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 (P _n ) 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 P _n . 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 P _n was significantly increased by soil-applied Zn EDTA compared with the control, but P _n was not different between the two soil-applied Zn-EDTA treatments. Leaf P _n in midseason did not increase at leaf tissue Zn concentrations above 14–22 mg·kg ⁻¹ . Leaf SPAD consistently followed a similar pattern to P _n . Soil Zn-EDTA application increased leaf stomatal conductance ( g _S ) compared with the Control early through midseason but not after August. Intercellular CO ₂ concentration was significantly lower for Zn-EDTA-treated trees than the Control even on dates when there was no significant difference in g _s , which suggests that soil application of Zn-EDTA alleviated nonstomatal limitations to P _n caused by Zn deficiency.

Pecan is a major crop in the Mesilla Valley, New Mexico. Due to prolonged droughts, growers face challenges related to water shortages. Therefore, irrigation management is crucial for farmers. Advancements in satellite-derived evapotranspiration (ET) models and accessibility to data from web-based platforms like OpenET provide farmers with new tools to improve crop irrigation management. This study evaluates the evapotranspiration (ET) of a mature pecan orchard using OpenET platform data generated by six satellite-based models and their ensemble. The ET values obtained from the platform were compared with the ET values obtained from the eddy covariance (ETec) method from 2017 to 2021. The six models assessed included Google Earth Engine implementation of the Surface Energy Balance Algorithm for Land (geeSEBAL), Google Earth Engine implemonthsmentation of the Mapping Evapotranspiration at High Resolution with Internalized Calibration (eeMETRIC) model, Operational Simplified Surface Energy Balance (SSEBop), Satellite Irrigation Management Support (SIMS), Priestley–Taylor Jet Propulsion Laboratory (PT-JPL), and Atmosphere–Land Exchange Inverse and associated flux disaggregation technique (ALEXI/DisALEXI). The average growing season ET of mature pecan estimated from April to October of 2017 to 2021 by geeSEBAL, eeMETRIC, SSEBop, SIMS, PT-JPL, ALEXI/DisALEXI, and the ensemble were 1061, 1230, 1232, 1176, 1040, 1016, and 1130 mm, respectively, and 1108 mm by ETec. Overall, the ensemble model-based monthly ET of mature pecan during the growing season was relatively close to the ETec (R² of 0.9477) with a 2% mean relative difference (MRD) and standard error of estimate (SEE) of 15 mm/month for the five years (N = 60 months). The high agreement of the OpenET ensemble of the six satellite-derived models’ estimates of mature pecan ET with the ETec demonstrates the utility of this promising approach to enhance the reliability of remote sensing-based ET data for agricultural and water resource management.

Pecan ( Carya illinoinensis ) is a tree nut native to North America. Although inhibited light exposure (most specifically as a result of overlapping tree canopies) has been shown to impair yield, the effect of this factor on nut antioxidant properties remains unknown. This study investigated effects of mechanical pruning and canopy height position of fruit on pecan kernel antioxidant contents and capacity. Beginning in 2006, trees in a ‘Western’ pecan orchard in New Mexico were subjected to three mechanical pruning frequency treatments (annual, biennial, and triennial) paralleling conventional practices, while other trees were maintained as unpruned controls. During the 2012 to 2014 seasons, pecans were sampled at fruit maturity from three canopy height zones (“low,” “middle,” and “high,” corresponding to 1.5 to 3.0 m, 3.0 to 4.5 m, and 4.5 to 6.0 m above the orchard floor). In vitro phenolics contents and antioxidant capacities of the nutmeats were evaluated by total phenolics content (TPC) and oxygen radical absorbance capacity (H-ORAC _FL ), respectively. Soluble ester- and glycoside-bound phenolics were quantified by reversed-phase high-performance liquid chromatography (HPLC). For both TPC and H-ORAC _FL , results determined pruned samples had significantly higher values than unpruned samples ( P < 0.001 for both comparisons), and that samples of “high” canopy height were significantly greater than those of “middle” height, which were in turn greater than those of “low” height ( P < 0.001 for all comparisons). HPLC findings showed that in all three phenolic fractions (free, esterified, and glycoside-bound phenolics), nuts acquired from pruned trees had substantially greater concentrations of ellagic acid and its derivatives. Our findings indicate mechanical pruning of pecan trees and higher tree canopy position of fruit increase nut antioxidant properties.

We would like to address a number of concerns regarding this paper (Savory et al., 2017)