including Banana and Cassava

Closed for proposals

Project Type

Coordinated Research Project

Project Code

D23027

CRP

1312

Approved Date

7 December 2004

Status

Closed

Start Date

1 May 2005

Expected End Date

22 July 2011

Completed Date

22 July 2011

Description

Vegetatively propagated crops, those crops whose planting materials include among others stem cuttings, vines, suckers, or tubers, rather than biological seeds arising from sexual reproduction, are critical for food security in the tropical and subtropical regions of Africa, Asia and Latin America. Increased and stable yields in these crops are required in order to meet the calorie needs of the rapidly growing populations in these regions. The challenges are particularly urgent in sub-Saharan Africa, where rapid population growth and an alarming rate of climate change are making vegetatively propagated crops even more vital for achieving food security. The production of improved varieties that are nutritionally acceptable, minimize post-harvest losses, show tolerance to such important abiotic stresses as drought and salinity, and biotic stresses such as pests and diseases, while still satisfying the diverse preferences and agro-ecologies across the tropics and sub-tropics is a daunting task. This is because starting materials in the genetic improvement of vegetatively propagated crops usually lack the uniform genetic background that greatly simplifies the genetic improvement of seed propagated crops. However, new powerful neutral tools of molecular biology that can circumvent the confounding effects of non-heritable factors while evaluating crop germplasm can, when applied in concert with induced mutations (deliberate artificial change to the genetic make up of individuals) and cell culture techniques, facilitate the improvement of these crops. This Coordinated Research Project (CRP) will make every effort to ensure that the existing molecular resources and information on the genetic make up of banana and cassava (i.e. genomics tools) are brought to bear on efforts to produce improved varieties of both crops. It will achieve this goal by the development of exhaustively characterized populations structured for the discovery of genes influencing traits of interest while building upon the experiences of the Agency in the use of induced mutations for the genetic improvement in both crops. This CRP will also facilitate access to information resources on the genetic make up of these 2 crops currently being held by advanced labs, and the development of plant populations that make genetic improvement easier and facilitate the location of the genes controlling traits of interest. The above tools will be aggressively applied to improve the efficiency of enhancing quality traits, and the equally important tolerance to biotic and abiotic stress constraints in banana and cassava in active cassava and banana breeding programs in Member States. The results of these activities will also be documented to provide a proof of concept on the use of these new methodologies and tools in concert with induced mutations to understand the biological bases of important genetic traits and their application in crop improvement.

Objectives

Together, banana and cassava are staple crops for over 1 billion people in developing countries particularly in tropical and subtropical regions. Largely vegetativley propagated, these crops face challenges not found in seed propagated crops. Genomics resources exist for cassava and banana, but they remain to be deployed widely in the aid of breeding and integration with mutant germplasm. There is a lack of well-defined genetic stocks with which to conduct functional genomics analysis that is critical for the application of genomics and nuclear technologies in plant breeding, and a need for a network of advanced labs and NARS in tropical countries to begin the process of putting these tools to work. The CRP was started in 2004 to bridge this gap and exploit opportunities for technology development, breeding and the use of mutations to advance progress in the crops, and to develop guidelines and strategies relevant to all vegetatively propagated species.

Specific objectives

To employ induced mutants and functional genomics, at the single gene level (conserved orthologous [COS] markers) and at the transcriptome level (a collection of ESTs), as well as appropriate genetic mapping populations, including doubled haploids, to identify molecular markers for marker-assisted selection (MAS) of quality and related traits.

Impact

The outputs of genomic sequences and cDNA (ESTs), and implementation of a variety of different marker systems, and their linkage to important agronomic traits provides a good foundation for continued efforts in using molecular tools to enhance the efficiency of mutation based improvement of banana and cassava. The development of mutant populations with improved traits (yield, starch quality, delayed post harvest physiological deterioration, etc) also provides the base material for the development of new varieties. Such successes should have a good impact within the circle of collaborators and should spread to groups not participating in the CRP and who are struggling to overcome the many bottlenecks of improvement of vegetatively propagated crops. While only focusing on cassava and banana, the methods employed in this CRP can be transferred to other important vegetatively propagated crops.

