Hybrid Rootstocks Research Articles

Diversity of microbial, biocontrol agents and nematode abundance on a susceptible Prunus rootstock under a Meloidogyne root gradient infection.

Root-knot nematodes (RKNs) of the genus Meloidogyne are one of the most damaging genera to cultivated woody plants with a worldwide distribution. The knowledge of the soil and rhizosphere microbiota of almonds infested with Meloidogyne could help to establish new sustainable and efficient management strategies. However, the soil microbiota interaction in deciduous woody plants infected with RKNs is scarcely studied. This research was carried out in six commercial almond groves located in southern Spain and infested with different levels of Meloidogyne spp. within each grove. Several parameters were measured: nematode assemblages, levels and biocontrol agents in Meloidogyne's eggs, levels of specific biocontrol agents in rhizoplane and soil, levels of bacteria and fungi in rhizoplane and soil, fungal and bacterial communities by high-throughput sequencing of internal transcribed spacer (ITS), and 16S rRNA gene in soil and rhizosphere of the susceptible almond hybrid rootstock GF-677 infested with Meloidogyne spp. The studied almond groves showed soil degradation by nematode assemblies and fungi:bacterial ratio. Fungal parasites of Meloidogyne eggs were found in 56.25% of the samples. However, the percentage of parasitized eggs by fungi ranged from 1% to 8%. Three fungal species were isolated from Meloidogyne eggs, specifically Pochonia chlamydosporia, Purpureocillium lilacinum, and Trichoderma asperellum. The diversity and composition of the microbial communities were more affected by the sample type (soil vs rhizosphere) and by the geographical location of the samples than by the Meloidogyne density, which could be explained by the vigorous hybrid rootstock GF-677 and a possible dilution effect. However, the saprotrophic function in the functional guilds of the fungal ASV was increased in the highly infected roots vs the low infected roots. These results indicate that the presence of biocontrol agents in almond fields and the development of new management strategies could increase their populations to control partially RKN infection levels.

Impact of Cucurbita and Cucumis rootstocks on the performance and quality of Piel de Sapo melon

Melon grafting represent an increasingly important strategy against biotic and abiotic stresses. Cucurbita hybrid rootstocks have been extensively developed for this purpose, but it is necessary to find new alternatives. In this work, several experimental rootstocks of cultivated and wild resources from the Cucurbita and Cucumis genera have been evaluated using Piel de Sapo melon as scion. Cucurbita rootstocks tended to increase fruit size and seed cavity and offered more rounded shapes at the early stages of ripening, but this effect was later minimised. Cucumis rootstocks tended to show less vigour than those of Cucurbita. C. metuliferus hybrid rootstock caused plant collapse at specific environmental conditions, probably due to differences in the growth of rootstock and scion. One of the Cucurbita maxima x C. moschata and the Cucurbita pepo experimental hybrids were also less vigorous, delaying flowering and fruit set, and compromising yield. The effects of Cucurbita and Cucumis rootstocks on sugar and acid accumulation of Piel de Sapo were almost negligible, but they altered the volatile profile. This last impact depended on the specific scion x rootstock interaction and the environmental conditions. Cucumis rootstocks tended to minimise it, especially the hybrid Cucumis melo subsp. melo x C. melo subsp. agrestis Pat 81, which offered a volatile profile highly resembling the non-grafted control. Among Cucurbita alternatives, the commercial hybrid Cucurbita maxima x C moschata had the lowest impact, while other experimental hybrids C. moschata x C. moschata and C. maxima x C. moschata increased levels of alcohols. Among Cucumis rootstocks, the hybrids of wild species Cucumis ficifolius x C. anguria and C. ficifolius x C. myriocarpus, and C. metuliferus had a higher impact on the volatile profile.

