Evaluation of Lipid Quality in Fruit: Utilizing Lipidomic Approaches for Assessing the Impact of Biotic Stress on Pecans (Carya illinoinensis)

There is a scarcity of data on how the lipid composition of oily seeds changes in response to biotic stress. Yellow peach moth (Conogethes punctiferalis) has caused massive economic losses on the pecan (Carya illinoinensis) industry. Lipidomics is used in this study to determine the lipid composition of pecan and how it changes in response to insect attack. Pecan had 167 lipids, including 34 glycerolipids (GL), 62 glycerophospholipids (GP), 17 fatty acyls (FA), 41 sphingolipids (SP), and 13 saccharolipids (SL). The effects of biotic stress on lipids, particularly GL and GP, were significant. Biotic stress significantly reduced the lipid content of chains longer than 48. Forty-four significantly different lipids were discovered as potential biomarkers for distinguishing non-infected pecans from infested pecans. In addition, we used bioinformatics to identify the five most important metabolic pathways in order to investigate the processes underlying the changes. Our discoveries may offer valuable insights for enhancing pecan production in the future and contribute novel perspectives towards enhancing the nutritional value of pecans.

Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories

The maintenance of stable mating type polymorphisms is a classic example of balancing selection, underlying the nearly ubiquitous 50/50 sex ratio in species with separate sexes. One lesser known but intriguing example of a balanced mating polymorphism in angiosperms is heterodichogamy - polymorphism for opposing directions of dichogamy (temporal separation of male and female function in hermaphrodites) within a flowering season. This mating system is common throughout Juglandaceae, the family that includes globally important and iconic nut and timber crops - walnuts (Juglans), as well as pecan and other hickories (Carya). In both genera, heterodichogamy is controlled by a single dominant allele. We fine-map the locus in each genus, and find two ancient (>50 Mya) structural variants involving different genes that both segregate as genus-wide trans-species polymorphisms. The Juglans locus maps to a ca. 20 kb structural variant adjacent to a probable trehalose phosphate phosphatase (TPPD-1), homologs of which regulate floral development in model systems. TPPD-1 is differentially expressed between morphs in developing male flowers, with increased allele-specific expression of the dominant haplotype copy. Across species, the dominant haplotype contains a tandem array of duplicated sequence motifs, part of which is an inverted copy of the TPPD-1 3' UTR. These repeats generate various distinct small RNAs matching sequences within the 3' UTR and further downstream. In contrast to the single-gene Juglans locus, the Carya heterodichogamy locus maps to a ca. 200-450 kb cluster of tightly linked polymorphisms across 20 genes, some of which have known roles in flowering and are differentially expressed between morphs in developing flowers. The dominant haplotype in pecan, which is nearly always heterozygous and appears to rarely recombine, shows markedly reduced genetic diversity and is over twice as long as its recessive counterpart due to accumulation of various types of transposable elements. We did not detect either genetic system in other heterodichogamous genera within Juglandaceae, suggesting that additional genetic systems for heterodichogamy may yet remain undiscovered.

Exploring the Core Bacteria and Functional Traits in Pecan (Carya illinoinensis) Rhizosphere

Pecan (Carya illinoinensis) and Chinese hickory (Carya cathayensis) are important commercially cultivated nut trees. They are phylogenetically closely related plants; however, they exhibit significantly different phenotypes in response to abiotic stress and development. The rhizosphere selects core microorganisms from bulk soil, playing a pivotal role in the plant's resistance to abiotic stress and growth. In this study, we used metagenomic sequencing to compare the selection capabilities of seedling pecan and seedling hickory at taxonomic and functional levels in bulk soil and the rhizosphere. We observed that pecan has a stronger capacity to enrich rhizosphere plant-beneficial microbe bacteria (e.g., Rhizobium, Novosphingobium, Variovorax, Sphingobium, and Sphingomonas) and their associated functional traits than hickory. We also noted that the ABC transporters (e.g., monosaccharide transporter) and bacterial secretion systems (e.g., type IV secretion system) are the core functional traits of pecan rhizosphere bacteria. Rhizobium and Novosphingobium are the main contributors to the core functional traits. These results suggest that monosaccharides may help Rhizobium to efficiently enrich this niche. Novosphingobium may use a type IV secretion system to interact with other bacteria and thereby influence the assembly of pecan rhizosphere microbiomes. Our data provide valuable information to guide core microbial isolation and expand our knowledge of the assembly mechanisms of plant rhizosphere microbes. IMPORTANCE The rhizosphere microbiome has been identified as a fundamental factor in maintaining plant health, helping plants to fight the deleterious effects of diseases and abiotic stresses. However, to date, studies on the nut tree microbiome have been scarce. Here, we observed a significant "rhizosphere effect" on the seedling pecan. We furthermore demonstrated the core rhizosphere microbiome and function in the seedling pecan. Moreover, we deduced possible factors that help the core bacteria, such as Rhizobium, to efficiently enrich the pecan rhizosphere and the importance of the type IV system for the assembly of pecan rhizosphere bacterial communities. Our findings provide information for understanding the mechanism of the rhizosphere microbial community enrichment process.

Genome-Wide Identification, Characterization, and Expression Analysis of Long-Chain Acyl-CoA Synthetases in Carya illinoinensis under Different Treatments

As crucial enzymes in the lipid metabolic network, long-chain acyl-CoA synthases (LACSs) are members of the acyl-activated enzyme superfamily and play a crucial role in epidermal wax synthesis, plant lipid anabolic metabolism, and stress tolerance. In this study, 11 pecan LACS genes were identified and categorized into five groups and located on nine chromosomes. The significant degree of conservation in the AtLACS and CiLACS protein sequences was demonstrated by multiple sequence alignment and conserved motif analysis. Cis-acting element analysis identified numerous stress-responsive and hormone-inducible elements in the promoter regions of CiLACS genes. The expression levels of CiLACS9 and CiLACS9-1 were considerably up-regulated under salt and drought stress, according to the qRT-RCR study. Treatment with ABA also led to increased expression levels of CiLACS1, CiLACS1-1, CiLACS2, and CiLACS9-1. Notably, CiLACS4, CiLACS4-1, CiLACS9, and CiLACS9-1 exhibited peak expression levels at 135 days after anthesis and are likely to have been crucial in the accumulation of seed kernel oil. Moreover, the CiLACS9 gene was shown to be located in the cytoplasm. These findings offer a theoretical framework for clarifying the roles of LACS genes in the processes of pecan kernel oil synthesis and response to abiotic stressors.

