The physiological roles of mycorrhizal fungi, including arbuscular mycorrhizal fungi on seedlings and nut trees, are increasingly studied. Mycorrhizal fungi provide beneficial symbiosis in the roots of nut trees, accelerate plant growth and biomass production, nutrient acquisition, and increase potential tolerance to abiotic stress, e.g., drought and salt tolerance. Consequently, future outlooks in this field seem optimistic.In pistachio, several fungal and bacterial diseases can infest both the above-ground and under-ground tree parts. Among these, Phytophthora root and crown rot , Armillaria root rot , and Verticillium wilt are the three most serious soil borne fungal diseases of pistachio trees worldwide. The P. vera is the only pistachio species that produces edible nuts large enough for commercial use . Initial evaluations demonstrated that the P. vera seedling trees were susceptible to soilborne pathogens Phytophthora spp.; Verticillium dahlia, and nematodes.Therefore, other available Pistacia spp. were used as root stocks. Verticillium wilt has killed a majority of the trees in the late 1970s and caused growers the most severe economic losses ever experienced in California. A small number of P. integerrima seedlings from an Iranian seedling tree selected and planted at the USDA Plant Introduction Station in Chico were found to be tolerant to Verticillium wilt; the trees can be infested but exhibit few symptoms and no mortality. This P. integerrima seedling root stock was quickly commercialized as Pioneer Gold 1 . Verticillium-tolerant P. integerrima was then used to produce UCB1 which is moderately resistant to this disease; it exhibits mild symptoms when infested but, as with PGI, no mortality. The P. atlantica and P. terebinthus root stocks are susceptible to Verticillium wilt . Armillaria root rot occasionally affects pistachio and resistant root stocks would offer the best protection.

Field trials indicate that P. terebinthus and UCB1 are tolerant,blueberry plant pot whereas P. atlantica and P. integerrima are susceptible to this pathogen. Root and crown rot caused by Phytophthora spp. also can affect pistachio trees. According to Ferguson et al., UCB1 and P. atlantica are more tolerant to Phytophthora root and crown rot than P. integerima. Epstein et al. studied the resistance of four root stocks to Verticillium dahlia. Yield, growth, incidence of Verticillium symptoms, and mortality rates were studied for 10 consecutive years. UCB1 and P. integerrima showed the greatest tree vigor, and UCB1 had the fewest symptoms. UCB1 is also resistant to Phytophthora. Thus, UCB1 has become the major root stock in California. However, a stunted and difficult-to-graft phenotype has emerged in California in clonally reproduced UCB1 root stocks from multiple sources. This has been at times, since 2010, a serious production problem which has been variously attributed to either somaclonal mutation during in vitro propagation or to Rhodoccus sp. bacterial infection, Chang et al.. The syndrome was identified by its appearance as Pistachio Bushy Top Syndrome, PBTS. However, as this problem proved to be non-transmissible in the field, and nurseries can now identify it in young root stocks, it is no longer a problem. Nouri et al. reported a new pathogen, Macrophomina phaseolina in Kern County of California which is characterized by wilted foliage combined with crown rot of the root stock. UCB1 is highly susceptible to M. phaseolina and this pathogen is now an emerging threat to pistachio production in California. One important biotic stress in Persian walnut is black line disease caused by Cherry leaf roll virus. Persian walnut tolerates this virus and is generally symptomless. In contrast, J. hindsii or its hybrids are resistant to CLRV. Blackline symptoms occur when a hypersensitive root stock [Northern California Black walnut , other black walnuts, or hybrids of these with J. regia, are used as root stock for Persian walnut. The virus is transmitted through infected pollen and scions. The pollenborne virus enters through flowers during pollination and is systemically transported to the graft union. The resulting hypersensitive reaction of the root stock and death of tissue at the graft union blocks nutrient and water transport between the root stock and scion.

The hypersensitive response to this virus is controlled by a single dominant gene. To develop CLRV-resistant scion cultivars capable of blocking the virus at the pistillate flower and/or movement toward the graft union, a breeding program was initiated in 1984 the University of California-Davis to backcross resistance from Paradox into scion cultivars with commercially acceptable horticultural traits. This program is still ongoing. A DNA marker related to CLRV-resistance that maps to ~6.2 Mb onchromosome 14 has been developed in order to accelerate selection of CLRV-resistant offspring. In continuation of work started by E. Germain , a hybrid resistant to black line is in evaluation to be registered in France. In California, screening of a huge multi-species Juglans population, J. regia, J. microcarpa, J. major, J. cathayensis, and others and targeted interspecies hybridization between the selected superior genotypes to produce root stocks resistant to the soil borne pathogens, Agrobacterium tumefaciens, Phytophthora spp.; Pratylenchus vulnus, and Armillaria mellea, has been in progress for several years and is continuing. Crown gall is a major root stock issue in walnuts, particularly when using Paradox hybrid root stocks. This bacterial disease can significantly reduce production and increase management costs. The RNAi technology, RNA interference has been used experimentally to suppress genes involved in the plant response to the bacterium. Silencing of tryptophan monooxygenase and isopentenyl transferase genes blocks bacterial induction of de novo auxin and cytokinin and therefore prevents gall development. Using RNAi-mediated silencing technology, walnut researchers at UC-Davis were also able to develop apparent nematode resistance in Paradox microshoots evaluated in vitro but this work has not been confirmed in the greenhouse or field trials. Nematodes are another serious problem for nut growers. Three separate root-knot nematode resistance genes have been identified in Prunus species, Ma in the Myrobalan plum clones ‘P29800 and ‘P21750 , RMia in the peach root stock ‘Nemared’, and RMja in the bitter almond ‘Alnem’. Pyramiding of these three genes by interspecific crosses of almond × peach × Myrobalan is the main objective of the French root stock breeding program. 

