A genomewide admixture mapping study for yield factors and morphological traits in a cultivated cocoa (Theobroma cacao L.) population

Abstract

The selection of productive varieties of modern Criollo cocoa, showing fine aromatic qualities in their beans, is of major interest for some producing countries, such as Venezuela. Cultivated populations of Modern Criollo or Trinitario varieties may be suitable for admixture mapping analysis, as large blocks of alleles derived from two identified divergent ancestors, recently admixed, are still preserved, after a few generations of recombination, similar to experimental mapping progenies. Two hundred and fifty-seven individuals from a cultivated population of Modern Criollo were selected and analysed with 92 microsatellite markers distributed along the genome. This population exhibited a wide range of variability for yield factors and morphological features. Population structure analysis identified two main subgroups corresponding to the admixture from the two ancestors Criollo and Forastero. Several significant associations between markers and phenotypic data (yield factors and morphological traits) were identified by a least squares general linear model (GLM) taking into account the population structure and the percentage of admixture of each individual. Results were compared with classical QTL analyses previously reported for other cacao populations. Most markers associated to quantitative traits were very close to QTLs detected formerly for the same traits. Associations were also identified between markers and several qualitative traits including the red pigmentation observed in different organs, mainly associated to common markers in linkage group 4.

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping

“…We demonstrate how these differences in sample-wide LD can practically impact the resolution of association mapping analyses. Using microsatellite haplotypes and phenotypic data on pod coloration, a wellunderstood cacao phenotype (Marcano et al 2008;Motamayor et al 2013), we show how association mapping analyses are far less precise in an F1-mapping population from Brazil (referred to as MP01) compared to a semi-cultivated population from Hawaii (referred to as Hawaii). Finally, given the existence of varying levels of LD in wild and cultivated cacao varieties, we highlight how careful sample selection will be a crucial factor in the efficacy of future association mapping analyses.…”

“…The Pod color phenotype in cacao have been mapped to LG 04 in various genetic backgrounds, including the MP01 population (Motamayor et al 2013), using both family-based linkage and association mapping approaches Marcano et al 2008;Motamayor et al 2013). In the most recent of these studies, extensive analysis of the trait led to the identification of four SNP variants (between 20,878,891 and 20,879,148 bp) within a MYB transcription factor gene (TcMYB113), which are strongly believed to affect pod color differences between cacao varieties (Motamayor et al 2013).…”

Cocoa Agronomy, Quality, Nutritional, and Health Aspects

“…Guiltinan (2007) and Clement et al (2004) described the value of the recently constructed cacao bacterial artificial chromosome (BAC) libraries for gene discovery in cacao. Marcano et al (2009) reported on a genome-wide mapping study for yield factors and morphological traits in cacao. Lanaud et al (2009) presented their findings on a meta-QTL analysis of resistance traits to Phytophthora spp.…”

A disease and production index (DPI) for selection of cacao (Theobroma cacao) clones highly productive and tolerant to pod rot diseases

“…Clone T1 has a higher estimated maximum annual number of pods per tree than the 36 to 40 reported by Philips‐Mora et al () and Ndoumbè‐Nkeng et al (). However, Marcano et al () have reported very high values of 72 pods per tree per year. This would result in a maximum DPI value around 518 assuming no disease losses.…”