Ammonium-nitrate mixtures dominated by NH4+-N promote the growth of pecan (Carya illinoinensis) through enhanced N uptake and assimilation

Nitrogen (N) limits plant productivity, and its uptake and assimilation may be regulated by N sources, N assimilating enzymes, and N assimilation genes. Mastering the regulatory mechanisms of N uptake and assimilation is a key way to improve plant nitrogen use efficiency (NUE). However, it is poorly known how these factors interact to influence the growth process of pecans. In this study, the growth, nutrient uptake and N assimilation characteristics of pecan were analyzed by aeroponic cultivation at varying NH4 +/NO3 - ratios (0/0, 0/100,25/75, 50/50, 75/25,100/0 as CK, T1, T2, T3, T4, and T5). The results showed that T4 and T5 treatments optimally promoted the growth, nutrient uptake and N assimilating enzyme activities of pecan, which significantly increased aboveground biomass, average relative growth rate (RGR), root area, root activity, free amino acid (FAA) and total organic carbon (TOC) concentrations, nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (Fd-GOGAT and NADH-GOGAT), and glutamate dehydrogenase (GDH) activities. According to the qRT-PCR results, most of the N assimilation genes were expressed at higher levels in leaves and were mainly significantly up-regulated under T1 and T4 treatments. Correlation analysis showed that a correlation between N assimilating enzymes and N assimilating genes did not necessarily exist. The results of partial least squares path model (PLS-PM) analysis indicated that N assimilation genes could affect the growth of pecan by regulating N assimilation enzymes and nutrients. In summary, we suggested that the NH4 +/NO3 - ratio of 75:25 was more beneficial to improve the growth and NUE of pecan. Meanwhile, we believe that the determination of plant N assimilation capacity should be the result of a comprehensive analysis of N concentration, N assimilation enzymes and related genes.

Water uptake in germinating pecan (Carya illinoinensis) seed

• Water uptake is the fundamental and essential requirement for seed germination. Pecan seed has a hard woody endocarp and plays an important role during water uptake. • To explore the laws of water uptake during germination, the spatiotemporal pattern of water and the effect of endocarp were analysed by water measuring, high-field magnetic resonance imaging (MRI), dye-tracing, blocking and scanning electron microscopy (SEM). • Isolated seeds finish water uptake in 8h while whole seeds take 6d, and the cracking of endocarp plays an important role. The hilum is the channel for water to enter the seed, the rest of the seed coat consist of cells covered with a waxy layer and act as a barrier that made it difficult to absorb water. The region with the highest water contents in pecan seed was the edge of the U-shaped region and the water progressively diffused from the edge of the U-shaped region to the whole kernel. • There seems to be a new water absorption stage between phase II and phase III of triphasic model of water uptake of pecan seeds. The cracking of endocarp changed the water distribution in pecan seeds, which may be the trigger for further water absorption and radicle elongation.

Transcriptome Analysis of Resistant and Susceptible Pecan (Carya illinoinensis) Reveals the Mechanism of Resistance to Black Spot Disease (Colletotrichum fioriniae)

Pecan, Carya illinoinensis (Wangenh.) K. Koch, is an important dried fruit and woody oil tree species grown worldwide. With continuous expansion of pecan cultivation, the frequency and scope of diseases, especially black spot disease, are increasing, damaging trees and reducing yields. In this study, the key factors in resistance to black spot disease (Colletotrichum fioriniae) were investigated between the high-resistance pecan variety "Kanza" and the low-resistance variety "Mahan". Leaf anatomy and antioxidase activities confirmed much stronger resistance to black spot disease in "Kanza" than in "Mahan". Transcriptome analysis indicated that the increased expression of genes associated with defense response, oxidation-reduction, and catalytic activity was involved in disease resistance. A connection network identified a highly expressed hub gene CiFSD2 (CIL1242S0042), which might participate in redox reactions to affect disease resistance. Overexpression of CiFSD2 in tobacco inhibited enlargement of necrotic spots and increased disease resistance. Overall, the expression of differentially expressed genes differed in pecan varieties with different levels of resistance to C. fioriniae infection. In addition, the hub genes associated with black spot resistance were identified and the functions clarified. The in-depth understanding of resistance to black spot disease provides new insights for early screening of resistant varieties and molecular-assisted breeding in pecan.

Quantitative Phosphoproteomic Analysis Reveals Potential Regulatory Mechanisms of Early Fruit Enlargement in Pecan (Carya illinoinensis)

Pecan (Carya illinoinensis) is a popular tree nut. Its fruit development undergoes slow growth, rapid expansion, core hardening, and kernel maturation stages. However, little is known about how pecan initiates fruit development and enlargement after pollination. In this study, we performed the first large-scale identification of potential phosphorylation sites and proteins at early development of pecan fruit by a label-free phosphoproteomic quantification technique. A total of 2155 phosphosites were identified from 1953 phosphopeptides covering 1311 phosphoproteins in unpollinated pistils and fruits at 5 and 9 weeks after pollination. Of these, 699 nonredundant phosphoproteins were differentially phosphorylated (DP). Furthermore, the phosphorylation intensity of DP proteins in brassinolide (BR) and auxin signaling were analyzed, and the function of CiBZR1 was investigated. Ectopic expression of CiBZR1 resulted in BR response phenotypes with curled leaves and fruit, while enlarged seed size in Arabidopsis. Subcellular localization and transcriptional activation activity assay demonstrated that CiBZR1 distributed in both the nucleus and cytoplasm with transcriptional activity. When two phosphosites mutated, CiBZR1^S201P,S205G moved to the nucleus completely, while the transcriptional activity remained unchanged. Taken together, our data reveal extensive phosphoproteins and lay a foundation to comprehensively dissect the potential post-translational regulation mechanism of early development of pecan fruit.

