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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Research Project #431653

Research Project: Identification of Molecular Markers Associated with Self-incompatibility in Theobroma Cacao

Location: Subtropical Horticulture Research

Project Number: 6038-21000-025-15-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 30, 2016
End Date: Dec 31, 2020

The primary goal this collaborative research project is to dissect the genetic mechanisms involve in inheritance of self-incompatibility in cacao. The project has three specific goals: (1) identify the genes responsible for the regulation of self-incompatibility in cacao; (2) develop SNP markers that could be used for selecting self-compatible cultivars; and (3) understand the dominance relationship between the self-compatible alleles within the cocoa population by analyzing the self-incompatibility status of progenies from 99 crosses between accessions from various genetic groups.

Cacao production is plagued by very serious losses globally from insects and pests. However, yield reduction in new cultivars selected for insect and disease resistance could be due to self-incompatibility (SI). Genes associated with the process of SI in cacao have not been identified yet; the discovery of molecular markers associated with alleles that are involved in SI will be useful for selecting self-compatible cultivars with higher yields within breeding populations. To attain these goals, 150 cacao clones were sequenced at Stanford University, and of these 117 clones are currently planted at the International Cacao Genebank in Trinidad (ICG, T). In addition, these clones belong to the ten genetic groups and their self-incompatibility status needs to be studied and correlated with genomic data so that candidate genes or markers associated with self-incompatibility could be ascertained and validated. Furthermore, this research project also presents an opportunity to investigate the relationship between self-incompatibility alleles in the genetically variable cacao collection. Therefore, this study aims at better understanding the genetics of self-incompatibility of selected cacao genotypes, as well as characterizing self-compatibility and yield evaluation of these clones. The project will allow for breeders to design mating design and select for self-compatibility at a seedling stage. This work through the understanding of allelic relationships will also allow for better deployment of cross compatible clones in farmer fields without the usual delays associated with conducting cross compatibility studies. Uniform pollination data are crucial for obtaining precision in the results of marker association studies. If we do not have uniform phenotypic pollination data, to use together with the sequence data from two cacao genomes, our marker association project results will lack the necessary precision to accomplish the primary goal of the cacao breeding program which is the development of high yielding cacao cultivars utilizing the new molecular genetic tools to increase the efficiency of the selection process. Phenotypic self-incompatibility data will be collected from the 117 accessions by selfing 8-12 flowers and harvesting the selfed flowers after 4-5 days and studying the proportion of successful fusions in the ovaries. The accessions will be subjected to the necessary agronomic practices to induce flowering and fruit set, six weeks prior to the initiation of the study. Unopened flower buds will be isolated/covered the day before pollination. The study will be also be conducted in grafted accessions in the greenhouse to further expedite the work. These accessions were grafted two years ago and are now flowering. In addition, selfing will be conducted on verified parents from the various crosses already established in the genebank. Approximately, five progeny from 25 selected crosses will be studied for the rates of successful fusions.