Relevance

Vegetatively propagated crops such as cassava and banana suffer from numerous bottlenecks including lack of meiotic propagation, that make their improvement through traditional or mutation breeding approaches less efficient and more time consuming that seed propagated crops. Together, Musa (banana and plantain) and cassava make up staple foods for over 1 billion people in developing countries. Climate change and variation, coupled with increased population growth in the least developed countries, means that pressures on agricultural production are likely to increase. With little investment from developed countries, the improvement of vegetatively propagated crops is at a distinct disadvantage. Further, rapid improvements that could potentially be achieved with GMOs is largely shunned by the public and requires heretofore non existent regulatory infrastructure in developing countries. Taken together, mutation based approaches can be considered a major area where successes can be achieved.

CRP Publications

Type

Conference proceedings

Year

2009

Description

Sudarmonowati, E., S. Hartati, Hartati, S. Kurniawati, S. Sugiharti. 2009. Developing Drought Resistant Cassava andEggplant Through Induced Variation and Cloning of Drought Resistance-related Genes. SEA-EU Net Conference. Bogor,10-12 November 2009.,

Country/Organization

Indonesia

Type

Published abstract

Year

2005

Description

AN ANALYSIS OF RESISTANCE GENE ANALOGS IN MUSA ACUMINATA VAR. CALCUTTA 4 In: Primeiro Encontro da Sociedade de Melhoramento de Plantas – Regional DF,

Country/Organization

Brazil

Type

Conference proceedings

Year

2008

Description

Sudarmonowati, E. N.S. Hartati, S. Sugiharti, A. Amsal. 2008. Altering amylosecontent in Indonesian Cassava through irradiation : role of genotypes, dosage,and planting materials. Presented at FAO/IAEA International Symposium ofInduced Mutations in Plants. Vienna, Austria, 12-15 August 2008.

Country/Organization

Indonesia

Type

Scientific Article

Year

2010

Description

R.N.G. Miller, M.A.N. Passos, F.L. Emediato, C. de Camargo Teixeira, G.J. Pappas Júnior, 2010. Candidate Resistance Gene Discovery: Resistance Gene Analog Characterization and DifferentialGene Expression Analysis in Musa-Mycosphaerella Host-Pathogen Interactions. Acta Hort. (ISHS).

Country/Organization

Brazil

Type

Conference proceedings

Year

2005

Description

Sudarmonowati, E., N.S. Hartati, Hartati, L. Sukmarini, H. Fitriani, D. Priadi, N.Rahman, N. Taryana. 2005. Genetic Improvement of Indonesian Cassavathrough Integrated Molecular Approach. Makalah dipresentasikan diSymposium on Application of Plant Biotechnology for AgribusinessDevelopment. Bogor, 28-29 September, 2005.

Country/Organization

Indonesia

Type

Peer-reviewed publication

Year

2010

Description

Bayoumi, S. A. L., Rowan, M. G., Beeching, J. R. and Blagbrough, I. S., 2010. Constituents and secondary metabolite natural products in fresh and deteriorated cassava roots. Phytochemistry, 71 (5-6), pp. 598-604.

Country/Organization

UK

Type

Conference proceedings

Year

2007

Description

Sudarmonowati, E., N.S. Hartati, Hartati and L. Sukmarini. 2007. Amylosecontent variation of Indonesian cassava genotypes and its correlation withRAPD and AFLP markers. Proceedings First International Meeting on CassavaBreeding, Biotechnology and Ecology. Brasilia, 11-15 November 2006

Country/Organization

Indonesia

Type

Peer reviewed article

Year

2009

Description

Sudarmonowati, E., H. Fitriani, Supatmi, N. Ardiyanti. 2009. Factors affecting friableembryogenic callus in several plant species. Journal of Biotechnology Research 2 (2): 1-5.

Country/Organization

Indonesia

Type

Peer-reviewed publication

Year

2007

Description

Hakkinen M, Doleželová M, Suchánková P, Hribová E, Doležel J. KaryologicalObservation in the New Variety of Musa beccarii (Musaceae). – Acta Phytotax Geobot58: 112-118, 2007.

Country/Organization

Czech Republic

Type

Peer-reviewed publication

Year

2008

Description

Bayoumi, S.A.L., Rowan, M.G., Beeching, J.R. and Blagbrough, I.S., 2008. Investigation of biosynthetic pathways to hydroxycoumarins during post-harvest physiological deterioration in Cassava roots by using stable isotope labelling. ChemBioChem, 9, pp. 3013-3022.

