Genome-wide association mapping of sexual incompatibility genes in cacao (Theobroma cacao L.)

Abstract

Sexual compatibility limits the production of cacao plantations, being an important selection criterion in breeding programs. However, the current method for characterizing compatibility, based on the frequency of flower setting after controlled pollination, is time consuming, requiring a long time to identify self-compatible individuals. The identification of molecular markers in genomic regions can be an alternative to allow early selection of self-compatible plants. The present study aimed to identify SNP markers associated with sexual compatibility in cacao, by utilizing genome-wide association (GWAS) mapping. A population of 295 individuals mostly from third-generation breeding populations, but also founder clones, was used. This population was phenotypically characterized by hand pollinating 8199 flowers and evaluating the flower retention 15 days after pollination. In addition, leaf samples of each individual were collected and DNA extracted for genotyping by sequencing, generating 5301 SNP markers after cleaning. Genome-wide association mapping analysis was performed using Synbreed, GCTA, and TASSEL softwares. Significant markers associated to incompatibility, likely in strong linkage disequilibrium, were found within a region of 196 kb, in the proximal end of chromosome 4, suggesting the existence of a major gene in that region. However, this result should be validated in a larger population, considering that only 295 trees were used here. When the SNP effects were treated as random in the estimation process, many other regions in the genome appears to be involved with sexual incompatibility in cacao. Candidate genes were found not only in the proximal end of chromosome 4 but also spread in several other regions of the genome.

A Larger Chocolate Chip—Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps

“…Previous QTL studies have hinted at the involvement of chromosome 4 in traits that may affect yield (Schnell et al, 2005 ; Yamada et al, 2010 ; da Silva et al, 2016 ); for example Royaert et al ( 2011 ) identified a flower drop QTL on the distal end of chromosome 4 (Royaert et al, 2011 ). In this study, we have also observed that traits related to yield, such as the number of healthy, infected, and small pods (cherelles), are associated with this same region on LG04.…”

Deciphering the Theobroma cacao self-incompatibility system: from genomics to diagnostic markers for self-compatibility

“…In this current work, we carried out fine mapping of these genome regions and identified candidate genes whose expression was then characterized during SC and SI reactions. In order to refine the existing predictive model for self-compatibility ( Da Silva et al , 2016 ), we searched for multi-allelic diagnostic simple sequence repeat (SSR) markers in the CH4 region identified by fine mapping.…”

Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases

“…GWA allows for the identification of markers in linkage disequilibrium (LD) with polymorphisms that cause phenotypic changes and can be used for quantitative trait dissection in diverse populations (Hirschhorn and Daly, 2005 ). Significant markers can then be used in marker-assisted selection programs to more efficiently integrate favorable alleles into a germplasm pool, and GWA has yielded significant markers associated with multiple agronomic and morphological traits in cacao (Marcano et al, 2007 , 2009 ; Motamayor et al, 2013 ; da Silva et al, 2016 ). Generally, GWA requires large number of individuals to tap into ancestral recombination for identifying variants associated with the phenotypes of interest, and although GWA is highly effective with low-complexity phenotypes, traits with many underlying genetic causal polymorphisms can be increasingly harder to identify, and complications such as false positives limit the application of this method.…”