Abstract
Cacao (Theobroma cacao) is a globally important crop, and its yield is severely restricted by disease. Two of the most damaging diseases, witches’ broom disease (WBD) and frosty pod rot disease (FPRD), are caused by a pair of related fungi: Moniliophthora perniciosa and Moniliophthora roreri, respectively. Resistant cultivars are the most effective long-term strategy to address Moniliophthora diseases, but efficiently generating resistant and productive new cultivars will require robust methods for screening germplasm before field testing. Marker-assisted selection (MAS) and genomic selection (GS) provide two potential avenues for predicting the performance of new genotypes, potentially increasing the selection gain per unit time. To test the effectiveness of these two approaches, we performed a genome-wide association study (GWAS) and GS on three related populations of cacao in Ecuador genotyped with a 15K single nucleotide polymorphism (SNP) microarray for three measures of WBD infection (vegetative broom, cushion broom, and chirimoya pod), one of FPRD (monilia pod) and two productivity traits (total fresh weight of pods and % healthy pods produced). GWAS yielded several SNPs associated with disease resistance in each population, but none were significantly correlated with the same trait in other populations. Genomic selection, using one population as a training set to estimate the phenotypes of the remaining two (composed of different families), varied among traits, from a mean prediction accuracy of 0.46 (vegetative broom) to 0.15 (monilia pod), and varied between training populations. Simulations demonstrated that selecting seedlings using GWAS markers alone generates no improvement over selecting at random, but that GS improves the selection process significantly. Our results suggest that the GWAS markers discovered here are not sufficiently predictive across diverse germplasm to be useful for MAS, but that using all markers in a GS framework holds substantial promise in accelerating disease-resistance in cacao.
Highlights
Cacao (Theobroma cacao) is tropical understory tree native to the Amazon basin that produces one of the world’s most valuable agricultural commodities: cacao beans
Malvinas had several significant associations (6) for monilia pod, spread over five chromosomes, including one on chromosome 9 that lay in relatively close proximity (∼750 kbp) to a similar marker found in Las Tecas
In a study of three related populations of cacao, several markers were identified for disease resistance and productivity via genomewide association studies (GWAS), but these were not consistent across populations, perhaps due to their distinctive germplasm structure
Summary
Cacao (Theobroma cacao) is tropical understory tree native to the Amazon basin that produces one of the world’s most valuable agricultural commodities: cacao beans. BPR is by far the most serious pathogen in terms of annual losses, WBD and FPRD may have the potential to be even more damaging due to the fact they have not yet spread to West Africa, the largest center of cacao production (Ploetz, 2007). Both WBD and FPRD are caused by basidiomycete fungi (Moniliophthora perniciosa and M. roreri, respectively), which are closely related (Aime and Phillips-Mora, 2005; Meinhardt et al, 2014). These strategies, are considered ‘short- to medium-term’ (Hebbar, 2007); longterm solutions will require the development of disease-resistant germplasm
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