Proteomic Analysis of Pecan (Carya illinoinensis) Nut Development

Pecan (Carya illinoinensis) nuts are an economically valuable crop native to the United States and Mexico. A proteomic summary from two pecan cultivars at multiple time points was used to compare protein accumulation during pecan kernel development. Patterns of soluble protein accumulation were elucidated using qualitative gel-free and label-free mass-spectrometric proteomic analyses and quantitative (label-free) 2-D gel electrophoresis. Two-dimensional (2-D) gel electrophoresis distinguished a total of 1267 protein spots and shotgun proteomics identified 556 proteins. Rapid overall protein accumulation occurred in mid-September during the transition to the dough stage as the cotyledons enlarge within the kernel. Pecan allergens Car i 1 and Car i 2 were first observed to accumulate during the dough stage in late September. While overall protein accumulation increased, the presence of histones diminished during development. Twelve protein spots accumulated differentially based on 2-D gel analysis in the weeklong interval between the dough stage and the transition into a mature kernel, while eleven protein spots were differentially accumulated between the two cultivars. These results provide a foundation for more focused proteomic analyses of pecans that may be used in the future to identify proteins that are important for desirable traits, such as reduced allergen content, improved polyphenol or lipid content, increased tolerance to salinity, biotic stress, seed hardiness, and seed viability.

The complete mitochondrial genome of Cladosporium anthropophilum (cladosporiaceae, dothideomycetes)

The genus Cladosporium (Cladosporiaceae, Capnodiales) is a large genus of Ascomycota. Although the genus is mostly reported as saprobes from a wide range of substrates with a worldwide distribution, members of this genus comprise infectious agents in animals and plants. Of those, Cladosporium anthropophilum is a common saprophytic fungus and has been found to be a human opportunistic pathogen and plant pathogen. The complete mitochondrial genome of C. anthropophilum is characterized through the de novo assembly of Illumina sequencing data. The mitochondrial genome is a circular molecule of 35,937 bp with 30.23% GC content and has a total of 47 genes including 16 protein-coding genes, 29 transfer RNA genes, and two ribosomal RNA genes. Based on protein-coding sequences of the mitochondrial genome sequence, a phylogenetic tree was constructed to demonstrate the phylogenetic relationship of C. anthropophilum and its related genera.

First report of leaf spot on pecan caused by Choanephora cucurbitarum in China

Pecan (Carya illinoinensis K. Koch) is an important and widely planted nut tree species in Jiangsu Province, China (Mo et al. 2018). In July 2020, leaf spot symptoms were frequently observed on pecan in Jurong, Jiangsu Province (119°15'36"E, 32°1'6"N). Disease incidences ranged from 40 to 65% among 150 mature pecan trees from three nurseries. The disease severity index (DSI, Jiang et al. 2019) reached 58.4. Symptoms began as small brown spots scattered on leaves that gradually expanded to large, circular to irregular black and brown necrotic lesions. In severe cases, lesions developed on large portions of a single leaf, and eventually the dead leaves fell from the trees. Three monoconidial isolates (Chen2346, Chen2347, Chen2348) were isolated from lesion margins and cultured on potato dextrose agar (PDA) medium. Colonies on PDA were white and cottony, later becoming light gray with abundant reproductive structures. Sporangiophores were aseptate, hyaline, unbranched, and apically dilated to form a clavate vesicle, which produced sporangia. Sporangia were globular to ellipsoid, brown to dark brown, 103 to 128 µm in length, and 88 to 114 µm in width (n = 30). Sporangiola were brown, ellipsoid to ovoid, with longitudinal striae, and measured 13.9 to 18.8 × 7.9 to 10.8 μm (n = 60). The morphological characteristics of these isolates agreed with descriptions of Choanephora cucurbitarum (Kirk 1984). Genomic DNA of these three monoconidial isolates was extracted, and the partial sequences of the internal transcribed spacer (ITS) and large subunit (LSU) of rDNA were amplified using primer pairs ITS1/ITS4 (White et al. 1990) and LR0R/LR7 (Vilgalys and Hester 1990), respectively. The consensus sequences (GenBank accession nos.: OP315248 to OP315250 for ITS and OP315251 to OP315253 for LSU) were aligned using BLASTn and showed100% identity with the sequences from C. cucurbitarum found in GenBank (accession nos.: MF942131 for ITS and ON025788 for LSU). To further confirm the identity, a phylogenetic analysis was performed with MEGA (v.7.0) and MrBayes (v.3.1.2) software, using the maximum likelihood and Bayesian inference methods, respectively. The multigene phylogeny revealed that the three isolates in this study, as well as, C. cucurbitarum specimen, clustered as a strongly supported monophyletic group (99 bootstrap value; 0.95 posterior probabilities). Based on the morphological and molecular data, the isolates were identified as C. cucurbitarum. To confirm pathogenicity, healthy pecan seedlings (2 years old) were each inoculated with a mycelial block (3 × 3 mm) excised from the margin of a colony on the vein of each leaf. Seedlings treated with non-colonized PDA blocks were used as controls. The inoculated seedlings were maintained in sterile plastic boxes with moistened sheets of filter paper at 25 ± 1°C and a 12-h photoperiod. Fifteen leaves per isolate were tested for each treatment. The experiment was repeated twice. Three days after inoculation, symptoms similar to those in the field appeared, whereas the control leaves remained symptomless. Subsequently, C. cucurbitarum was reisolated from the lesions and morphologically identified, confirming Koch's postulates. To the best of our knowledge, this is the first report of C. cucurbitarum causing leaf spot on C. illinoinensis in China. This study provides the foundation to further investigate the biology, epidemiology, and management of this disease.

