In perennial plants such as pecan, once reproductive maturity is attained, there are genetic switches that are regulated and required for flower development year after year. Pecan trees are ...heterodichogamous with both pistillate and staminate flowers produced on the same tree. Therefore, defining genes exclusively responsible for pistillate inflorescence and staminate inflorescence (catkin) initiation is challenging at best. To understand these genetic switches and their timing, this study analyzed catkin bloom and gene expression of lateral buds collected from a protogynous (Wichita) and a protandrous (Western) pecan cultivar in summer, autumn and spring. Our data showed that pistillate flowers in the current season on the same shoot negatively impacted catkin production on the protogynous 'Wichita' cultivar. Whereas fruit production the previous year on 'Wichita' had a positive effect on catkin production on the same shoot the following year. However, fruiting the previous year nor current year pistillate flower production had no significant effect on catkin production on 'Western' (protandrous cultivar) cultivar. The RNA-Seq results present more significant differences between the fruiting and non-fruiting shoots of the 'Wichita' cultivar compared to the 'Western' cultivar, revealing the genetic signals likely responsible for catkin production. Our data presented here, indicates the genes showing expression for the initiation of both types of flowers the season before bloom.
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.
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.
Changes in gene dosage are a major driver of cancer, known to be caused by a finite, but increasingly well annotated, repertoire of mutational mechanisms. This can potentially generate correlated ...copy-number alterations across hundreds of linked genes, as exemplified by the 2% of childhood acute lymphoblastic leukaemia (ALL) with recurrent amplification of megabase regions of chromosome 21 (iAMP21). We used genomic, cytogenetic and transcriptional analysis, coupled with novel bioinformatic approaches, to reconstruct the evolution of iAMP21 ALL. Here we show that individuals born with the rare constitutional Robertsonian translocation between chromosomes 15 and 21, rob(15;21)(q10;q10)c, have approximately 2,700-fold increased risk of developing iAMP21 ALL compared to the general population. In such cases, amplification is initiated by a chromothripsis event involving both sister chromatids of the Robertsonian chromosome, a novel mechanism for cancer predisposition. In sporadic iAMP21, breakage-fusion-bridge cycles are typically the initiating event, often followed by chromothripsis. In both sporadic and rob(15;21)c-associated iAMP21, the final stages frequently involve duplications of the entire abnormal chromosome. The end-product is a derivative of chromosome 21 or the rob(15;21)c chromosome with gene dosage optimized for leukaemic potential, showing constrained copy-number levels over multiple linked genes. Thus, dicentric chromosomes may be an important precipitant of chromothripsis, as we show rob(15;21)c to be constitutionally dicentric and breakage-fusion-bridge cycles generate dicentric chromosomes somatically. Furthermore, our data illustrate that several cancer-specific mutational processes, applied sequentially, can coordinate to fashion copy-number profiles over large genomic scales, incrementally refining the fitness benefits of aggregated gene dosage changes.
Pecan bacterial leaf scorch, caused by
subsp.
, is an economically significant disease of pecan with known detrimental effects on the yield of susceptible cultivars. In this study, endosperm was ...harvested from developing pecan seeds, and direct qPCR and sequencing were used to detect and confirm the presence of
. DNA was isolated from mature seeds originating from seven trees, revealing a positivity rate up to 90%, and transmission of
from infected seed to the germinated seedlings was found to be over 80%. Further epidemiological analyses were performed to determine where
localizes in mature seed and seedlings. The highest concentrations of
DNA were found in the hilum and outer integument of the seeds and the petioles, respectively. High-, medium-, and low-density seeds were harvested to determine the impact of the bacterium on seed density and seedling growth rate. The growth rate of seedlings originating from low-density seeds was significantly reduced compared to the medium- and high-density seeds. Despite the increased growth and germination rates, the high-density seed group had a greater proportion of samples that tested positive for the presence of
by qPCR. The results demonstrate the ability of
to colonize developing seeds and be efficiently transmitted from well-developed seeds to germinated seedlings. Continued research is needed to understand the plant-microbe interactions involved in the colonization of pecan seeds by
and to develop effective phytosanitary approaches to reduce the risks posed by seed transmission.
