Genome-wide association study and marker development for adventitious root formation in rose

Garden and cut roses often have to be propagated via costly and laborious grafting, among others due to limited adventitious root (AR) formation of cuttings. The complex process of AR formation is not fully understood and reasons for genotypic differences in rooting ability are not identified for rose yet. In this study, a garden rose population and a cut rose population of 96 genotypes each were phenotyped for AR formation in hydroponic rooting experiments. The genotypic information based on single nucleotide polymorphisms (SNPs) of the WagRhSNP 68k Axiom^® SNP array was used to perform genome-wide association studies (GWAS). During the six weeks rooting period, some cuttings turned black and rotted. Therefore, the effect of including or excluding these cuttings that do not survive on GWAS results and on variance components for rooting percentages after five weeks of cultivation was evaluated. We could show that differences in GWAS results were negligible between the two ways of calculating the rooting percentage, both for garden and cut roses. Although we could not find any significantly associated SNPs for rooting when applying a conservative p-value, six promising SNP clusters forming distinctive peaks could be defined. Within these SNP clusters, homologs for genes that were already described to be involved in AR formation in literature, for example ARF16 (AUXIN RESPONSE FACTOR 16), ERF1 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 1), SCR (GRAS family transcription factor) or GH3 (GRETCHEN HAGEN3) were found. They are the basis of future research aiming at developing markers for AR formation, but also for functional studies.