Identification and Expression Analysis of MPK and MKK Gene Families in Pecan (Carya illinoinensis)

Mitogen-activated protein kinases consist of three kinase modules composed of MPKs, MKKs, and MPKKKs. As members of the protein kinase (PK) superfamily, they are involved in various processes, such as developmental programs, cell division, hormonal progression, and signaling responses to biotic and abiotic stresses. In this study, a total of 18 MPKs and 10 MKKs were annotated on the pecan genome, all of which could be classified into four subgroups, respectively. The gene structures and conserved sequences of family members in the same branch were relatively similar. All MPK proteins had a conserved motif TxY, and D(L/I/V)K and VGTxxYMSPER existed in all MKK proteins. Duplication events contributed largely to the expansion of the pecan MPK and MKK gene families. Phylogenetic analysis of protein sequences from six plants indicated that species evolution occurred in pecan. Organ-specific expression profiles of MPK and MKK showed functional diversity. Ka/Ks values indicated that all genes with duplicated events underwent strong negative selection. Seven CiPawMPK and four CiPawMKK genes with high expression levels were screened by transcriptomic data from different organs, and these candidates were validated by qRT-PCR analysis of hormone-treated and stressed samples.

fructicola that cause anthracnose in pecan

Pecan (Carya illinoinensis Wang. K. Koch) is a deciduous tree of the Juglandaceae family with important economic value worldwide. Anthracnose of the pecan leaves and shuck is a devastating disease faced by pecan-growing areas in China. However, the causal species occurring on pecan remain largely unidentified. we collected samples of diseased pecan from the provinces of China, Leaves and fruits affected by anthracnose were sampled and subjected to fungus isolation, The morphological characters of all strains were observed and compared; Multi-locus phylogenetic analyses [Internally transcribed spacer (ITS), Actin (ACT), Calmodulin (CAL), Chitin synthase (CHS1), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and b-tubulin (TUB2)] were performed on selected representative strains; examine their pathogenicity on leaves of pecan.The results showed that: (1) resulting in a total of 11 Colletotrichum isolates, Two Colletotrichum species were identifified to be C. fioriniae and C. fructicola; (2) Pathogenicity tests revealed that both species caused black spots on pecan leaves and fruit, The virulence of the different isolates varied substantially, with C. fioriniae PCJD179 being the most virulent; (3) The susceptibility levels of pecan tree varieties, 'Mahan' and 'Kanza', were determined, No significant differences were observed in the lesion sizes produced by the various isolates in 'Kanza', while there were signifificant differences in 'Mahan'. This study is thefifirst to determine that C. fructicola and C. fioriniaecan cause anthracnose in pecan in China. It improves the understanding of the species that cause anthracnose in pecan and provides useful information for the effective control of this disease in China.

Transcriptomic Analysis to Unravel Potential Pathways and Genes Involved in Pecan (Carya illinoinensis) Resistance to Pestalotiopsis microspora

Fruit black spot (FBS), a fungal disease of pecan (Carya illinoinensis (Wangenh) K. Koch) caused by the pathogen Pestalotiopsis microspora, is a serious disease and poses a critical threat to pecan yield and quality. However, the details of pecan responses to FBS infection at the transcriptional level remain to be elucidated. In present study, we used RNA-Seq to analyze differential gene expression in three pecan cultivars with varied resistance to FBS infection: Xinxuan-4 (X4), Mahan (M), and Wichita (W), which were categorized as having low, mild, and high susceptibility to FBS, respectively. Nine RNA-Seq libraries were constructed, comprising a total of 58.56 Gb of high-quality bases, and 2420, 4380, and 8754 differentially expressed genes (DEGs) with |log2Fold change| ≥ 1 and p-value < 0.05 were identified between M vs. X4, W vs. M, and W vs. X4, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed to further annotate DEGs that were part of specific pathways, which revealed that out of 134 total pathways, MAPK signaling pathway, plant−pathogen interaction, and plant hormone signal transduction were highly enriched. Transcriptomic profiling analysis revealed that 1681 pathogen-related genes (PRGs), including 24 genes encoding WRKY transcription factors, potentially participate in the process of defense against Pestalotiopsis microspora infection in pecan. The correlation of WRKY TFs and PRGs was also performed to reveal the potential interaction networks among disease-resistance/pathogenesis-related genes and WRKY TFs. Expression profiling of nine genes annotated as TIFY, WRKY TF, and disease-resistance protein-related genes was performed using qRT-PCR, and the results were correlated with RNA-Seq data. This study provides valuable information on the molecular basis of pecan−Pestalotiopsis microspora interaction mechanisms and offers a repertoire of candidate genes related to pecan fruit response to FBS infection.

Study on pecan seed germination influenced by seed endocarp

Nondeep physiological dormancy exists in freshly harvested pecan (Carya illinoinensis) seed, and the endocarp inhibits the seed germination. New methods were tried to detect if "chemical dormancy" or "mechanical dormancy" was caused by the endocarp. The germination of freshly harvested pecan seed with the removal of different parts of the endocarp and the fracture pressure of the endocarp of pecan seed soaked in water at different temperatures were tested. The results showed that (1) there was no significant difference in germination rate between the pecan kernel keeping in touch and out of touch with the same part of the endocarp, (2) whether a part of endocarp was removed to expose the radicle, preventing endocarp from splitting by glue inhibited the radicle elongation significantly, (3) the fracture pressure of the endocarp decreased significantly over water uptake time, and (4) little difference in the fracture pressure of the endocarp between different soaking temperatures. In conclusion, it suggested that (1) the endocarp caused "mechanical dormancy" but "chemical dormancy," (2) the prevention of radicle elongation was due to the endocarp pressuring the cotyledon rather than the direct physical restriction on the radicle, and (3) the radicle elongation seemed to be able to respond to the suture split and the pressure on the cotyledon.

Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus

Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.

Identification and Analysis of the AP2 Subfamily Transcription Factors in the Pecan (Carya illinoinensis)

The AP2 transcriptional factors (TFs) belong to the APETALA2/ ethylene-responsive factor (AP2/ERF) superfamily and regulate various biological processes of plant growth and development, as well as response to biotic and abiotic stresses. However, genome-wide research on the AP2 subfamily TFs in the pecan (Carya illinoinensis) is rarely reported. In this paper, we identify 30 AP2 subfamily genes from pecans through a genome-wide search, and they were unevenly distributed on the pecan chromosomes. Then, a phylogenetic tree, gene structure and conserved motifs were further analyzed. The 30 AP2 genes were divided into euAP2, euANT and basalANT three clades. Moreover, the cis-acting elements analysis showed many light responsive elements, plant hormone-responsive elements and abiotic stress responsive elements are found in CiAP2 promoters. Furthermore, a qPCR analysis showed that genes clustered together usually shared similar expression patterns in euAP2 and basalANT clades, while the expression pattern in the euANT clade varied greatly. In developing pecan fruits, CiAP2-5, CiANT1 and CiANT2 shared similar expression patterns, and their expression levels decreased with fruit development. CiANT5 displayed the highest expression levels in developing fruits. The subcellular localization and transcriptional activation activity assay demonstrated that CiANT5 is located in the nucleus and functions as a transcription factor with transcriptional activation activity. These results help to comprehensively understand the pecan AP2 subfamily TFs and lay the foundation for further functional research on pecan AP2 family genes.

