Unravelling the genetic basis of <i>Rhizobium rhizogenes</i>-mediated transformation and hairy root formation in rose using a genome-wide association study

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. <i>Rhizobium rhizogenes</i>-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 <i>in vitro</i> grown rose genotypes was transformed with <i>R. rhizogenes</i> 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.解析植物转化的遗传机制，对于生物技术领域始终具有重要意义。这一点对于玫瑰及其他在转化流程中表现出顽拗性的木本观赏植物而言尤为关键。发根农杆菌（*Rhizobium rhizogenes*）介导的转化可诱导发状根（hairy root, HR）形成，是研究植物转化过程与宿主-病原体互作的优秀模型体系。因此，本研究旨在鉴定与发状根形成相关的数量性状位点（quantitative trait loci, QTLs），并以玫瑰作为木本观赏植物的模式物种，探究其与不定根（adventitious root, AR）形成的关联关系。本研究采用由104份体外培养（in vitro）的玫瑰基因型组成的多样性关联群体，使用携带绿色荧光蛋白报告基因的发根农杆菌菌株ATCC 15834进行转化。针对叶片与叶柄，收集愈伤组织形成及根系形成的表型数据。利用23419个单核苷酸多态性标记开展全基因组关联分析，结果在1号和2号染色体上发现了与根系形成性状相关的显著QTLs。5个关键基因组区域可解释12.0%~26.9%的性状变异，其中部分峰值与此前报道的不定根形成相关QTLs存在重叠。发状根与不定根形成性状之间存在弱至中等程度的相关性，这一结果支持了上述遗传重叠现象，尤其在叶柄组织中更为显著。通过文献调研与转录组数据分析开展候选基因筛选，共鉴定得到10个参与细菌响应、激素信号转导及应激反应的候选基因。本研究结果为解析玫瑰发状根形成的遗传调控机制提供了新视角，并为提升观赏作物的转化效率指明了潜在靶点，从而可为后续相关研究与育种应用提供助力。