Unraveling the genetic basis of Rhizobium rhizogenes-mediated transformation and hairy root formation in rose using a genome-wide association study

Multiple QTLs reveal the polygenic nature of R. rhizogenes-mediated transformation and hairy root formation in roses, with five key regions explaining 12.0-26.9% of trait variability and transformation-related candidate genes identified. Understanding genetic mechanisms of plant transformation remains crucial for biotechnology. This is particularly relevant for roses and other woody ornamentals that exhibit recalcitrant behavior in transformation procedures. Rhizobium rhizogenes-mediated transformation leading to hairy root (HR) formation provides an excellent model system to study transformation processes and host-pathogen interactions. Therefore, this study aimed to identify quantitative trait loci (QTLs) associated with HR formation and explore their relationship with adventitious root (AR) formation in rose as a model for woody ornamentals. A diversity panel of 104 in vitro grown rose genotypes was transformed with R. rhizogenes strain ATCC 15834 carrying a green fluorescent protein reporter gene. Phenotypic data on callus and root formation were collected for laminae and petioles. A genome-wide association study using 23,419 single-nucleotide polymorphism markers revealed significant QTLs on chromosomes one and two for root formation traits. Five key genomic regions explained 12.0-26.9% of trait variability, with some peaks overlapping previously reported QTLs for AR formation. This genetic overlap was supported by weak to moderate correlations between HR and AR formation traits, particularly in petioles. Candidate gene identification through literature review and transcriptomic data analysis revealed ten candidate genes involved in bacterial response, hormone signaling, and stress responses. Our findings provide new insights into the genetic control of HR formation in roses and highlight potential targets for improving transformation efficiency in ornamental crops, thereby facilitating future research and breeding applications.