Country/Organization

UK

Type

Peer-reviewed publication

Year

2008

Description

Bayoumi, S.A.L., Rowan, M.G., Blagbrough, I.S. and Beeching, J.R., 2008. Biosynthesis of scopoletin and scopolin in cassava roots during post-harvest physiological deterioration: The E-Z-isomerisation stage. Phytochemistry, 69 (17), pp. 2928-2936.

Country/Organization

UK

Type

Peer reviewed publication

Year

2009

Description

Miller, R.N.G., Bertioli, D.J., Baurens, F.C., Quirino, B.F., Ciampi, A.Y., Santos, C.M.R., Martins, N.F., Souza Jr., M.T. and Pappas Jr., G.J. 2009. UNDERSTANDING PLANT RESPONSES TOBIOTIC STRESS: ONGOING RESEARCH IN MUSA. Acta Hort. (ISHS) 828:255-272

Country/Organization

Brazil

Type

Peer-reviewed publication

Year

2008

Description

Azhar, M., Heslop-Harrison, J.S. 2008 Genomes, diversity and resistance gene analogues in Musa species. Cytogenet Genome Res. 121:59-66

Country/Organization

UK

Type

Conference Abstract

Year

2007

Description

Abstract Plant GEM 2007:Comparative genomics of Musa and rice genomes: insight into an RGA cluster.Franc-Christophe BAURENS , Robert Neil Gerard MILLER, Magali LESCOT, Mathieu ROUARD, Georgios Joannis PAPPASJr, Takashi MATSUMOTO , Nicolas ROUX, Takuji SASAKI, Stéphanie SIDIBE BOCS and Angélique D’HONT.

Country/Organization

Brazil

Type

Peer-reviewed article

Year

2010

Description

Hippolyte, Isabelle ; Bakry, Frederic ; Seguin, Marc ; Gardes, Laetitia ; Rivallan, Ronan ; Risterucci, Ange-Marie; Jenny, Christophe ; Perrier, Xavier ; Carreel, Francoise ; Argout, Xavier ;PIFFANELLI, Pietro ; Khan, Imtiaz ; Miller, Robert NG ; Pappas, Georgios J ; Mbeguie-a-mbeguie, Didier ; Matsumoto, Takashi ; De Bernardinis, Veronique ; Huttner, Eric ; Kilian, Andrzej ; Baurens,Franc-Christophe ; D´Hont, A ; Cote, Francois ; Courtois, Brigitte ; Glaszmann, Jean-Christophe. 2010. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangementsamong bananas. BMC Plant Biology 10: 65.

Country/Organization

Brazil

Type

Peer reviewed article

Year

2010

Description

Baurens, Franc-Christophe ; Bocs, Stephanie ; Rouard, Mathieu ; Matsumoto, Takashi ; Miller, Robert NG; Rodier-Goud, Marguerite ; Mbeguie-a-mbeguie, Didier ; Yahiaoui, Nabila. 2010.Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana). BMC Plant Biology 10: 149.

Country/Organization

Brazil

Type

Peer reviewed article

Year

2008

Description

Priadi, D., Hani Fitriani dan Enny Sudarmonowati. 2008. Growth of cassava shoot In Vitro(Manihot esculenta Crantz) on various alternative gelling agents to replace agar .BIODIVERSITAS Journal of Biological Diversity 9(1): 9-12.7..

Country/Organization

Indonesia

Type

Conference proceedings

Year

2009

Description

Improved Production and Agrobacterium - mediated Transformation of friable embryogeniccallus (FEC) of cassava genotypes Iding and Gebang. Proceedings of Symposium & NationalCongres of PERIPI. Bogor, November 17-19, 2009.9.