Response of selected scion and rootstock grape (<i>Vitis </i>spp.) genotypes to induced drought stress

Climate change is expected to elevate drought frequency, straining agricultural freshwater resources. Developing drought-tolerant grapevine varieties is crucial. This study examined grape scion and rootstock genotypes under well-watered (WW) and induced-drought (ID) conditions. ID treatment reduced vine length by 11.34-35.15%, with Vitis parviflora, 110R, and Male Hybrid rootstocks showing superior growth. Root length increased under ID, indicating an adaptive moisture-seeking response. The ID treatment led to substantial reduction in leaf count and average leaf area, especially in Flame Seedless (27.71 and 19.07 cm2, respectively). Drought stress elevated chlorophyll a:b ratio, affecting chlorophyll degradation in different genotypes. Significant variations were observed in leaf and root iron (Fe) and zinc (Zn) contents. Enzyme activities particularly peroxidase and polyphenol oxidase especially rose under drought, particularly in V. parviflora (3.39 μM guaiacol min-1 mg-1 protein and 1.33EU/ml/min respectively) likely to be contributing in drought tolerance mechanism. Principal component analysis (PCA) highlighted impact of traits on genotypes, emphasizing V. parviflora, Male Hybrid and Pusa Navrang as superior drought stress tolerant genotypes. Genotype clustering confirmed distinct groupings, while, correlation analysis unveiled intricate trait interactions.

Citrus rootstock breeding in an HLB-endemic environment with an industry in crisis

The arrival (2005) and rapid establishment in Florida of the most devastating disease known to citriculture, namely Huanglongbing or Citrus Greening Disease, has caused dramatic changes to the long-term citrus rootstock breeding program at the University of Florida’s Citrus Research and Education Center (UF-CREC). Since all commercial scion/rootstock combinations have proven to be susceptible to the disease, there is an urgent need to quickly develop improved rootstocks with good horticultural attributes that can mitigate the disease in trees grafted with commercial scions. This report describes our efforts to achieve this goal. Our approach is to rapidly develop and screen a large population of genetically-diverse hybrid rootstock candidates. Multiple available sources of potential rootstock germplasm are being exploited in our efforts. We have identified several good rootstock candidates that are showing improved HLB tolerance. These are now being propagated either by seed or micropropagation as needed for advanced multi-site trials with multiple scions. This research offers potential for the ultimate solution to HLB, leading to sustainable and profitable citriculture in HLB-endemic areas

Inoculation with arbuscular mycorrhiza did not affect growth, root traits or gas exchange of grafted almond saplings when exposed to drought stress

Very little is known about potential benefits of using AM inoculation as a tool to alleviate drought stress of trees grown under nursery conditions. There is some evidence that benefits of mycorrhiza on gas exchange parameters and growth of trees are proportionally greater when trees are subjected to drought stress. We hypothesized that inoculation with mycorrhiza would increase growth, nutrition, stem water potential and gas exchange of containerized almond (Prunus dulcis (Mill.) D.A. Webb) when young trees are grown under low water availability.In the spring of 2015 and 2016, forty containerized almond trees (Nonpareil scion grafted on Hansen 536, a peach/almond hybrid rootstock) were either inoculated or not with a commercially available arbuscular mycorrhizal inoculum and kept well-watered for 60 days in 2015 and 54 days in 2016, after which half of the plants were exposed to gradually reduced water availability over 38 days in 2015 and 61 days in 2016. Measurements included growth metrics, stem water potential, stomatal density, leaf NPK concentration, light saturated photosynthesis, and parameters calculated from CO2 response curves (Vcmax, J, TPU, Rd, gm, and stomatal limitation).The low-water treatment decreased stem water potential and reduced trunk diameter growth, light saturated photosynthesis (A), stomatal conductance (gs), Vcmax, J, TPU, gm, specific root length, leaf N and K concentration and total leaf N, P, and K content. Inoculation decreased root mass, increased leaf mass fraction, and decreased root mass fraction in 2015, but not in 2016. Neither stem water potential nor gas exchange were significantly altered by inoculation. Inoculation decreased leaf stomatal density, and slightly elevated leaf N and P concentrations in the low water treatments, although not consistently across years. Contrary to expectations we did not find substantially greater benefits from mycorrhizal inoculation in young drought stressed almond trees and conclude that the potential for mycorrhizal inoculant to alleviate drought stress in containerized trees is minimal.

Identification and diversity analysis of interspecific citrus rootstock hybrids with combination of morphological traits and microsatellite markers

Identification and diversity analysis of interspecific citrus rootstock hybrids with combination of morphological traits and microsatellite markers

Transcriptomic Evidence of a Link between Cell Wall Biogenesis, Pathogenesis, and Vigor in Walnut Root and Trunk Diseases.

