Dissecting the genetic architecture of early root-related traits in grapevine rootstocks across propagation methods and different scion

Root traits are fundamental to plant establishment and survival, influencing resource acquisition, anchorage, and stress resilience. In grapevine, a perennial grafted fruit crop, early growth-related traits, such as rooting and grafting success, are crucial for both vineyard establishment and nursery production, which require well-developed rootstock mother vines and grafted plants. An understanding of the genetic variability underlying these traits is therefore important. We investigated the genetic architecture of early growth-related traits in a Vitis berlandieri × V. rupestris mapping population of 449 genotypes, using hardwood cuttings and grafted plants with two scion cultivars: V. vinifera cvs. Cabernet Sauvignon and Riesling. Our results indicate that the genetic control of these traits was polygenic and varied with the method of propagation (cuttings vs grafts), with individual QTLs explaining from 3.1% to 14.1% of the phenotypic variance. In particular, we detected largely non-overlapping genomic regions associated with similar traits across propagation methods and observed rootstock × scion interactions, suggesting an influence of scion genotype on root development. Two overlapping roots number QTLs were identified in grafts with different scions accounted for 7 and 14% of the variance in Cabernet Sauvignon and Riesling, respectively. Our results highlight the challenge of applying marker-assisted selection in rootstock breeding programs, due to the different genetic determinants underlying the same traits across the different propagation methods. Here, we found that QTLs colocalized with genes involved in growth and stress responses. Finally, eight genotypes with root-related performance superior to that of commercial rootstocks were identified, providing promising candidates for further evaluation in grapevine rootstock breeding programs.