Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)

Abstract

Cacao (Theobroma cacao L.), the source of chocolate, is one of the most important commodity products worldwide that helps improve the economic livelihood of farmers. Diseases like frosty pod rot caused by Moniliophthora roreri and witches’ broom caused by Moniliophthora perniciosa limit the cacao productivity, this can be solved by using resistant varieties. In the current study, we sequenced 229 cacao accessions using genotyping-by-sequencing to examine the genetic diversity and population structure employing 9,003 and 8,131 single nucleotide polymorphisms recovered by mapping against two cacao genomes (Criollo B97-61/B2 v2 and Matina 1-6 v1.1). In the phenotypic evaluation, three promising accessions for productivity and 10 with good tolerance to the frosty pod rot and witches’ broom diseases were found. A genome-wide association study was performed on 102 accessions, discovering two genes associated with productivity and seven to disease resistance. The results enriched the knowledge of the genetic regions associated with important cacao traits that can have significant implications for conservation and breeding strategies like marker-assisted selection.

Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses

“…The GBS method that uses two restriction enzymes is a highly effective method for reducing genome complexity and generating high-quality SNP markers in several crops, including barley, wheat ( Poland et al, 2012 ), and cacao ( Osorio-Guarin et al, 2020 ), which was also demonstrated in the present study. The GBS method has been used previously for simultaneous SNP discovery and genotyping in finger millet ( Kumar A. et al, 2016 ; Gimode et al, 2016 ; Qi et al, 2018 ; Tiwari et al, 2020 ).…”

Prioritizing Colombian plant genetic resources for investment in research using indicators about the geographic origin, vulnerability status, economic benefits, and food security importance

“…The cocoa collection conserved in the BGVCOL has 565 accessions characterized at the genomic level. The analysis demonstrated a high genetic diversity among groups, supporting that some genetic groups originated in Colombia, which probably is a center of origin for this crop [78].Moreover, this collection has association studies that support a breeding program [79,80]. In addition, researchers from Agrosavia conducted two expeditions in the upper Amazon and the Pacific, searching for wild cacao relatives.…”

Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacaoL.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential

“…Da Silva et al [96] identified markers on chromosome 4, which were putatively colocalized with a major gene encoding self-incompatibility. Osorio-Guarín et al [97] detected two genes putatively associated with productivity (number of healthy fruits) and seven encoding Frosty Pod disease resistance. It must be borne in mind that genetic variation of quantitative (polygenic, continuous) traits such as yield and disease resistance are controlled by the combined effects of QTL, epistasis (interactions between QTLs) [14], the environment and interaction between environment and QTL [98].…”