Crown gall disease (Agrobacterium tumefaciens), crown/root rot disease (Phytophthora spp.), root lesion disease (Pratylenchus vulnus) and tree vigor are key traits affecting the productivity and quality of walnuts in California. Unchallenged hybrid rootstocks were analyzed by RNA-seq to examine pre-formed factors affecting these traits. Enrichment analysis of the differentially expressed genes revealed that the increased expression of cell wall biogenesis-related genes plays a key role in susceptibility to A. tumefaciens, susceptibility to Phytophthora spp. and increased vigor. Analysis of the predicted subcellular loci of the encoded proteins revealed that many gene products associated with vigor and susceptibility were targeted to the plasma membrane and extracellular space, connecting these traits to sustaining barrier function. We observed that RNA processing and splicing, along with predicted nuclear targeting, were associated with resistance to A. tumefaciens, resistance to Phytophthora spp. and low vigor. Four genes within the J. microcarpa QTL region for resistance to A. tumefaciens and Phytophthora spp. were represented among our transcripts, with two of the genes being differentially expressed in association with resistance to A. tumefaciens and decreased vigor. No differential expression related to Phytophthora spp. or P. vulnus resistance was observed in this region. Additionally, the J. microcarpa haplotype expressed more transcripts associated with resistance to A. tumefaciens, Phytophthora spp. and low vigor, but not P. vulnus, than the J. regia haplotype. We also report unique and shared hormone and defense responses associated with each trait. This research suggests a link between cell wall biogenesis, vigor and critical root diseases of walnut.

Interspecific Hybrid Rootstocks Improve Productivity of Tomato Grown under High-temperature Stress

Grafting can be a useful technology to improve productivity of vegetable crops, including tomato, particularly under the serious challenges of climate change for agricultural systems. This study aimed to evaluate the impact of some local tomato interspecific hybrid rootstocks along with Maxifort on the vegetative growth, productivity, and fruit quality of tomato under field production conditions. Heat-tolerant tomato hybrid 023 F1 was used as a scion over the two late summer seasons of 2021 and 2022. Grafting 023 F1 onto Maxifort or KFS-16 rootstocks resulted in the maximum plant growth. Similarly, Maxifort and KFS-16 rootstocks significantly increased the fruit setting percentage from 22.2% to 23.5% and 17.8% to 24.6%, total fruit yield from 33.5% to 53.7% and 29.6% to 51.6%, and marketable yields from 34.1% to 56.0% and 27.3% to 56.7%, respectively, during both seasons compared with nongrafted plants. These two rootstocks enhanced nutrient (nitrogen, phosphorus, potassium) uptake compared with nongrafted planted. However, grafting with the interspecific hybrid rootstocks (KFS-8 and KWS-9) significantly decreased the content of catalase, peroxidase, and proline, which might be associated with lower plant vigor and yield in these rootstocks. All rootstocks had an impact on fruit chemical composition; however, generally, Maxifort and KFS-16 had greater contents of vitamin C, β-carotene, and total antioxidants than nongrafted plants. KFS-16 had also greater lycopene content than nongrafted plants. These results demonstrate the potential use of Maxifort and local rootstock KFS-16 to boost the growth and yield of tomato plants under high-temperature stress in the late summer season.

Seasonal Dynamics and Distribution of Xylella fastidiosa in Infected Almond Trees.

This research focused on studying the dynamics of the bacterial pathogen Xylella fastidiosa in almond trees across different developmental stages. The objective was to understand the seasonal distribution and concentration of X. fastidiosa within almond trees. Different tree organs, including leaves, shoots, branches, fruits, flowers, and roots, from 10 X. fastidiosa-infected almond trees were sampled over 2 years. The incidence and concentration of X. fastidiosa were determined using qPCR and isolation. Throughout the study, X. fastidiosa was consistently absent from fruits, flowers, and roots, whereas it was detected in leaves as well as in shoots and branches. We demonstrate that the absence of X. fastidiosa in the roots is likely linked to the inability of this isolate to infect the peach-almond hybrid rootstock GF677. X. fastidiosa incidence in shoots and branches remained consistent throughout the year, whereas in leaf petioles, it varied across developmental stages, with lower detection during the early and late stages of the season. Similarly, viable X. fastidiosa cells were isolated from shoots and branches at all developmental stages, but no successful isolations were achieved from leaf petioles during the vegetative and nut growth stage. Studying the progression of almond leaf scorch symptoms in trees with initial infections showed that once symptoms emerged on one branch, symptomless branches were likely already infected by the bacterium. Therefore, selectively pruning symptomatic branches is unlikely to cure the tree. This study enhances our understanding of X. fastidiosa dynamics in almond trees and may have practical applications for its detection and control.