Chromosome-scale assembly reveals asymmetric paleo-subgenome evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan

Pecan (Carya illinoinensis) is a tree nut crop of worldwide economic importance that is rich in health-promoting factors. However, pecan production and nut quality are greatly challenged by environmental stresses such as the outbreak of severe fungal diseases. Here, we report a high-quality, chromosome-scale genome assembly of the controlled-cross pecan cultivar 'Pawnee' constructed by integrating Nanopore sequencing and Hi-C technologies. Phylogenetic and evolutionary analyses reveal two whole-genome duplication (WGD) events and two paleo-subgenomes in pecan and walnut. Time estimates suggest that the recent WGD event and considerable genome rearrangements in pecan and walnut account for expansions in genome size and chromosome number after the divergence from bayberry. The two paleo-subgenomes differ in size and protein-coding gene sets. They exhibit uneven ancient gene loss, asymmetrical distribution of transposable elements (especially LTR/Copia and LTR/Gypsy), and expansions in transcription factor families (such as the extreme pecan-specific expansion in the far-red impaired response 1 family), which are likely to reflect the long evolutionary history of species in the Juglandaceae. A whole-genome scan of resequencing data from 86 pecan scab-associated core accessions identified 47 chromosome regions containing 185 putative candidate genes. Significant changes were detected in the expression of candidate genes associated with the chitin response pathway under chitin treatment in the scab-resistant and scab-susceptible cultivars 'Excell' and 'Pawnee'. These findings enable us to identify key genes that may be important susceptibility factors for fungal diseases in pecan. The high-quality sequences are valuable resources for pecan breeders and will provide a foundation for the production and quality improvement of tree nut crops.

Advances in Rootstock Breeding of Nut Trees: Objectives and Strategies

The production and consumption of nuts are increasing in the world due to strong economic returns and the nutritional value of their products. With the increasing role and importance given to nuts (i.e., walnuts, hazelnut, pistachio, pecan, almond) in a balanced and healthy diet and their benefits to human health, breeding of the nuts species has also been stepped up. Most recent fruit breeding programs have focused on scion genetic improvement. However, the use of locally adapted grafted rootstocks also enhanced the productivity and quality of tree fruit crops. Grafting is an ancient horticultural practice used in nut crops to manipulate scion phenotype and productivity and overcome biotic and abiotic stresses. There are complex rootstock breeding objectives and physiological and molecular aspects of rootstock-scion interactions in nut crops. In this review, we provide an overview of these, considering the mechanisms involved in nutrient and water uptake, regulation of phytohormones, and rootstock influences on the scion molecular processes, including long-distance gene silencing and trans-grafting. Understanding the mechanisms resulting from rootstock × scion × environmental interactions will contribute to developing new rootstocks with resilience in the face of climate change, but also of the multitude of diseases and pests.

Effects of Trap, and Ethanol Lure Type and Age on Attraction of Ambrosia Beetles (Coleoptera: Curculionidae)

Ambrosia beetles (Xylosandrus spp.) are pests of woody ornamental nurseries and tree nut orchards. Growers use ethanol-infused bolts and ethanol-mediated bottle traps for monitoring ambrosia beetles in the spring. To refine these monitoring tools, we investigated the 1) sensitivity of the commercially available ethanol pouches placed on bolts compared with that of ethanol-infused bolts for ambrosia beetle attacks; and 2) the effect of aging of ethanol pouches on ambrosia beetle captures in bottle traps. Experiments were conducted in ornamental nurseries and pecan orchards in 2019 and 2020. For objective 1, the treatments included a bolt infused with locally purchased ethanol, an ethanol pouch attached to a bolt, and a control (bolt without ethanol). For objective 2, ethanol pouches were initially field-aged for 0, 1, 2, 3, and 4 wk and ambrosia beetle captures were documented weekly for 4 wk. Ethanol pouches older than 5 wk were replaced with fresh pouches at the pecan sites while ethanol pouches at nursery sites were aged up to 8 wk. The ethanol-pouch comparison study showed that the number of ambrosia beetle attacks was significantly greater on ethanol-infused bolt traps than with the ethanol pouches on bolts at the nursery and pecan sites in both years. The age of the ethanol pouches did not affect captures of Xylosandrus crassiusculus (Motschulsky) and X. germanus (Blandford) in bottle traps within 8 wk of deployment. Results provide practical implications into the sensitivity of the different ethanol lure types in association with bolt traps and the longevity of the ethanol pouches for grower use.

Phytophthora cathayensis sp. nov., a new species pathogenic to Chinese Hickory (Carya cathayensis) in southeast China

Crown decline and mortality associated with collar lesions were observed on Carya cathayensis (Chinese hickory) trees in a plantation in Zhejiang province, China. Examination of active lesions resulted in the isolation of a homothallic, papillate Phytophthora sp. Detailed morphological and physiological studies and phylogenetic analysis, using ITS, beta-tubulin, cytochrome oxidase I, and heat shock protein 90 gene regions, revealed that all isolates belonged to an undescribed species residing in phylogenetic Clade 4, which is described here as Phytophthora cathayensis sp. nov. Inoculation trials were conducted under greenhouse conditions on C. cathayensis and C. illinoensis (pecan) plants to fulfill Koch postulates and hypothesize a possible pathway of the incursion. An existing report of a Phytophthora species with the same ITS sequence was reported on C. illinoensis from the USA in 2009. The difference in susceptibility of the two inoculated Carya species, and the report from the USA, suggest a possible introduction with plant material from the USA to China. Citation: Morales-Rodríguez C, Wang Y, Martignoni D, Vannini A (2020). Phytophthora cathayensis sp. nov., a new species pathogenic to Chinese Hickory (Carya cathayensis) in southeast China. Fungal Systematics and Evolution 7: 99-111. doi: 10.3114/fuse.2021.07.05.