To ensure the presence of the three genes in the same root stock, it has been necessary to develop effective molecular markers. The identification of intra-gene markers for nematode-resistance genes Ma and RMia has allowed the application of marker-assisted selection for these two genes. The RMja gene is located on linkage group 7 of the Prunus genome in the same region as the Ma gene. Chestnut cultivation has been threatened by chestnut blight and root rot diseases. The first pandemic disease for chestnut was root rot. Today two species of root rot are widelyspread in Europe and Asia Minor. The most effective method against root rot disease is using resistant root stocks. Due to the resistance to root rot, C. crenata and C. mollissima trees were imported into Europe at the beginning of the 19th century. The following years showed that their nut quality was low, and they were sensitive to spring frosts. Therefore, they were used as root stocks. However, graft incompatibility was observed. In France, two of these genotypes were registered as ‘Ipharra’ and ‘Marki’. Schad et al. planted some superior genotypes in orchards infected with Phytophthora spp. in 1946. As a result of this study, natural hybrids of C. crenata × C. sativa were obtained [260,261]. Amongst those, ‘Marsol’ and ‘Maraval’ have been used as resistant root stocks. ‘Marigoule’ has been used in forest areas due to its fast-growing characteristic. Now, ‘Marigoule’ is also used as root stocks in many countries due to its resistance to root rot and tolerance to the chestnut blight . However, seedlings of the ‘Marigoule’ are not tolerant or resistant to these diseases as a scion cultivar. Ten years of observation have demonstrated that ‘Marigoule’ seedling survival from root rot is only 10% greater than European chestnut seedlings. As a continuation of these studies, in 1980,plastic gardening pots a new breeding program was initiated in France. Early results showed that ‘Maridonne’ and ‘Marlhac’ root stocks could also be used against root rot . This breeding program is continuing. A similar program was also initiated in Spain by Gallasteguie in 1926 and continued by Urquijo. They imported some chestnut genotypes from Korea and Japan between 1917 and 1940. In this study, 263,000 genotypes were tested and 12,000 of these were found resistant to Phytophthora. As a result of this study, genotypes 111-1, 7521, and 1483 were selected for both resistance to root rot and better graft compatibility with chestnut cultivars. Genotypes ‘CHR-1510 , ‘CHR-1370 , ‘CHR-1680 , ‘CHR-1610 , ‘CHR-310 , ‘CHR-1490 , ‘CHR-1470 , ‘CHR-1670 , and ‘7760 also were found promising. Hybridization has been undertaken in several countries, including Portugal, Italy, Australia, and USA, to obtain root rot-resistant root stocks. A limited number of resulting hybrids were used commonly but most of them exhibited graft incompatibility problems. One example is ‘Menzies’ , commonly used as a seedling root stock source in Australia for its resistance to root rot. In Asia, chestnut production is from C. crenata and C. mollissima trees which are naturally resistant to chestnut blight and root rot but are sensitive to the Asian chestnut gall wasp . In Japan, seedlings of ‘Shibaguri’ have been used as scions for production but devastation from the gall wasp has reduced yield. In recent years, due to graft incompatibility problems, they have started using seedlings of the chosen scion cultivar as seedling root stocks. Scions and root stocks can interact at trans-graft-union movement at the molecular level in different ways. In some cases, mobile macromolecules and large signaling molecules can move through the graft union via the vascular system and regulate various physiological processes in scion including vigor, yield, water use efficiency, biotic and abiotic resistance, etc..

RNAs and proteins can be targeted to move up through the graft union and this process has been studied in various vegetable and fruit trees. In addition, some studies have focused on protein production in transgenic root stocks with targeted delivery to scions to control disease. Transgenic root stocks expressing a polygalacturonidase inhibitory protein , were able to protect wild type scion from both a bacterial disease caused by Xylella fastidiosa and a fungal disease caused by Botrytis cinereal, both pathogens use polygalacturonase as a virulence factor. Recently, the strategy of delivering therapeutic proteins from a root stock to a scion was validated in the field where transgenic root stocks were able to transgraft protected a sensitive wild type scion variety from succumbing to Pierces Disease.Transgrafting also holds great promise for the improvement of nut tree root stocks. Commercially accepted scion cultivars grafted onto transgenic root stocks could benefit from the root stock-mediated increase in productivity and/or disease resistance while avoiding potential consumer concerns regarding use of any transgenic scion. Rootstocks can also be improved with enhanced features while simultaneously designed to avoid transmission of macromolecules or products to the scion. As discussed in the biotic stress section, a crown gall resistant root stock was generated by silencing ipt and iaaM genes responsible for tumor formation. Examination for movement from the transgenic root stock to a standard untransformed scion showed that none of the genes or their products transfer through graft union. This method can produce root stocks with enhanced disease resistance or other features while avoiding concerns about changes in the scion or food product.The technique of producing trees on root stocks means two species are genetically joined and therefore can affect one another’s performance. The selection of root stock is an important aspect of orchard management. In nut tree crops, root stocks influence vigor, rooting ability, water and nutrient uptake, bud break timing, yield, nut quality, susceptibility to abiotic factors including temperatures, drought, waterlogging and salinity, and biotic factors, including crown gall, root rot, root-knot nematodes and soil borne fungal infections, harvest efficiency and post harvest nut quality. And now, producing sustainable orchards which can meet the challenges of climate change and economic production, producing better root stocks is even more important. Breeding tree nut crop root stocks began many years ago when local growers near the centers of a species origins started collecting and domesticating the best wild species tolerant to abiotic and biotic stresses and that also produced good nuts.