Fig. 2: Illustrative scheme for gene cloning by combining genetic, genomic and transcriptomic approaches.

a Using genetic approaches (such as quantitative trait loci (QTL) mapping in F1 progenies or association analysis across a panel of accessions), major genes or QTLs can be detected for important ornamental traits and located on the seven rose linkage groups. b In the corresponding region of the rose genome sequence, using the functional annotation of the rose genome (each purple box represent an annotated gene), putative candidate genes can be identified based on similarities with genes known to be involved in the studied process in model plants such as Arabidospis thaliana. In the candidate genomic region, five genes have been identified with possible roles (pink boxes), as transcription factors. c By transcriptomic approach, a differentially expressed gene between two contrasting conditions for the studied trait can be identified. d For the gene with contrasting expression, allelic variants can be identified by sequencing mutant pairs or diversity panels. In this example, two alleles are detected, which differ by an indel. Other variants can be single-nucleotide polymorphisms (SNPs) (synonymous or non-synonymous) or insertions of transposable elements