Abstract
Cacao is a crop of global relevance that faces constant demands for improved bean yield. However, little is known about the genomic regions controlling the crop yield and genes involved in cacao bean filling. Hence, to identify the quantitative trait loci (QTL) associated with cacao yield and bean filling, we performed a QTL mapping in a segregating mapping population comprising 459 trees of a cross between ‘TSH 1188’ and ‘CCN 51’. All variables showed considerable phenotypic variation and had moderate to high heritability values. We identified 24 QTLs using a genetic linkage map that contains 3526 single nucleotide polymorphism (SNP) markers. Haplotype analysis at the significant QTL region on chromosome IV pointed to the alleles from the maternal parent, ‘TSH 1188’, as the ones that affect the cacao yield components the most. The recombination events identified within these QTL regions allowed us to identify candidate genes that may take part in the different steps of pod growth and bean filling. Such candidate genes seem to play a significant role in the source-to-sink transport of sugars and amino acids, and lipid metabolism, such as fatty acid production. The SNP markers mapped in our study are now being used to select potential high-yielding cacao varieties through marker-assisted selection in our existing cacao-breeding experiments.
Highlights
Breeding programs for many crops focus on the improvement of crop yield components
The main objectives of this study were (1) to map quantitative trait loci (QTL) regions associated with cacao yield components, (2) to identify candidate genes that have a higher probability of affecting the phenotypic variation of those traits, and (3) to provide reliable single nucleotide polymorphism (SNP) markers to support the selection of high-yielding cacao genotypes via marker-assisted selection
QTL mapping analysis In our QTL mapping analysis, we found 24 genomic positions spread over eight chromosomes associated with cacao yield components, and those regions may contain the primary candidate genes that control the phenotypic variation observed in MP01
Summary
Breeding programs for many crops focus on the improvement of crop yield components. Cacao yield components refer to the tree’s organs that are harvested and converted into final crop production, such as the total number of healthy pods, the fresh and dry bean weight, and the final yield. Besides resistance to biotic and abiotic stress and bean quality, yield (measured as dry bean weight in kilograms per hectare (kg/ha)) is the most economically important crop trait, and it depends on a complex interaction between different factors that include genetics, environment, crop management, and growth and development processes[1]. A primary objective is to identify reliable molecular markers flanking the regions that control such traits. Few molecular markers have been associated with cacao yield components, such as pod traits and tree vigor[2], and bean size and bean weight[3], these studies did not report any candidate genes that control these traits. The expectation is to integrate the information from QTL regions to identify gene sequences controlling the phenotypic variation of traits of interest
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