Regarding pecan ( Carya illinoinensis ), alternate bearing, which is a biennial fluctuation of crop yield, is a major hindrance for the pecan industry. Little is known about the internal cues that ...trigger pecan shoots to become reproductive. This 2-year study approached the mysteries of alternate bearing of pecan by determining whether pecan homologs of three genes known to control floral initiation in other species are expressed differently at various times of the growing season or in distinct plant tissues, and whether expression of these genes can be manipulated by plant growth regulator (PGR) application when compared with an untreated control group. The flowering genes of interest were pecan homologs of leafy ( CpLFY ), apetala1 ( CpAP1 ), and flowering locus t ( CpFT ). During year 1 (2014), PGRs ethephon and gibberellin GA 3 were applied at the shoot level 1 week before each of three tissue sampling dates (13 June, 3 July, 29 July). During the following year (2015), two more PGRs were added to the study a second double rate (2X) of gibberellin GA 3 and ethylene inhibitor aminoethoxyvinylglycine (AVG) for a total of four PGRs (applied on 10 June, 1 July, and 23 July) plus the untreated control. Experimental leaf and bud tissues were sampled from fruiting and nonfruiting shoots on mature ‘Western’ pecan trees and analyzed separately. Normalized expression levels of CpLFY and CpAP1 were significantly higher in buds than in leaves. Normalized expression of CpLFY in bud tissues differed statistically based on the sampling date in 2014, with the earliest date (13 June) having higher expression than the two later dates that year. In 2015, a treatment × date interaction revealed that, compared with the untreated control, CpLFY expression was significantly lower in shoots treated with both gibberellin GA 3 dosages on 1 July. A few weeks later (23 July), CpLFY expression was lower in the 2X GA 3 treatment group and higher in samples treated with AVG. In 2014, CpAP1 expression in buds was significant, with a treatment × date interaction in which ethephon increased CpAP1 expression, but only on one date (29 July). In 2015, bud CpAP1 expression was significantly higher in fruiting than in nonfruiting shoots; however, again, only on one date. The results reveal differential expression of these key flowering genes based on tissue type, sampling date, and fruiting status of the shoot and PGR treatment. Results suggest that more research of the effects of PGRs is necessary for understanding the flowering behavior of pecan and mitigating the intensity of alternate bearing.
Many growers fertigating their orchards with zinc–ethylenediaminetetraacetic acid (Zn-EDTA) are still using supplemental zinc foliar sprays because of a lack of confidence that soil-applied Zn-EDTA ...is supplying enough Zn to the trees. A field study was conducted in a pecan orchard located near San Simon, AZ, on 8-year-old ‘Wichita’ trees growing in an alkaline, calcareous Vekol loam soil to evaluate the effectiveness of supplemental foliar Zn sprays. All trees were fertigated with 6.0 kg⋅ha –1 Zn in the form of Zn-EDTA in 2018 and 11.0 kg⋅ha –1 Zn in 2019 and did not exhibit visible signs of Zn deficiency. Foliar treatments of 3.75 mL⋅L –1 urea–ammonium nitrate (UAN), 3.6 g⋅L –1 zinc sulfate monohydrate (ZnSO 4 ·H 2 O), 3.6 g⋅L –1 ZnSO 4 ·H 2 O with 3.75 mL⋅L –1 UAN, 11 mL⋅L –1 Zn-EDTA, and water alone were applied to individual fruiting shoot terminals of trees on two dates each in 2018 and 2019. Treatments were sprayed directly onto the leaves of the selected terminals. Zn-EDTA was included as a foliar treatment in 2019 only. Leaf photosynthesis was measured to determine the impact of leaf Zn concentrations on plant function. Midday stem water potential (MDSWP) was measured to verify that water stress was not limiting photosynthesis. Both measurements were taken about 2 to 4 weeks after the application of foliar treatments. MDSWP measurements indicated a lack of water stress and therefore no effect on photosynthesis. Leaf samples collected from untreated branches indicated that the average foliar Zn concentration of untreated leaves was 21.3 mg⋅kg –1 in 2018 and 15.7 mg⋅kg –1 in 2019. No differences were observed in photosynthesis rates of treated branches. No additional benefit to leaf photosynthetic function or appearance was observed from spraying Zn on foliage of trees fertigated with Zn-EDTA.
