Abstract
Chocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and widespread pathogens. A panel of 148 improved cacao clones was assembled based on productivity and disease resistance, and phenotypic single-tree replicated clonal evaluation was performed for 8 years. Using high-density markers, the diversity of clones was expressed relative to 10 known ancestral cacao populations, and significant effects of ancestry were observed in productivity and disease resistance. Genome-wide association (GWA) was performed, and six markers were significantly associated with frosty pod disease resistance. In addition, genomic selection was performed, and consistent with the observed extensive linkage disequilibrium, high predictive ability was observed at low marker densities for all traits. Finally, quantitative trait locus mapping and differential expression analysis of two cultivars with contrasting disease phenotypes were performed to identify genes underlying frosty pod disease resistance, identifying a significant quantitative trait locus and 35 differentially expressed genes using two independent differential expression analyses. These results indicate that in breeding populations of heterozygous and recently admixed individuals, mapping approaches can be used for low complexity traits like pod color cacao, or in other species single gene disease resistance, however genomic selection for quantitative traits remains highly effective relative to mapping. Our results can help guide the breeding process for sustainable improved cacao productivity.
Highlights
The perennial tree Theobroma cacao is an important crop for tropical small-holder farmers
The 121 superior clones were chosen among closely related selections in order to maximize allele replication, which in turn placed most segregating alleles in high minor allele frequency (MAF) (Supplementary Figure 1), where there is the highest statistical power for association (Korte and Farlow, 2013)
The use of genetic markers to increase breeding program efficiency remains limited in tropical tree crops
Summary
The perennial tree Theobroma cacao is an important crop for tropical small-holder farmers. Unlike M. roreri, the presence of sexual structures (Vujicic, 1971) have shown that P. palmivora can undergo sexual reproduction, similar to most Phytophthora species the majority of spores produced by P. palmivora are asexual (Judelson and Blanco, 2005) Both diseases can be controlled to a certain extent through laborintensive sanitation combined with optimal crop management practices(Evans, 2007), the use of clonal cultivars with genetic disease resistance can provide a cost- and labor-efficient approach for farmers to manage both diseases, and multiple QTL have been mapped for disease resistance in cacao (Brown et al, 2007; Lanaud et al, 2009)
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