Characterization of Almond Scion/Rootstock Communication in Cultivar and Rootstock Tissues through an RNA-Seq Approach.

The rootstock genotype plays a crucial role in determining various aspects of scion development, including the scion three-dimensional structure, or tree architecture. Consequently, rootstock choice is a pivotal factor in the establishment of new almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) intensive planting systems, demanding cultivars that can adapt to distinct requirements of vigor and shape. Nevertheless, considering the capacity of the rootstock genotype to influence scion development, it is likely that the scion genotype reciprocally affects rootstock performance. In the context of this study, we conducted a transcriptomic analysis of the scion/rootstock interaction in young almond trees, with a specific focus on elucidating the scion impact on the rootstock molecular response. Two commercial almond cultivars were grafted onto two hybrid rootstocks, thereby generating four distinct combinations. Through RNA-Seq analysis, we discerned that indeed, the scion genotype exerts an influence on the rootstock expression profile. This influence manifests through the modulation of genes associated with hormonal regulation, cell division, root development, and light signaling. This intricate interplay between scion and rootstock communication plays a pivotal role in the development of both scion and rootstock, underscoring the critical importance of a correct choice when establishing new almond orchards.

Cucumber grafting on indigenous cucurbit landraces confers salt tolerance and improves fruit yield by enhancing morpho-physio-biochemical and ionic attributes

Pakistan is the 8th most climate-affected country in the globe along with a semi-arid to arid climate, thereby the crops require higher irrigation from underground water. Moreover, ~ 70% of pumped groundwater in irrigated agriculture is brackish and a major cause of secondary salinization. Cucumber (Cucumis sativus L.) is an important vegetable crop with an annual growth rate of about 3.3% in Pakistan. However, it is a relatively salt-sensitive crop. Therefore, a dire need for an alternate environment-friendly technology like grafting for managing salinity stress in cucumber by utilizing the indigenous cucurbit landraces. In this regard, a non-perforated pot-based study was carried out in a lath house to explore indigenous cucurbit landraces; bottle gourd (Lagenaria siceraria) (cv. Faisalabad Round), pumpkin (Cucurbit pepo. L) (cv. Local Desi Special), sponge gourd (Luffa aegyptiaca) (cv. Local) and ridge gourd (Luffa acutangula) (cv. Desi Special) as rootstocks for inducing salinity tolerance in cucumber (cv. Yahla F1). Four different salts (NaCl) treatments; T0 Control (2.4 dSm–1), T1 (4 dSm–1), T2 (6 dSm–1) and T3 (8 dSm–1) were applied. The grafted cucumber plants were transplanted into the already-induced salinity pots (12-inch). Different morpho-physio-biochemical, antioxidants, ionic, and yield attributes were recorded. The results illustrate that increasing salinity negatively affected the growing cucumber plants. However, grafted cucumber plants showed higher salt tolerance relative to non-grafted ones. Indigenous bottle gourd landrace (cv. Faisalabad Round) exhibited higher salt tolerance compared to non-grafted cucumber plants due to higher up-regulation of morpho-physio-biochemical, ionic, and yield attributes that was also confirmed by principal component analysis (PCA). Shoot and root biomass, chlorophylls contents (a and b), activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POX) enzymes, antioxidants scavenging activity (ASA), ionic (↑ K and Ca, ↓ Na), and yield-related attributes were found maximum in cucumber plants grafted onto indigenous bottle gourd landrace. Hence, the indigenous bottle gourd landrace ‘cv. Faisalabad round’ may be utilized as a rootstock for cucumber under a mild pot-based saline environment. However, indigenous bottle gourd landrace ‘cv. Faisalabad round’ may further be evaluated as rootstocks in moderate saline field conditions for possible developing hybrid rootstock and, subsequently, sustainable cucumber production.