Analysis of composite pecan leaf samples typically used to determine need for nutrient applications does not account for variability among trees in the sampled area. To account for this unmeasured ...variability, pecan orchard block nutrient standards are greater than actual single tree nutrient requirements. In 2018 and 2019, we measured variability in a pecan orchard block by evaluating nutrient status of all trees in a study area consisting of two cultivars (Wichita and Western) grafted on open-pollinated ‘Ideal’ seedlings. Foliar zinc (Zn) coefficient of variation ( cv ) ranged from 0.186 to 0.255 within individual cultivars and years but was as high as 0.30 when combining cultivars within a year. The ‘Western’ cultivar had higher foliar Zn concentrations than ‘Wichita’, but Zn concentrations were not consistently associated with other leaf nutrient levels, soil Zn status, or other soil properties. Using observed foliar Zn variability, we determined that it is necessary to sample 35 trees for a composite sample to achieve a relative margin of error of 10% and 95% confidence level in a pecan orchard block with more than 1000 trees. We developed field scale foliar Zn recommendations based on individual tree research that indicates a minimum acceptable leaf Zn concentration of ≈15 mg·kg –1 is needed to maintain optimal photosynthetic function in Zn chelate fertigated pecan trees. Assuming a Zn cv of 0.30 and a composite sample comprised of leaves from 35 trees, the minimum acceptable orchard block Zn level to ensure that less than 5% of trees had suboptimal levels of Zn was 27.6 mg·kg –1 . An orchard block Zn level below 23.4 mg·kg –1 indicates that more than 5% of trees in the block had suboptimal foliar Zn concentrations.
A field study was conducted to evaluate tolerance of pecan rootstocks to soil salinity and sodicity. Seven cultivars—Elliott, Giles, Ideal, Peruque, Riverside, ‘Shoshoni, and VC1-68—were selected ...from a range of geographic regions of origin. The soil of the experimental plot was a poorly drained, saline–sodic Pima silty clay variant. The irrigation water was a moderately saline mix of Gila River and local groundwater with an electrical conductivity of 2.8 dS⋅m –1 , containing primarily ions of Na and Cl. Eighty seeds of each cultivar were planted in a greenhouse in late Feb. 2016; 48 seedlings of each cultivar were transplanted into field plots in Feb. 2017. Half the trees received a soil-based application of Zn–ethylenediaminetetraacetic acid (EDTA) at planting. The trees were observed and rated for both vigor and resistance to salt injury on seven separate occasions. Trunk diameter was measured each dormant season. Leaf samples were collected on 9 Oct. 2019 and 6 Oct. 2020, and were analyzed for nutrient content. Zn-EDTA was not found to have a significant effect on growth, vigor, or resistance to salt injury. ‘Elliott’ seedlings exhibited greater tolerance for the alkaline, saline–sodic soil conditions than other cultivars. ‘Giles’ and ‘Peruque’ were most severely affected. Resistance to salt injury (ranging from marginal leaf burn to necrosis of entire leaf), vigor, and growth correlated more strongly with foliar concentrations of Na than Cl or K during 2019. Vigor and growth were not significantly correlated with foliar Na, Cl, or K concentrations in 2020. The foliar K:Na ratio had a nearly equal correlation with resistance to salt injury and a greater correlation with growth than that of Na alone in 2019. However, although the correlation of the K:Na ratio with vigor was stronger than that of Cl or K, Na had the strongest correlation with vigor in 2019. In 2020, the only significant correlation of growth and vigor was with the K:Na ratio. The strongest correlation with resistance to salt injury in 2020 was with foliar Na concentration.
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.
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