Country/Organization

Indonesia

Type

Peer reviewed publication

Year

2008

Description

Miller RNG, Bertioli DJ, Baurens FC, Santos CM, Alves PC, Martins NF, Togawa RC, Souza MT Junior, Pappas GJ Junior. 2008 . Analysis of non-TIR NBS-LRR resistance gene analogs in Musaacuminata Colla: Isolation, RFLP marker development, and physical mapping.. BMC Plant Biology 8:15

Country/Organization

Brazil

Type

Conference proceedings

Year

2008

Description

Priadi, D., Djumhawan Ratman Permana, Sri Elin Dona, N. Sri Hartati dan EnnySudarmonowati. 2008. Selection of Indonesian local cassava (Manihot esculenta Crantz)genotypes as ß-Karoten source. Proc, of National Seminar on Biochemistry “The role ofBiochemistry on increasing added value, Efficiency, and quality of Industries”, UniversitasIndonesia ,9 January 2008 (ISBN 978-979-8768-07-1).

Country/Organization

Indonesia

Type

Peer-reviewed publication

Year

2008

Description

Hribová, E., Doleželová, M., Doležel, J.: FISH with BAC clones on mitoticchromosomes of banana (Musa acuminata). – Biol. Plant. 52: 445-452, 2008.

Country/Organization

Czech Republic

Type

Book chapter

Year

2011

Description

Andrew James, Rodomiro Ortiz, Robert Miller, Franc Baurens and Angelique d’Hont. 2011. Map-Based or Positional Cloning. In: Encyclopedia of Plant Genomics (Ed. Prof. Chittaranjan Kole)

Country/Organization

Brazil

Type

Published abstract

Year

2006

Description

Analysis of Resistance Gene Analogs in Musa acuminata subsp. burmannicoides, var. Calcutta 4. 2nd Musa Workshop, XIV International Plant and Animal genome conference (PAG),

Country/Organization

Brazil

Type

Book chapter

Year

2009

Description

EMEDIATO, Flavia Leonel ; NUNES, Francisca Aline Carvalho ; TEIXEIRA, C. C. ; PASSOS, Marco Aurelio N ; BERTIOLI, David J. ; PAPPAS JÚNIOR, Georgios J. ; MILLER, R. N. G. 2009.Characterization of resistance gene analogs in Musa acuminata cultivars contrasting in resistance to biotic stresses. In: Food and Agriculture Organization of the United Nations. (Org.). Induced PlantMutations in the Genomics Era.. Rome: Food and Agriculture Organization of the United Nations, 2009, p. 443-445.

Country/Organization

Brazil

Type

Peer-reviewed publication

Year

2007

Description

Reilly, K., Bernal, D., Cortes, D. F., Gomez-Vasquez, R., Tohme, J. and Beeching, J. R., 2007. Towards identifying the full set of genes expressed during cassava post-harvest physiological deterioration. Plant Molecular Biology, 64 (1-2), pp. 187-203.

Country/Organization

UK

Type

Review book chapter

Year

2008

Description

Roux, N., Baurens, F.C., Doležel, J., Hribová, E., Heslop-Harrison, J.S., Town, C.,Sasaki, T., Matsumoto, T., Aert, R., Remy, S., Souza, M., Lagoda, P.: Genomics ofBanana and Plantain (Musa spp.), Major Staple Crops in the Tropics. In: Moore, P.H. &Ming, R. (eds). Genomics of Tropical Crop Plants. Springer, Heidelberg, Germany,

Country/Organization

Bioviersity Internationa, UK, Czech Republic, IAEA

Type

Scientific Article

Year

2010

Description

Roberto C. Togawa, Candice Mello Romero Santos, Robert N. G. Miller, Manoel Teixeira Souza Júnior, Natália Florêncio Martins. 2010. DATAMusa - a Database for Ortholog Genes from Musa.Tree and Forestry Science and Biotechnology.

Country/Organization

Brazil

Type

Conference proceedings

Year

2008

Description

Sudarmonowati, E., N.S. Hartati, A. Amsal. 2008. Casaava Improvement and itsdevelopment for health nutrition and food security. Proceedings of 9th WidyaKarya Pangan dan Gizi, Jakarta, 27-28 August 2008

Country/Organization

Indonesia

Type

Peer-reviewed publication

Year

2007

Description

Isolation and characterization of the highly repeated fraction of the banana genome. E Hribová, M Dolezelová, C D Town, J Macas, J Dolezel Cytogenetic and Genome Research (2007) Volume: 119, Issue: 3-4, Pages: 268-274

Country/Organization

Czech Republic

Type

Peer reviewed article

Year

2011

Description

E.K. Sales, N.G. Butardo, H.G. Paniagua, H. Jansen and J.Dolezel. Assessment of Ploidy and Genome Constitution of Some Musa balbisiana Cultivars using DArT Markers. The Philippine Journal of Crop Science. Volume 36 No.1 April 2011, Volume 36 (1):11-18.