Antioxidant Properties of Pecan Shell Bioactive Components of Different Cultivars and Extraction Methods

Pecan shells are a rich source of various bioactive compounds with potential antioxidant and antimicrobial properties. This study investigated the effect of pecan variety and method extraction on the antioxidant property of shell extracts. Twenty different varieties of pecan shells were subjected to either aqueous or ethanolic extraction and were examined for total phenolics and antiradical activity. The phenolic content and antiradical activity of shell extracts were significantly (p < 0.05) varied with different pecan cultivars. The total phenolic content of ethanol extracts ranged from 304.2 (Caddo) to 153.54 (Cherokee) mg GAE/g of dry extract and was significantly greater (p < 0.05) than those obtained by aqueous extraction. The antiradical activity of ethanol extracts ranged from 840.6 (Maramec) to 526.74 (Caper Fear) mg TEg-1, while aqueous extracts ranged from 934.9 (Curtis) to 468.3 (Elliot) mg TEg-1. Chemical profiling of the crude and acid hydrolyzed extracts was performed by reverse phase high performance liquid chromatography and flow injection electrospray ionization mass spectrometry. Lignin degradation products such as lignols, dilignols, trilignols, and oligolignols were found to be the major components of tested extracts. Phenolic content and antiradical activity of pecan shell extracts are significantly varied with cultivars and methods of extraction.

Extending the Cultivation Area of Pecan (Carya illinoinensis) Toward the South in Southeastern Subtropical China May Cause Increased Cold Damage

Pecan (Carya illinoinensis) is an important nut tree species in its native areas in temperate and subtropical North America, and as an introduced crop in subtropical southeastern China as well. We used process-based modeling to assess the effects of climatic warming in southeastern China on the leaf-out phenology of pecan seedlings and the subsequent risk of "false springs," i.e., damage caused by low temperatures occurring as a result of prematurely leafing out. In order to maximize the biological realism of the model used in scenario simulations, we developed the model on the basis of experiments explicitly designed for determining the responses modeled. The model showed reasonable internal accuracy when calibrated against leaf-out observations in a whole-tree chamber (WTC) experiment with nine different natural-like fluctuating temperature treatments. The model was used to project the timing of leaf-out in the period 2022-2099 under the warming scenarios RCP4.5 and RCP8.5 in southeastern China. Two locations in the main pecan cultivation area in the northern subtropical zone and one location south of the main cultivation area were addressed. Generally, an advancing trend of leaf-out was projected for all the three locations under both warming scenarios, but in the southern location, a delay was projected under RCP8.5 in many years during the first decades of the 21st century. In the two northern locations, cold damage caused by false springs was projected to occur once in 15-26 years at most, suggesting that pecan cultivation can be continued relatively safely in these two locations. Paradoxically, more frequent cold damage was projected for the southern location than for the two northern locations. The results for the southern location also differed from those for the northern locations in that more frequent cold damage was projected under the RCP4.5 warming scenario (once in 6 years) than under the RCP8.5 scenario (once in 11 years) in the southern location. Due to the uncertainties of the model applied, our conclusions need to be re-examined in an additional experimental study and further model development based on it; but on the basis of our present results, we do not recommend starting large-scale pecan cultivation in locations south of the present main pecan cultivation area in southeastern subtropical China.

Pecan pericarp extract protects against carbon tetrachloride-induced liver injury through oxidative mechanism in rats

The purpose of this study was to quantify the proanthocyanidin content of pecan (Carya illinoinensis) pericarp extract (PPE) and to assess its useful impacts against carbon tetrachloride (CCl₄)-induced hepatotoxicity. Rats were randomly divided into four groups: Group 1: received intraperitoneal injection of saline solution, Group 2: was injected with PPE (25 mg/kg body weight) for 10 consecutive days, Group 3: received CCl₄ (0.5 ml/kg, subcutaneous injection), Group 4: was coadministred with PPE + CCl₄. The CCl₄ was administered every 3 days during 10 days. Results revealed the presence of a high amount of total proanthocyanidins in the PPE (81.01 ± 0.21 mg TAE.g^-1DW). CCl₄ injection induced significant reductions in hepatic antioxidants but increased hepatic lipid peroxidation (LPO) as well as serum injury biomarkers. However, cotreatment with PPE significantly (P < 0.05) inverted CCl₄-induced increase in plasma alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, and lactate dehydrogenase activities, respectively to 74%, 77%, 60%, and 82% compared with CCl₄ group. No significant toxic effects were observed following treatment with plant extract alone. PPE cotreatment also decreased significant (P < 0.05) the hepatic malondialdehyde formation (21%) and enhanced the liver catalase activity (107%) in CCl₄-intoxicated rats. The histopathological examination showed inflammatory infiltration and degenerative changes in the hepatic tissue following CCl₄ injection. The hepatoprotective activity of PPE against CCl₄ exposure was supported by the maintenance of structural integrity of liver histopathology. In conclusion, the current study illustrated that PPE pretreatment significantly improved all examined parameters, restored the hepatic architecture and successfully alleviates oxidative damage induced by CCl₄ intoxication.

Photosystem Disorder Could be the Key Cause for the Formation of Albino Leaf Phenotype in Pecan

Pecan is one of the most famous nut species in the world. The phenotype of mutants with albino leaves was found in the process of seeding pecan, providing ideal material for the study of the molecular mechanisms leading to the chlorina phenotype in plants. Both chlorophyll a and chlorophyll b contents in albino leaves (ALs) were significantly lower than those in green leaves (GLs). A total of 5171 differentially expression genes (DEGs) were identified in the comparison of ALs vs. GLs using high-throughput transcriptome sequencing; 2216 DEGs (42.85%) were upregulated and 2955 DEGs (57.15%) were downregulated. The expressions of genes related to chlorophyll biosynthesis (HEMA1, encoding glutamyl-tRNA reductase; ChlH, encoding Mg-protoporphyrin IX chelatase (Mg-chelatase) H subunit; CRD, encoding Mg-protoporphyrin IX monomethylester cyclase; POR, encoding protochlorophyllide reductase) in ALs were significantly lower than those in GLs. However, the expressions of genes related to chlorophyll degradation (PAO, encoding pheophorbide a oxygenase) in ALs were significantly higher than those in GLs, indicating that disturbance of chlorophyll a biosynthesis and intensification of chlorophyll degradation lead to the absence of chlorophyll in ALs of pecan. A total of 72 DEGs associated with photosynthesis pathway were identified in ALs compared to GLs, including photosystem I (15), photosystem II (19), cytochrome b6-f complex (3), photosynthetic electron transport (6), F-type ATPase (7), and photosynthesis-antenna proteins (22). Moreover, almost all the genes (68) mapped in the photosynthesis pathway showed decreased expression in ALs compared to GLs, declaring that the photosynthetic system embedded within the thylakoid membrane of chloroplast was disturbed in ALs of pecan. This study provides a theoretical basis for elucidating the molecular mechanism underlying the phenotype of chlorina seedlings of pecan.