Improvement of Citrus Rootstock Hybrids Derived by 2x × 2x Intra Crosses with the Aid of Embryo Rescue and Ploidy Detection

Diploid Citrus × Poncirus hybrids have significantly contributed to citrus rootstock evaluation. In Türkiye, common sour orange rootstock is used in many different climates and soil conditions at almost 85% of citrus plantations, but this rootstock is susceptible to Citrus tristeza virus disease. This study was conducted to improve new rootstock genotypes by traditional hybridization. Common sour orange (CSO) and Common mandarin (Citrus deliciosa Ten.) (CM) were crossed with Troyer citrange (TC) while King mandarin (KM) was crossed with Carrizo citrange (CC). Embryos obtained from crosses were taken on 110, 120 and 130 days after artificial pollination (DAP), and were germinated on MT culture media. The embryos of 120 DAP of combinations had the highest germination rate within CSO×TC, 95.15%; CM×TC, 96.25%; KM×CC, 95.23%. The trifoliate rates for each combination at subculture (CSO×TC, 17.40%; CM×TC, 11.11%; KM×CC; 6.17%) were obtained from 110 DAP embryos. Survival rates of the genotypes were ranged between 72.13% and 90.28% in subculture and varied from 40.17% and 64.71% in the greenhouse. As a result of the ploidy analysis by flow cytometry, the nuclear DNA content of diploid genotypes were found between 0.78 pg/2C and 0.93 pg/2C. One of the genotypes derived from CM×TC hybridization on 120 DAP was determinated as a triploid plant.

Identification of genes involved in almond scion tree architecture influenced by rootstock genotype using transcriptome analysis

The emergence of almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) intensive and semi-intensive cropping systems has created a necessity for new almond cultivars with vigor and shape adapted to these new circumstances. Hence, it is important to unravel which mechanisms are behind the regulation of the tree three-dimensional structure, or tree architecture, and what factors may play a role, like the choice of rootstock. In this study, we have analyzed the rootstock influence on the scion transcriptome, regarding the biological processes that control almond tree architecture. Three commercial almond cultivars were grafted onto three hybrid rootstocks known to confer different architecture to the scion, resulting in nine combinations, whose gene expression in shoot tips was analyzed via RNA-Seq. We report that differences in tree architecture phenotype are correlated with differential expression of genes involved in hormonal and molecular responses associated with the regulation of apical dominance, branch formation, plant growth, cell wall formation, or nitrogen assimilation. These results highlight the importance of the rootstock choice in selecting a desirable scion architecture and in establishing almond orchards.

Responses of Potential Rootstock Hybrids (Vinifera × American) to Drought and Salt Stress

Responses of Potential Rootstock Hybrids (Vinifera × American) to Drought and Salt Stress

Transcriptomics reveal the genetic coordination of early defense to Armillaria root rot (ARR) in Prunus spp.

Armillaria root rot (ARR) poses a significant threat to the long-term productivity of stone-fruit and nut crops in the predominant production area of the United States. To mitigate this issue, the development of ARR-resistant and horticulturally-acceptable rootstocks is a crucial step towards the maintenance of production sustainability. To date, genetic resistance to ARR has been found in exotic plum germplasm and a peach/plum hybrid rootstock, 'MP-29'. However, the widely-used peach rootstock Guardian® is susceptible to the pathogen. To understand the molecular defense mechanisms involved in ARR resistance in Prunus rootstocks, transcriptomic analyses of one susceptible and two resistant Prunus spp. were performed using two causal agents of ARR, including Armillaria mellea and Desarmillaria tabescens. The results of in vitro co-culture experiments revealed that the two resistant genotypes showed different temporal response dynamics and fungus-specific responses, as seen in the genetic response. Gene expression analysis over time indicated an enrichment of defense-related ontologies, including glucosyltransferase activity, monooxygenase activity, glutathione transferase activity, and peroxidase activity. Differential gene expression and co-expression network analysis highlighted key hub genes involved in the sensing and enzymatic degradation of chitin, GSTs, oxidoreductases, transcription factors, and biochemical pathways likely involved in Armillaria resistance. These data provide valuable resources for the improvement of ARR resistance in Prunus rootstocks through breeding.