Country/Organization

Philippines

Type

Peer-reviewed publication

Year

2010

Description

Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencingEva Hribová,1 Pavel Neumann,2 Takashi Matsumoto,3 Nicolas Roux,4 Jirí Macas,2 and Jaroslav Doležel1BMC Plant Biol. 2010; 10: 204.

Country/Organization

Czech Republic

Type

Peer reviewed publication

Year

2006

Description

Priadi, D. dan Enny Sudarmonowati. 2006. Effect of media composition and explant size on embryogenic callusformation in several local genotypes of cassava (Manihot esculenta Crantz). BIODIVERSITAS 7(3): 269-272.2.

Country/Organization

Indonesia

Type

Conference Abstract

Year

2007

Description

Abstract Jobim 2007:Comparison of hom(oe)ologous regions containing clusters of duplicated RGAs within Musa species and with riceStéphanie Sidibe Bocs, Georgios Joannis Pappas Jr, Mathieu Rouard, Fabrice Legeai, Gaëtan Droc, Vincent Jouffe, OlivierGarsmeur, Céline Cardi, Angélique d’Hont, Takashi Matsumoto, Robert Neil Gerard Miller and Franc-Christophe Baurens

Country/Organization

Brazil

Type

Conference proceedings

Year

2009

Description

Sudarmonowati, E., Supatmi and Reny. H. Zul. 2009. Induction and Regeneration of primarysomatic embryos (PSE) and secondary somatic embryos (SSE) of local cassava genotypesIding and Gebang for genetic transformation materials. Proceedings of Symposium &National Congres of PERIPI. Bogor, November 17-19, 2009.

Country/Organization

Indonesia

Type

Conference proceedings

Year

2009

Description

Hartati, N.S., H. Fitriani, S. Sugiharti, E. Sudarmonowati. 2009. Cassava genetic improvement efforts (Manihot esculentaCrantz) to develop high beta karoten genotypes through selection and molecular approaches. Proceedings ofSimposium & Kongres Nasional PERIPI. Bogor, November 17-19, 2009.8.

Country/Organization

Indonesia

Type

Peer reviewed article

Year

2010

Description

Miller, Robert NG ; Passos, Marco AN ; Menezes, Natalia NP ; Souza, Manoel T ; do Carmo Costa, Marcos M; Rennó Azevedo, Vânia C ; Amorim, Edson P ; Pappas, Georgios J ; Ciampi, Ana Y.2010. Characterization of novel microsatellite markers in Musa acuminata subsp. burmannicoides, var. Calcutta 4. BMC Research Notes 3: 148.

Country/Organization

Brazil

Type

Peer-reviewed publication

Year

2008

Description

Miller RNG, Bertioli DJ, Baurens FC, SantosCM, Alves PC, Martins NF, Togawa RC, SouzaMT Junior, Pappas GJ Junior. (2008). Analysis ofnon-TIR NBS-LRR resistance gene analogs inMusa acuminata Colla: Isolation, RFLP markerdevelopment, and physical mapping. BMC PlantBiology 8:15 doi:10.1186/1471-2229-8-15

Country/Organization

Brazil

Type

Peer-reviewed publciation

Year

2008

Description

Bayoumi, S.A.L., Rowan, M.G., Beeching, J.R. and Blagbrough, I.S., 2008. Investigation of biosynthetic pathways to hydroxycoumarins during post-harvest physiological deterioration in Cassava roots by using stable isotope labelling. ChemBioChem, 9, pp. 3013-3022.

Country/Organization

UK

Type

Peer-reviewed publication

Year

2010

Description

Blagbrough, I. S., Bayoumi, S. A. L., Rowan, M. G. and Beeching, J. R., 2010. Cassava: an appraisal of its phytochemistry and its biotechnological prospects. Phytochemistry, 71 (17-18), pp. 1940-1951.

Country/Organization

UK

Type

Short report

Year

2007

Description

Molecular tools for quality improvement in vegetatively propagatedcrops, including banana and cassava*

Country/Organization

India, IAEA

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