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United States Department of Agriculture

Agricultural Research Service


item Brown, James
item Kuhn, David
item Motamayor, Juan
item Borrone, James
item Lopes, Uilson
item Schnell Ii, Raymond

Submitted to: Proceedings of the International Cocoa Producer's Conference
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/11/2003
Publication Date: 10/20/2003
Citation: Brown, J.S., Kuhn, D., Motamayor, J.C., Borrone, J., Lopes, U., Schnell II, R.J. 2003. A preliminary genomic map based on SSR markers, Resistance Gene Homologues, and Stress-related WRKY genes in an F2 population of T. cacao L. Proceedings of the International Cocoa Producer's Conference.

Interpretive Summary: Genomic maps based on molecular markers have become basic tools for modern plant breeding. As this technology has progressed, the types of markers hve become more informative and less labor-intensive. This molecular marker map consists of 120 microsatellite (SSR) markers, and eleven markers coming from the candidate gene research; seven resistance gene homologues (RGH), and four WRKY genes, a type of gene that codes for stress resistance. The latter two types of genes were adapted to function as molecular markers. The population used for the map consisted of 146 trees of Theobroma cacao L. from the F2 population, derived from selfing the clone, TSH516, a cross between SCA6 and ICS1. SCA6 is considered to be an important donor of resistance to witch's broom disease (Crinipellis perniciosa(Stahel)), a disease which has ravaged the cocoa industry in South America. The map was composed of 10 linkage groups corresponding to the 10 chromosomes of cacao. This preliminary map covered 664.07 centimorgans, slightly shorter than the high-density reference map (885.4 cM) and had six blocks with significant segregation distortion. We plan to add an additional set of approximately 100 more SSR markers to the map produced at CIRAD, Montpellier, France. With these addtional markers, the length of the mpa should be quite close to the reference map.

Technical Abstract: A genetic linkage map has been created with 151 trees from an F2 population of a cross between SCA6 and ICS1. Simple sequence repeat markers were used principally for this map with a total of 131 SSR markers. In addition, seven markers developed from Resistance Gene Homologues (RGH) and four markers developed from WRKY (stress-related) genes were included. Joinmap software from Plant Breeding International was used to create the map from the scored data, and 10 linkage groups were obtained in the preliminary map. The 10 linkage groups were found to correspond well to the map of Lanaud, etal., and cover approximately 715 centimorgans, as opposed to 759 in the map of Lanaud, et al. Approximately 30% of the markers showed serious segregation distortion, however, and this distortion tended to map towards six areas of the genome. Three different factors were identified which could explain this segregation distortion, namely population size, factors involved in circumbenting the self-incompatability mechanism of the F1, and possibly genetically based segregation distortion. Nonetheless, a basic map exists which could be used to locate the inheritance of resistance to Crinipellis, as phenotypic data does exist from both field scores for one-half of the population, and for seedling inoculation response for the entire population. Our future plans involve the creation and addition of addtional SSR markers in house, and the addition of all possible publicly available SSR markers.

Last Modified: 10/18/2017
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