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Current challenges of tropical tree crop improvement: Integrating genomics into an applied cacao breeding program

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 17th and 18th 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 tropical 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.