o Risterucci et al. (2000) protocol.Genotyping by SSRThis population was genotyped using SSR markers by Loor (2007). SSR loci have been scored individually and alleles have been recorded by the presence of polymorphic DNA fragments (alleles) among the men and women of each population. Only these alleles that showed constant amplification have been used in the evaluation of final results and smeared or weak bands were ignored.Sensorial AnalysisOne hundred and forty-six individuals have been characterised by sensory mGluR7 custom synthesis analyses determined by blind tastings carried out on three repetitions per sample. The tastings had been carried out on cocoa liquor. The cocoa liquor corresponds to merchant cocoa (dried fermented beans) which have been roasted and crushed. Sixteen floral notes have been judged using a score ranging from zero (no floral notes detected) to ten. We applied the typical on the 3 replicates for the phenotype with the GWAS analysis (ISCQF, 2020). This study was managed by Mr. Edward Seguine, whose perform consists of conducting sensory analyses of chocolate samples (see attached documents). This study doesn’t call for the approval of an ethics committee.Genotyping by SequencingDNA samples have been genotyped by sequencing (GBS) working with DArTseq (Diversity Arrays Technologies Sequencing) technology (Kilian et al., 2012). This strategy is based on enzymatic restriction of coding regions from the genome by the restriction enzymes: Pst1 and Mse1. The restriction generated lots of brief fragments, with each locus represented extra than ten NPY Y5 receptor medchemexpress instances. Then, illumina Hiseq2000 machine sequenced all the fragments plus the outcome was analysed. Reads had been aligned with all the V2 sequence of the Criollo genome (Argout et al., 2017). Reads that have a lot more than one location were discarded. Markers with unknown places have been discarded for analysis. Each of the markers applied are offered on http://tropgenedb.cirad.fr/tropgene/JSP/interface.Volatile Compound Evaluation by GC-MSPreparation of Cocoa SamplesThe evaluation of VOCs was carried out on dried fermented beans and roasted beans. For every sample, 50 g of beans were taken. The beans were deshelled and crushed to acquire nibs. Then,Frontiers in Plant Science | frontiersin.orgSeptember 2021 | Volume 12 | ArticleColonges et al.Floral Aroma Cocoa Genetic Determinismjspmodule=COCOAinthegenotypessectionandtheCocoaNacional-aromasub-section.Population’s Structure AnalysisThe phylogenetic tree was generated utilizing DARwin computer software (Perrier and Jacquemoud-Collet, 2006). The genetic distances have been calculated applying the Dice coefficient and also the NeighbourJoining technique (Dice, 1945; Saitou and Nei, 1987).parameters. The haplotypic block data was made use of to establish the confidence intervals of association locations. The physical maps with the QTL representation were developed working with SpiderMap v1.7.1 computer software (Rami, 2007 unpublished). The size of the dots is correlated to the R2. The identification of candidate genes was performed using the Theobroma cacao genome sequence (Argout et al., 2017).Association MappingThe graphic representation of the markers along the 10 chromosomes was created with all the R package “CMplot” (Yin, 2020). Quite a few analyses of associations with SNP or SSR markers happen to be performed:Statistical AnalysisPrincipal element analyses evaluation and visualisation have been made with the “mixOmics” R package. Calculation of correlation was created with “agricolae” R package and visualisation of correlation matrix with “corrplot” R package.SNP GWASFirst, we performed a GWAS analysis with SNP