Feature Review Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes Emily J. Warschefsky, 1,2 Laura L. Klein, 3,4 Margaret H. Frank, 5 Daniel H. Chitwood, 5 Jason P. Londo, 6 Eric J.B. von Wettberg, 1,2,7 and Allison J. Miller 3,4,@, * Grafting is an ancient agricultural practice that joins the root system (rootstock) of one plant to the shoot (scion) of another. It is most commonly employed in woody perennial crops to indirectly manipulate scion phenotype. While recent research has focused on scions, here we investigate rootstocks, the lesser- known half of the perennial crop equation. We review natural grafting, grafting in agriculture, rootstock diversity and domestication, and developing areas of rootstock research, including molecular interactions and rootstock micro- biomes. With growing interest in perennial crops as valuable components of sustainable agriculture, rootstocks provide one mechanism by which to improve and expand woody perennial cultivation in a range of environmental conditions. Getting to the Root of the Matter Roots anchor plants in the ground, acquire water and nutrients from the soil, serve as storage organs, and are the primary zone of contact with soil organisms. Root systems vary substantially in architecture and function, both within and between species, and they are a crucial component in coordinating plant responses to a range of abiotic and biotic stressors, including pathogens, water and nutrient shortages, and potentially toxic compounds such as salt or heavy metals (e.g., [1–4]). In perennial crops and some annuals, grafting is used to join resilient root systems (rootstocks) to shoots (scions) that produce the harvested product (e.g., fleshy or dry fruits). The vast majority of woody perennial plant cultivation involves clonal propagation [5–7], a technique that facilitated the domestication of the earliest woody crops including olive, grape, and fig [8]. In these and many other species, grafting is an important part of the propagation process. Grafting typically joins two plant organs (root system and shoot) from different individuals that form vascular connections and survive in a unique symbiotic relationship as a genetic chimera [8]. The development of grafting around 1800 BCE facilitated a ‘second wave’ of woody perennial domestication and resulted in the wide-scale cultivation of new woody crops, including many Rosaceae (apple, pear, plum, and cherry), and the improvement of previously ungrafted, clonally propagated perennials [8,9]. In long-lived woody plants, grafting is a common means to clonally propagate desirable scions, thus side-stepping challenges traditionally associated with breeding of woody perennials, including prolonged juvenile phases and primarily outcrossing reproductive systems [5]. It is becoming increasingly apparent that the use of genetically distinct individuals as rootstocks serves to improve perennial crops, with different rootstocks conferring unique traits in both belowground and aboveground components of the plant [8]. In addition to reducing the time to Trends As concerns mount about food secur- ity in a changing climate, attention is refocusing on perennial crops as important components of sustainable agriculture. In many economically important woody perennial crops (e.g., many Rosaceae, Citrus, and grapes), a fruit-bearing shoot (scion) is grafted to a root system (rootstock) that is genetically distinct from the scion. Rootstocks are selected for rooting and grafting capacity, abiotic and biotic stress tolerance, and their ability to beneficially alter scion phenotypes. Relatively little is known about the diversity of rootstocks used for any given crop, the geographic origins or current distribution of cultivated root- stocks, or their domestication. A common scion can be grafted to segregating rootstock populations to produce a genetic map of both the traits of the rootstocks themselves and their effects on scion phenotype. 1 Florida International University, Department of Biological Sciences, 11200 Southwest 8th Street, Miami, FL 33199-2156, USA 2 Fairchild Tropical Botanic Garden, Kushlan Tropical Science Institute, 10901 Old Cutler Road, Coral Gables, FL 33156-4233, USA 3 Saint Louis University, Department of Biology, 3507 Laclede Avenue, St. Louis, MO 63103-2010, USA 418 Trends in Plant Science, May 2016, Vol. 21, No. 5 http://dx.doi.org/10.1016/j.tplants.2015.11.008 © 2015 Elsevier Ltd. All rights reserved.