A comparison of fatty acid and sensory profiles of raw and roasted pecan cultivars

Five fatty acids comprise the bulk of the lipid content in pecans: palmitic acid, stearic acid, oleic acid, linoleic acid, and linolenic acid. Understanding the profiles of these fatty acids and how they relate to sensory characteristics may offer an explanation for flavor and flavor defects that may exist in certain cultivars of pecans. The objective of this study was to examine and compare fatty acid profiles of three cultivars of pecans (Major, Lakota, and Chetopa), over two crop years, under raw and roasted preparation methods, and understand the fatty acids association with sensory attributes. Percentages of palmitic, stearic, oleic, linoleic, and linolenic acids to total fatty acid content were determined using gas chromatography, and sensory profiles were generated using descriptive sensory analysis. Similar trends were seen across samples, with oleic acid comprising the majority of the total fatty acids and linolenic acid comprising the smallest percentage. There were significant differences in fatty acid content among cultivars and between pecans in the first and second crop year. Few associations were found between the fatty acids and sensory attributes, which suggest that combinations of the fatty acids contribute to certain pleasant or undesirable flavor attributes in the pecans. Subtle differences in fatty acid composition may lead to variation in flavor and flavor intensity or draw attention to or from certain attributes during consumption. Differences in crop year indicated that fatty acid content and therefore flavor are variable year to year. PRACTICAL APPLICATION: This study will help understand how fatty acid content of pecans varies from year to year. This should be taken into account when manufacturing products with pecans as the nutritional content of the product may change as the result.

The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts

As the apparent incidence of tree nut allergies rises, the development of MS methods that accurately identify tree nuts in food is critical. However, analyses are limited by few available tree nut protein sequences. We assess the utility of translated genomic and transcriptomic data for library construction with Juglans regia, walnut, as a model. Extracted walnuts were subjected to nano-liquid chromatography-mass spectrometry (n-LC-MS/MS), and spectra were searched against databases made from a six-frame translation of the genome (6FT), a transcriptome, and three proteomes. Searches against proteomic databases yielded a variable number of peptides (1156-1275), and only ten additional unique peptides were identified in the 6FT database. Searches against a transcriptomic database yielded results similar to those of the National Center for Biotechnology Information (NCBI) proteome (1200 and 1275 peptides, respectively). Performance of the transcriptomic database was improved via the adjustment of RNA-Seq read processing methods, which increased the number of identified peptides which align to seed allergen proteins by ~20%. Together, these findings establish a path towards the construction of robust proxy protein databases for tree nut species and other non-model organisms.

Effects of Moisture, Temperature, and Salt Content on the Dielectric Properties of Pecan Kernels During Microwave and Radio Frequency Drying Processes

Dielectric properties of materials influence the interaction of electromagnetic fields with and are therefore important in designing effective dielectric heating processes. We investigated the dielectric properties (DPs) of pecan kernels between 10 and 3000 MHz using a Novocontrol broadband dielectric spectrometer in a temperature range of 5–65 °C and a moisture content range of 10–30% wet basis (wb) at three salt levels. The dielectric constant (ε′) and loss factor (ε″) of the pecan kernels decreased significantly with increasing frequency in the radio frequency (RF) band, but gradually in the measured microwave (MW) band. The moisture content and temperature increase greatly contributed to the increase in the ε′ and ε″ of samples, and ε″ increased sharply with increasing salt strength. Quadratic polynomial models were established to simulate DPs as functions of temperature and moisture content at four frequencies (27, 40, 915, and 2450 MHz), with R² > 0.94. The average penetration depth of pecan kernels in the RF band was greater than that in the MW band (238.17 ± 21.78 cm vs. 15.23 ± 7.36 cm; p < 0.01). Based on the measured DP data, the simulated and experimental temperature-time histories of pecan kernels at five moisture contents were compared within the 5 min RF heating period.

Isolation and Characterization of Three Chalcone Synthase Genes in Pecan (Carya illinoinensis)

Phenolics are a group of important plant secondary metabolites that have been proven to possess remarkable antioxidant activity and to be beneficial for human health. Pecan nuts are an excellent source of dietary phenolics. In recent years, many studies have focused on the separation and biochemical analysis of pecan phenolics, but the molecular mechanisms of phenolic metabolism in pecans have not been fully elucidated, which significantly hinders quality breeding research for this plant. Chalcone synthase (CHS) plays crucial roles in phenolic biosynthesis. In this study, three Carya illinoinensisCHSs (CiCHS1, CiCHS2, and CiCHS3), were isolated and analyzed. CiCHS2 and CiCHS3 present high expression levels in different tissues, and they are also highly expressed at the initial developmental stages of kernels in three pecan genotypes. A correlation analysis was performed between the phenolic content and CHSs expression values during kernel development. The results indicated that the expression variations of CiCHS2 and CiCHS3 are significantly related to changes in total phenolic content. Therefore, CiCHSs play crucial roles in phenolic components synthesis in pecan. We believe that the isolation of CiCHSs is helpful for understanding phenolic metabolism in C. illinoinensis, which will improve quality breeding and resistance breeding studies in this plant.

The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition

BACKGROUND

Pecan (Carya illinoinensis) and Chinese hickory (C. cathayensis) are important commercially cultivated nut trees in the genus Carya (Juglandaceae), with high nutritional value and substantial health benefits.

