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.
ABSTRACT
ABSTRACT Cacao (Theobroma cacao L.) breeding programmes in Ecuador have focused on obtaining high-yield clones with improved disease resistance. Cacao clones should also have photosynthetic characteristics which support increased productivity. Regarding the weather conditions at the coast of Ecuador, where most of the year there are overcasts and low air evaporative demand, there is the possibility to grow cacao without overhead shade. This study focused on the photosynthetic response at two different photosynthetic photon flux densities (PPFD) of Ecuadorian cacao clones. Seven-year old cacao clones were evaluated: eight clones of Nacional type and two commercial clones (CCN 51 and EET 103), used as controls. All clones showed an increase of 35 % on average in net photosynthetic rate (A)with increasing PPFD from the light saturation point for cacao (i.e. 400 μmol m-2 s-1) to high values (1000 μmol 2 s-1). Such light responsiveness in A has not been reported before. Higher A was associated with higher apparent electron transport rate, while high stomatal conductance was maintained under both PPFD conditions. Under high PPFD, low non-photochemical quenching values were found, suggesting low energy dissipation. All clones showed high maximum quantum yields of PSII (Fv/Fm), suggesting the absence of damage of the photochemical system.
RESUMEN Los programas de mejoramiento de cacao (Theobroma cacao L.) en Ecuador se han centrado en la obtención de clones de alto rendimiento con mayor resistencia a las enfermedades. Estos clones también deben tener características fotosintéticas que apoyen una mayor productividad. En las condiciones climáticas en la costa de Ecuador, donde la mayor parte del año hay alta densidad de nubes y baja demanda evaporativa, existe la posibilidad de cultivar cacao sin sombra. Este estudio se centró en la respuesta fotosintética de clones de cacao del Ecuador en dos diferentes densidades de flujo de fotones fotosintéticos (PPFD). Se evaluaron diez clones de cacao de siete años de edad: ocho clones de tipo Nacional recientemente desarrollados por el Instituto Nacional de investigaciones Agropecuarias, y dos clones comerciales utilizados como controles (CCN 51 y EET 103). Todos los clones de cacao mostraron un aumento del 35 % en promedio en la tasa fotosintética neta (A) con el incremento del PPFD desde el punto de saturación de luz para el cacao (400 μmol m -2 s -1) hasta valores altos (1000 μmol m -2 s- 1). Dicha respuesta de A a estas condiciones de luz alta no se ha reportado en cacao. La tasa fotosintética neta se asoció con una mayor velocidad aparente de transporte de electrones (J), mientras que la alta conductancia estomática (gs) se mantuvo en ambas condiciones de PPFD. En condiciones de alto PPFD, se encontraron bajos valores del coeficiente de extinción no fotoquímico (NPQ), lo que sugiere una baja disipación de energía, además de presentarse altos rendimientos cuánticos máximos de PSII (Fv / Fm), indicando la ausencia de daño del sistema fotoquímico.
