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United States Department of Agriculture

Agricultural Research Service

Title: Current Challenges of Tropical Tree Crop Improvement: Integrating Genomics into An Applied Cacao Breeding Program

Authors
item Schnell Ii, Raymond
item Brown, James
item Kuhn, David - FLORIDA INT'L UNIVERSITY
item Cervantesmartinez, Cuauhtemoc
item Borrone, James
item Tondo, Cecile
item Motamayor, Juan - MASTERFOODS USA
item Phillips, Wilbert - CATIE
item Johnson, Elizabeth - CATIE
item Monteverde-Penso, Edgardo - CATIE
item Amores, Freddy - INIAP
item Lopes, Uilson - CEPLAC

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 16, 2006
Publication Date: June 1, 2007
Citation: Schnell II, R.J., Brown, J.S., Kuhn, D.N., Cervantesmartinez, C., Borrone, J.W., Olano, C.T., Motamayor, J.C., Phillips, W., Johnson, E., Monteverde-Penso, E.J., Amores, F., Lopes, U. 2007. Current challenges of tropical tree crop improvement: integrating genomics into an applied cacao breeding program. Acta Horticulturae: Proc IS on biotechnology of temperate fruit crops and tropical species. 738:p129-144.

Interpretive Summary: The seeds of the cacao tree are used as raw material for chocolate containing products. Cacao cultivation and production of cacao beans for the American Chocolate Industry is a multibillion-dollar effort, mainly centered in Africa, Asia, and South America. Substantial quantities of U.S. produced agricultural commodities, including milk, sugar, almonds, peanuts, and corn syrup sweeteners, are used in the chocolate and confectionery industry. Cacao production is plagued by very serious losses globally from pests and diseases. For the long term welfare of the industry, there is a need to promote international collaboration among producers, and to develop superior trees that can stand up to disease and still produce high quality cocoa beans. In 1999, the USDA-ARS in collaboration with Mars Inc. initiated a project to apply modern molecular genetic techniques to cacao breeding. The primary goal of this project is to develop a Marker Assisted Selection (MAS) program and to disseminate new, productive, disease resistant varieties of cacao. Use of MAS decreases the time and expense of traditional breeding by allowing selection of the best seedlings at early stages of development, based on genetic information. Molecular markers have been developed and are being used for DNA fingerprinting and for analysis of the genetic diversity that exists in cacao. Cooperative projects have been developed with national agricultural research services and international organizations. Cacao families generated for evaluation of disease resistance, quality and productivity traits have been identified and are being used to produce genetic linkage maps and to locate markers for the traits. These markers have been identified for a number of productivity and quality traits, as well as for two important diseases (witches’ broom and frosty pod) and are currently being used in MAS. An alternative method for mapping, association mapping, has been demonstrated to be successful in cacao. Work is underway to identify the genes involved in the disease resistance mechanism. This shorter time line and marker enhanced selection for field testing is far superior to traditional cacao selection techniques currently in use. The expected outcomes from the MAS are to produce new, high yielding, high quality, disease resistant cultivars which will in turn diminish crop losses and produce a stable supply of cocoa beans for the industry.

Technical Abstract: Theobroma cacao L. is an understory tree from the Amazon basin that can be cultivated in a sustainable agro-forestry system, providing income to small farmers while maintaining biodiversity. Four main genetic groups of cacao are traditionally described: Criollo, Trinitario, and lower and upper Amazon Forastero. During the seventeenth and eighteenth centuries, plants derived from a small number of parents were distributed to many tropical regions of the world, resulting in commercial plantings with a narrow genetic base. Production of cacao in tropical America has been severely affected by two fungal pathogens causing diseases known as witches’ broom (WB) and frosty pod (FP). These, along with another pan-tropical fungal disease, black pod (BP), were responsible for over 700 million USD in losses in 2001. Currently, WB and FP are confined to Central and South America; however, commercial populations in West Africa and South Asia are highly susceptible to both diseases. Traditional cacao breeding programs have only been marginally successful in producing resistant material with suitable commercial characteristics. In 1999, the USDA-ARS in collaboration with Mars Inc. initiated a project to apply modern molecular genetic techniques to cacao breeding. The objectives were to develop an international Marker Assisted Selection (MAS) breeding program focusing on disease resistance, to identify new sources of resistance in unexploited germplasm, and to identify the genes involved with disease resistance. Over 320 microsatellite and 50 candidate gene markers are being used to map families segregating for resistance to WB, FP, and BP diseases. Quantitative Trait Loci (QTL) have been identified for resistance to WB and FP and these are being employed in MAS. The utility of Association Mapping for productivity traits has been demonstrated providing an alternative method to traditional mapping. Microsatellite and candidate gene markers have also been used to estimate the genetic diversity in over 1,300 individuals representing 70 different domesticated and semi-domesticated/wild cacao populations. Genetic diversity has been found to be much higher in the semi-domesticated/wild populations from the upper Amazon which may contain new sources of disease resistance. For the gene discovery effort, a Bacterial Artificial Chromosome (BAC) library has been produced from ‘LCTEEN37’, resistant to WB, and work is underway to identify and sequence gene(s) responsible for a major WB QTL. Large evaluation trials, developed using MAS, are located in Costa Rica, Ecuador, Brazil, and Papua New Guinea with additional QTL evaluation studies in Ghana, Nigeria, Costa Rica, and Ecuador. All these projects are collaborations with national agricultural institutes in the respective countries. The international MAS project is expected to produce new disease resistant cultivars by 2012. Genetic stocks developed in this project will be distributed to areas currently free of WB and FP in anticipation of the arrival of these diseases. International collaboration and sharing of genetic resources will ensure that crop losses due to these pathogens are manageable and will contribute to stability in the supply of cocoa beans.

Last Modified: 9/20/2014
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