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United States Department of Agriculture

Agricultural Research Service


item Brown, James
item Schnell ii, Raymond
item Motamayor, J
item Lopes, Uilson
item Kuhn, David

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer reviewed journal
Publication Acceptance Date: 9/30/2004
Publication Date: 5/1/2005
Citation: Brown, J.S., Schnell II, R.J., Motamayor, J.C., Lopes, U., Kuhn, D.N. 2005. Resistance gene mapping for witches' broom disease in Theobroma cacao L. in an f2 population using ssr markers and candidate genes. Journal of the American Society for Horticultural Science. 130(3):366-373.

Interpretive Summary: The disease known as witches' broom has been devastating to cocoa growers in South and Central America. This disease has reduced production of cocoa in the state of Bahia, Brazil by as much as 80%. If this disease were to spread to cocoa growing areas in West Africa, the result would be catastrophic for native producers as well as for cocoa users. Control of this disease by sanitation and fungicides is difficult and minimally effective, therefore the search for genetic resistance began in the late 1940's. One clone, Sca6, which comes from the Upper Amazon region, was found to have stable resistance to most strains of the pathogen. This clone was crossed with a Trinitario type known as ICS1, and a resistant, productive clone known as TSH516 was selected from the progeny. TSH516, though self-incompatible like its maternal parent, Sca6, was self-pollinated using the "mentor pollen" technique to circumvent the incompatibility. A population of 100 trees was planted in Bahia, Brazil, and data measuring resistance of the progeny was taken over a six year period. Data for tree trunk diameter, a character related to disease resistance to witches's broom disease, was taken at the end of the study. Eighty additional trees were produced in 2000 to enlarge the population, making it sufficiently large for production of a genomic map. Using molecular markers known as "Simple sequence repeat" (SSR) markers, together with marker constructed from candidate resistance genes produced in our lab, a relatively densely saturated genomic map was constructed. We used this map and the phenotypic data, to identify two "quantitative trait loci" (QTL's) for resistance to witches' broom disease, and one for tree trunk diameter. These results provide evidence that Sca6 does contain genes for resistance to witches' broom disease, and gives the location of two of them, one of which appeared to be a gene with a major effect. Breeders using Sca6 as a donor have surmised from breeding results and observations that this was the case, and the molecular results confirm it. This research shows the importance of evaluating the second group of trees for resistance, also, which will increase the precision of localization of these genes, and will likely locate more genes, accounting for more of the resistance seen in the phenotypic data. This work also shows that we have a good population, in which agronomic traits could be mapped, as well. As all previously produced cacao genomic maps were from F1 populations of trees from crosses of heterozygous clones, this constitutes the first map from a segregating F2 population. Using an F2 population allows the determination of type of gene action (additive or dominant) in addition to localization, which is not possible in populations of F1 trees. This information is important for breeders using Sca6 to introgress resistance into new clones.

Technical Abstract: A genetic linkage map was created with 146 trees of cacao (T. cacao L.) from an F2 population of a cross between the clones, Sca6 and ICS1. Simple sequence repeat (SSR) markers were used principally for this map with a total of 170 SSR markers. Twelve markers developed from candidate genes (Resistance Gene Homologues (RGH) and stress related WRKY genes) were also used, for a total of 182 markers. Joinmap software from Plant Breeding International was used to create the map, and 10 linkage groups were clearly obtained, corresponding to the 10 chromosomes of cacao and to 10 linkage groups in the high-density cacao map of Risterucci et al. (2000). The map covered approximately 671.9 centimorgans, as opposed to 885.4 in the high-density map. Approximately 27% of the markers showed serious segregation distortion, however, and this distortion tended to map towards six areas of the genome. Two QTL (quantitative trait loci) for resistance were found, one being rather strong and highly repeatable, and one for trunk diameter, which was only 10.2 cM away from the stronger gene for witches' broom resistance. The use of cofactors indicated these two genes, though rather closely linked, to be independent loci and not one true locus with penetrance in two underlying, related traits. One of the RGH, RGH11, flanked the second QTL for witches' broom resistance, and another, RGH2, flanked the QTL for trunk diameter, and was therefore also relatively close to the other QTL for witches' broom resistance (24.6 cM away). This is the only F2 cacao population mapped to date, and will constitute a very useful conrnerstone population for future cacao research, as well.

Last Modified: 8/24/2016
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