New insights into short-term water stress tolerance through transcriptomic and metabolomic analyses on pepper roots

In the current climate change scenario, water stress is a serious threat to limit crop growth and yields. It is necessary to develop tolerant plants that cope with water stress and, for this purpose, tolerance mechanisms should be studied. NIBER® is a proven water stress- and salt-tolerant pepper hybrid rootstock (Gisbert-Mullor et al., 2020; López-Serrano et al., 2020), but tolerance mechanisms remain unclear. In this experiment, NIBER® and A10 (a sensitive pepper accession (Penella et al., 2014)) response to short-term water stress at 5 h and 24 h was studied in terms of gene expression and metabolites content in roots. GO terms and gene expression analyses evidenced constitutive differences in the transcriptomic profile of NIBER® and A10, associated with detoxification systems of reactive oxygen species (ROS). Upon water stress, transcription factors like DREBs and MYC are upregulated and the levels of auxins, abscisic acid and jasmonic acid are increased in NIBER®. NIBER® tolerance mechanisms involve an increase in osmoprotectant sugars (i.e., trehalose, raffinose) and in antioxidants (spermidine), but lower contents of oxidized glutathione compared to A10, which indicates less oxidative damage. Moreover, the gene expression for aquaporins and chaperones is enhanced. These results show the main NIBER® strategies to overcome water stress.

Pathogenicity of Oomycete Species to Different Prunus Hybrid Rootstocks.

Diseases caused by soilborne oomycetes are a limiting factor for the cultivation of Prunus spp., which makes the choice of a suitable rootstock a key factor. The objective of this study was to evaluate the pathogenicity of 12 oomycete species belonging to the genera Globisporangium, Phytophthora (Ph.), and Phytopythium (Pp.) to three Prunus hybrid rootstocks: 'Garnem', 'GF-677', and 'Rootpac-40'. These three rootstocks are widely used to grow stone fruit and almond in the Mediterranean Basin. Pathogenicity tests were conducted using 15 oomycete isolates and 1-year-old rootstock seedlings. Ninety days after inoculation, disease symptoms were evaluated on a severity scale, and the area under the disease progression curve and the survival probability of the inoculated seedlings were calculated. Moreover, root dry weight was recorded. All the isolates included in the pathogenicity tests were pathogenic on the rootstock seedlings and were reisolated from root lesions. Large differences in virulence were detected among the different oomycete species and isolates of Ph. niederhauserii for each rootstock. Phytophthora multivora and Pp. helicoides were generally the most virulent species. The results of the present research offer substantial contribution to increase our knowledge about the pathogenicity of several oomycete species that are frequently isolated in Prunus orchards and the potential risks that they pose for Prunus spp. crops.

A Chronological Study on Grapevine Leafroll-Associated Virus 2 in Australia.

Grapevine leafroll disease affects the health status of grapevines worldwide. Most studies in Australia have focused on grapevine leafroll-associated viruses 1 and 3, while little attention has been given to other leafroll virus types, in particular, grapevine leafroll-associated virus 2 (GLRaV-2). A chronological record of the temporal occurrence of GLRaV-2 in Australia since 2001 is reported. From a total of 11,257 samples, 313 tested positive, with an overall incidence of 2.7%. This virus has been detected in 18 grapevine varieties and Vitis rootstocks in different regions of Australia. Most varieties were symptomless on their own roots, while Chardonnay showed a decline in virus-sensitive rootstocks. An isolate of GLRaV-2, on own-rooted Vitis vinifera cv. Grenache, clone SA137, was associated with severe leafroll symptoms after veraison with abnormal leaf necrosis. The metagenomic sequencing results of the virus in two plants of this variety confirmed the presence of GLRaV-2, as well as two inert viruses, grapevine rupestris stem pitting-associated virus (GRSPaV) and grapevine rupestris vein feathering virus (GRVFV). No other leafroll-associated viruses were detected. Among the viroids, hop stunt viroid and grapevine yellow speckle viroid 1 were detected. Of the six phylogenetic groups identified in GLRaV-2, we report the presence of four groups in Australia. Three of these groups were detected in two plants of cv. Grenache, without finding any recombination event. The hypersensitive reaction of certain American hybrid rootstocks to GLRaV-2 is discussed. Due to the association of GLRaV-2 with graft incompatibility and vine decline, the risk from this virus in regions where hybrid Vitis rootstocks are used cannot be overlooked.

