The international marker assisted selection program for cacao

Authors: Schnell Ii, Raymond; MOTAMAYOR, JUAN - Mars, Inc; Brown, James; Kuhn, David; Tondo, Cecile; Livingstone, Donald; NAGAI, CHIFUMI - Hawaii Agricultural Research Center; PHILLIPS, WILBERT - Catie Tropical Agricultural Research; AMORES, FREDDY - National Institute For Agricultural Research (INIAP); SUAREZ-CAPELLO, CARMITA - National Institute For Agricultural Research (INIAP); LOPES, UILSON - M & M Mars Company - Brazil; TAKRAMA, JEMMY - Cocoa Research Institute Of Ghana; PADI, FRANCIS - Cocoa Research Institute Of Ghana; OPOKU, STEPHAN - Cocoa Research Institute Of Ghana; EFOMBAGAN, IVES - Institute Of Agricultural Research For Development (IRAD); AIKPOKPODION, PETER - Cocoa Research Institute Of Nigeria; POKOU, DESIRE - Centre National De Recherche Agronomique (NCAR); EPAINA, PETER - Png Cocoa And Coconut Institute (CCRI); MARFU, JEFFERY - Png Cocoa And Coconut Institute (CCRI)

Submitted to: Proceedings of the International Cocoa Producer's Conference
Publication Type: Proceedings
Publication Acceptance Date: 1/4/2010
Publication Date: 3/15/2010
Citation: Schnell Ii, R.J., Motamayor, J.C., Brown, J.S., Kuhn, D.N., Tondo, C.L., Livingstone, D., Royaert, S.E., Nagai, C., Phillips, W., Amores, F., Suarez-Capello, C., Lopes, U., Takrama, J., Padi, F., Opoku, S., Efombagan, I.B., Aikpokpodion, P., Pokou, D., Epaina, P., Marfu, J. 2010. The international marker assisted selection program for cacao. Proceedings of the International Cocoa Producer's Conference.

Interpretive Summary: In 2000, the USDA and Mars Inc. initiated a program combining traditional and modern molecular based breeding methodologies with the long-term objective of genetically improving Theobroma cacao L. Molecular markers and genetic linkage maps have been developed and using this information we are accelerating breeding efforts and increasing the efficiency of cacao selection. The primary constraints to bean production are the fungal pathogens causing diseases known as witches’ broom (WB), frosty pod (FP) and black pod (BP). These three diseases are responsible for yearly losses amounting to hundreds of millions in U.S. dollars. 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. We are now using the molecular genetic information to breed for resistance to all three diseases even in areas where the diseases are not yet present. Two new cultivars have been released from the CATIE project in Costa Rica and four new cultivars have been released from the INIAP project in Ecuador. All six new cultivars are high yielding, good quality and are resistant to local diseases.

Technical Abstract: In 2000, the USDA and Mars Inc. initiated a program combining traditional and Marker Assisted Selection (MAS) breeding methodologies with the long-term objective of genetically improving Theobroma cacao L. Molecular markers and genetic linkage maps were developed and used to verify parentage, germplasm accessions, and to identify Quantitative Trait Loci (QTL) for disease resistance and productivity. These markers are accelerating breeding efforts and increasing the efficiency of cacao selection. The primary constraints to bean production in tropical America are the fungal pathogens causing diseases known as witches’ broom (WB) and frosty pod (FP). These, along with black pod (BP) are responsible for yearly losses amounting to hundreds of millions in U.S. dollars. 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. QTLs have been identified for resistance to WB, FP, BP and productivity traits, and these are being employed in MAS. Using next generation sequencing methods 285,000 Single Nucleotide Polymorphism (SNP) markers have been identified from diverse cacao germplasm. These new SNP markers are being used to saturate current linkage maps, for association studies to identify additional QTL for disease resistance and productivity and to establish a cost efficient MAS platform. The cacao physical map has been completed and using known molecular marker locations, the physical and genetic maps have been aligned allowing the identification of important gene-containing areas of the genome. Preventative breeding is occurring in West Africa where we are using the QTLs for WB and FP to identify potentially resistant material in existing breeding populations. We have developed a reference database of genotypes with emphasis on Central and South American germplasm and are continuing with the existing and new field and MAS trials in Hawaii, Costa Rica, Ecuador, Brazil, Ghana, Cameroon, Nigeria, Cote d'Ivoire, and PNG with the goal of releasing superior varieties with high yield, disease resistance and the quality attributes required by the confectionary industry.