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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF AN INTERNATIONAL MARKER ASSISTED SELECTION PROGRAM FOR CACAO

Location: Subtropical Horticulture Research

Title: Characterization of reproductive self-compatibility in Theobroma cacao L.

Authors
item Royaert, Stefan
item Cariaga, Kathleen
item Freeman, Barbara
item Phillips, Wilberth -
item Lopes, Uilson -
item Brown, James
item Kuhn, David
item Schnell Ii, Raymond
item Motamayor, Juan -

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 15, 2010
Publication Date: January 15, 2010
Citation: Royaert, S.E., Cariaga, K.A., Freeman, B.L., Phillips, W., Lopes, U.V., Brown, J.S., Kuhn, D.N., Schnell Ii, R.J., Motamayor, J.C. 2010. Characterization of reproductive self-compatibility in Theobroma cacao L.. Plant and Animal Genome Conference. 1.

Interpretive Summary: Self-fertilization in plants is often times not possible due to a genetic mechanism called self-incompatibility (SI). SI in cacao is sporo-gametophetic, and so far, no genes regulating this phenomenon have been identified. To continue further progress in cacao breeding it is a necessity to identify the genes that are involved in this mechanism. Therefore, to understand the genetics of SI we are studying several mapping populations. A preliminary analysis on available data from 79 individuals out of 256 trees from the cross Pound-7 x UF-273, identified a QTL on chromosome 4. Further phenotypic data collection needs to be done to confirm the statistical significance of the identified QTL. Phenotyping and genotyping of another mapping population between TSH-1188 x CCN-51 is in progress. A second approach is to look for candidate genes. Twenty-five major candidate sequences were identified after a homology search between the ESTtik database and SI genes of other plant species. Those candidate genes were amplified in cacao by PCR and sequence polymorphisms, mainly SNPs, were identified between compatible and incompatible clones. The identified SNPs were analyzed in a subset of the CATIE mapping population and mapped. Preliminary results, with less than half of the sequences analyzed, showed no correlation between the studied SNPs and SI. A third approach is to identify differentially expressed sequences using mRNA of unpollinated and compatibly or incompatibly pollinated pistils, harvested at different time points. The mRNA has been sequenced on an Illumina Genome Analyzer. Up- or down-regulated sequences will be later analyzed for SNPs and subsequently mapped onto the genome. Lastly, different microscopy techniques are used to study morphological differences in intact ovules after self-incompatible pollinations. Our goal is to identify SNPs correlated with self-(in)compatibility for marker assisted selection and allele mining of the available germplasm for breeding purposes.

Technical Abstract: Self-incompatibility (SI) in plants prevents self-fertilization. SI in cacao is sporo-gametophetic, and so far, no genes regulating this phenomenon have been identified. To understand the genetics of SI we are studying several mapping populations. A preliminary analysis on available data from 79 individuals out of 256 trees from the cross Pound-7 x UF-273, identified a QTL on chromosome 4, but further phenotypic data collection is necessary to confirm its statistical significance. We are also using a candidate gene approach. An ESTtik database search for homology with SI genes of other plant species identified 25 major candidate sequences. Those were amplified in cacao by PCR and sequence polymorphisms, mainly SNPs, were identified between compatible and incompatible clones. Subsequently, identified SNPs were analyzed in a subset of the CATIE mapping population and mapped. Preliminary results, with less than half of the sequences analyzed, showed no correlation between the studied SNPs and SI. Our third approach is to identify differentially expressed sequences using mRNA of unpollinated and compatibly or incompatibly pollinated pistils, harvested at different time points. The mRNA has been sequenced on an Illumina Genome Analyzer. Pistil-specific sequences will be identified via comparison of the pistil transcriptome with the available leaf transcriptome. Up- or down-regulated sequences will be later analyzed for SNPs and subsequently mapped. Lastly, CLSM is used to study morphological differences in intact ovules after self-incompatible pollinations. Our goal is to identify SNPs correlated with self-(in)compatibility for marker assisted selection and allele mining of the available germplasm for breeding purposes.

Last Modified: 4/20/2014
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