Haplotyping interspecific hybrids by dual alignment to both parental genomes.

Sequencing-based genotyping of heterozygous diploids requires sufficient depth to accurately call heterozygous genotypes. In interspecific hybrids, alignment of reads to both parental genomes simultaneously can generate haploid data, potentially eliminating the problem of heterozygosity. Two populations of interspecific hybrid rootstocks of walnut (Juglans) and pistachio (Pistacia) were genotyped using alignment to the maternal genome, paternal genome, and dual alignment to both genomes simultaneously. Downsampling was used to examine concordance of imputed genotype calls as a function of sequencing depth. Dual alignment resulted in datasets essentially free of heterozygous genotypes, simplifying the identification and removal of cross-contaminated samples. Concordance between full and downsampled genotype calls was always highest after dual alignment. Nearly all single nucleotide polymorphisms (SNPs) in dual alignment datasets were shared with the corresponding single-parent datasets, but 60%-90% of single-parent SNPs were private to that dataset. Private SNPs in single-parent datasets had higher rates of heterozygosity, lower levels of concordance, and were enriched in fixed differences between parental genomes ("homeo-SNPs") compared to shared SNPs in the same dataset. In multi-parental walnut hybrids, the paternal-aligned dataset was ineffective at resolving population structure in the maternal parent. Overall, the dual alignment strategy effectively produced phased, haploid data, increasing data quality and reducing cost.

Relative Influence of Rootstock and Scion on Asian Citrus Psyllid Infestation and Candidatus Liberibacter asiaticus Colonization

The citrus industry in Florida faces a destructive endemic disease, known as huanglongbing (HLB), associated with Candidatus Liberibacter asiaticus (CLas), a phloem-limited bacterium, and transmitted by the Asian citrus psyllid (ACP). Rootstocks are regarded as critical to keep citrus production commercially viable and help trees cope with the disease. Although most scions are susceptible, some rootstocks are HLB-tolerant and may influence ACP infestation and CLas colonization and therefore the grafted tree tolerance. This study aimed to elucidate the relative influence of rootstock and scion on insect vector infestation and CLas colonization under natural HLB-endemic conditions. Seven commercial rootstock cultivars with different genetic backgrounds were grafted with ‘Valencia’ sweet orange (Citrus sinensis) or were self-grafted (non-‘Valencia’) and planted in an open field where ACP and CLas were abundant. ACP infestation was determined weekly during periods of leaf flushing, and leaves and roots were analyzed every 3 months to determine CLas titers. Trees with ‘Valencia’ scion were more attractive to the psyllids than non-‘Valencia’ scions. This was also associated with a higher number of bacteria and a larger abundance of foliar HLB symptoms. The influence of the rootstock on the psyllid attraction of grafted ‘Valencia’ scion was less evident, and leaf CLas titers were similar regardless of the rootstock. Among the non-‘Valencia’ scions, Carrizo had the lowest and US-942 the highest leaf CLas titers. Root CLas titers also varied among cultivars, and standard sour orange roots harbored more bacteria than some trifoliate orange hybrid rootstocks such as US-942. In some trees, CLas was detected first in the roots 4 months after planting, but root CLas titers remained low throughout the study. In contrast, leaf CLas titers increased over time and were considerably higher than root titers from 7 months until the end of the study, 15 months after planting. Overall, the results of this study demonstrate a greater relative influence of the scion than the rootstock on ACP infestation and CLas colonization during the early stages of infection. This suggests that other cultivar-specific traits, such as the ability to tolerate other stresses and to absorb water and nutrients more efficiently, along with influences on the scion phenology, may play a larger role in the rootstock influence on the grafted tree tolerance during the later stages of HLB progression.