‘UCB-1’ (Pistacia atlantica × Pistacia integerrima) rootstock is a hybrid cultivar widely used by the U.S. pistachio industry. In the last three years, a large number of micropropagated UCB-1 pistachio rootstocks planted in California and Arizona orchards exhibited shortened internodes, stunted growth, swollen lateral buds, bushy/bunchy growth, stem galls with multiple buds, and twisted roots with minimal lateral branching. Field T-budding success in affected orchards was reduced to approximately 30% with unusual bark cracking often observed around the bud-union. The percentage of abnormal rootstocks within affected orchards varied from 10 to 90%. We have termed the cumulative symptoms “pistachio bushy top syndrome” (PBTS) to describe these affected trees. Two isolates, both containing virulence factors from the phytopathogen Rhodococcus fascians, were identified on symptomatic trees in field and nursery samples. Micropropagated UCB-1 trees inoculated with the Rhodococcus isolates exhibited stunted growth, shortened internode length, swollen lateral buds, sylleptic branching, and differences in root morphology, compared with control UCB-1 trees. To our knowledge, this is the first report of Rhodococcus isolates, related to Rhodococcus fascians, causing disease on a commercial tree crop and the results presented indicate that this organism is responsible at least in part for PBTS in California and Arizona.

Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

Zinc deficiency is common in pecan (Carya illinoinensis) grown in alkaline, calcareous soils. Zinc (Zn)-deficient pecan leaves exhibit interveinal chlorosis, decreased leaf thickness, and reduced photosynthetic capacity. Low photosynthesis (Pn) contributes to restricted vegetative growth, flowering, and fruiting of Zn-deficient pecan trees. Our objectives were to measure effects of soil-applied ethylenediaminetetraacetic acid (EDTA)-chelated Zn fertilizer on gas exchange of immature ‘Wichita’ pecan and characterize the relationship between leaf Zn concentration and Pn. The study orchard had alkaline and calcareous soils and was planted in Spring 2011. Zinc was applied throughout each growing season as Zn EDTA through microsprinklers at rates of 0 (Control), 2.2, or 4.4 kg·ha−1 Zn. Leaf gas exchange and SPAD were measured on one occasion in the 2012 growing season, four in 2013, and five in 2014. Soil Zn-EDTA applications significantly increased the leaf tissue Zn concentration throughout the study. On all measurement occasions, net Pn was significantly increased by soil-applied Zn EDTA compared with the control, but Pn was not different between the two soil-applied Zn-EDTA treatments. Leaf Pn in midseason did not increase at leaf tissue Zn concentrations above 14–22 mg·kg−1. Leaf SPAD consistently followed a similar pattern to Pn. Soil Zn-EDTA application increased leaf stomatal conductance (gS) compared with the Control early through midseason but not after August. Intercellular CO2 concentration was significantly lower for Zn-EDTA-treated trees than the Control even on dates when there was no significant difference in gs, which suggests that soil application of Zn-EDTA alleviated nonstomatal limitations to Pn caused by Zn deficiency.

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