RESULTS

We obtained >187.22 and 178.87 gigabases of sequence, and ∼288× and 248× genome coverage, to a pecan cultivar ("Pawnee") and a domesticated Chinese hickory landrace (ZAFU-1), respectively. The total assembly size is 651.31 megabases (Mb) for pecan and 706.43 Mb for Chinese hickory. Two genome duplication events before the divergence from walnut were found in these species. Gene family analysis highlighted key genes in biotic and abiotic tolerance, oil, polyphenols, essential amino acids, and B vitamins. Further analyses of reduced-coverage genome sequences of 16 Carya and 2 Juglans species provide additional phylogenetic perspective on crop wild relatives.

CONCLUSIONS

Cooperative characterization of these valuable resources provides a window to their evolutionary development and a valuable foundation for future crop improvement.

RNA-Seq Reveals Flavonoid Biosynthesis-Related Genes in Pecan ( Carya illinoinensis) Kernels

Pecan ( Carya illinoinensis) is an important tree nut throughout the world. The high concentration of flavonoid in its kernels makes it an excellent food with health benefits. However, the molecular basis of flavonoid biosynthesis in pecan remains unclear, which hinders quality breeding in this plant. Therefore, in order to find the crucial genes involved in flavonoid biosynthesis, the changes in flavonoid profiles and the transcriptomes of pecan kernels at four developmental stages (late water, gel, dough, and mature stages) were analyzed. As a result, the highest levels of total phenolic, condensed tannin, and flavan-3-ols were observed at the "late water stage". Catechin was the most abundant flavan-3-ol at different development stages. In total, 64 773 unigenes were obtained, and 46 924 (72.44%) unigenes were annotated. After differentially expressed gene (DEG) analysis, 12 750 unique DEGs were identified. Flavonoid-related DEGs of 36 structural genes and eight MYBs were obtained. The structural gene set contained three PALs, three CHSs, two CHIs, one F3H, two F3'Hs, two F3'5'Hs, one DFR, one ANS, two LARs, and two ANRs. The expression patterns of most of the structural genes were consistent with the changes in flavonoid profiles during kernel development. We believe that this RNA-Seq data set will provide valuable resources for unraveling the molecular mechanism of flavonoid metabolism in pecan and will significantly promote genetic studies and quality breeding in this plant.

Metabolomics of Two Pecan Varieties Provides Insights into Scab Resistance

UHPLC-MS-based non-targeted metabolomics was used to investigate the biochemical basis of pecan scab resistance. Two contrasting pecan varieties, Kanza (scab-resistant) and Pawnee (scab-susceptible), were profiled and the metabolomics data analyzed using multivariate statistics. Significant qualitative and quantitative metabolic differences were observed between the two varieties. Both varieties were found to have some unique metabolites. Metabolites that were only present or more abundant in Kanza relative to Pawnee could potentially contribute to the scab resistance in Kanza. Some of these metabolites were putatively identified as quercetin derivatives using tandem mass spectrometry. This suggests that quercetin derivatives could be important to pecan scab resistance.

BSACI guideline for the diagnosis and management of peanut and tree nut allergy

Peanut nut and tree nut allergy are characterised by IgE mediated reactions to nut proteins. Nut allergy is a global disease. Limited epidemiological data suggest varying prevalence in different geographical areas. Primary nut allergy affects over 2% of children and 0.5% of adults in the UK. Infants with severe eczema and/or egg allergy have a higher risk of peanut allergy. Primary nut allergy presents most commonly in the first five years of life, often after the first known ingestion with typical rapid onset IgE-mediated symptoms. The clinical diagnosis of primary nut allergy can be made by the combination of a typical clinical presentation and evidence of nut specifc IgE shown by a positive skin prick test (SPT) or specific IgE (sIgE) test. Pollen food syndrome is a distinct disorder, usually mild, with oral/pharyngeal symptoms, in the context of hay fever or pollen sensitisation, which can be triggered by nuts. It can usually be distinguish clinically from primary nut allergy. The magnitude of a SPT or sIgE relates to the probability of clinical allergy, but does not relate to clinical severity. SPT of ≥ 8 mm or sIgE ≥ 15 KU/L to peanut is highly predictive of clinical allergy. Cut off values are not available for tree nuts. Test results must be interpreted in the context of the clinical history. Diagnostic food challenges are usually not necessary but may be used to confirm or refute a conflicting history and test result. As nut allergy is likely to be a long-lived disease, nut avoidance advice is the cornerstone of management. Patients should be provided with a comprehensive management plan including avoidance advice, patient specific emergency medication and an emergency treatment plan and training in administration of emergency medication. Regular re-training is required.

A Pecan-Rich Diet Improves Cardiometabolic Risk Factors in Overweight and Obese Adults: A Randomized Controlled Trial

Evidence from observational and intervention studies has shown a high intake of tree nuts is associated with a reduced risk of cardiovascular disease (CVD), mortality from type 2 diabetes (T2DM), and all-cause mortality. However, there is limited data regarding their effects on indicators of cardiometabolic risk other than hypercholesterolemia, and little is known about the demonstrable health benefits of pecans (Carya illinoensis (Wangenh.) K.Koch). We conducted a randomized, controlled feeding trial to compare the effects of a pecan-rich diet with an isocaloric control diet similar in total fat and fiber content, but absent nuts, on biomarkers related to CVD and T2DM risk in healthy middle-aged and older adults who are overweight or obese with central adiposity. After 4 weeks on a pecan-rich diet, changes in serum insulin, insulin resistance (HOMA-IR) and beta cell function (HOMA-β) were significantly greater than after the control diet (p < 0.05). Pecan consumption also lowered the risk of cardiometabolic disease as indicated by a composite score reflecting changes in clinically relevant markers. Thus, compared to the control diet, the pecan intervention had a concurrent and clinically significant effect on several relevant markers of cardiometabolic risk.

Transcriptomic Analysis Provides Insights into Grafting Union Development in Pecan (Carya illinoinensis)

Pecan (Carya illinoinensis), as a popular nut tree, has been widely planted in China in recent years. Grafting is an important technique for its cultivation. For a successful grafting, graft union development generally involves the formation of callus and vascular bundles at the graft union. To explore the molecular mechanism of graft union development, we applied high throughput RNA sequencing to investigate the transcriptomic profiles of graft union at four timepoints (0 days, 8 days, 15 days, and 30 days) during the pecan grafting process. After de novo assembly, 83,693 unigenes were obtained, and 40,069 of them were annotated. A total of 12,180 differentially expressed genes were identified between by grafting. Genes involved in hormone signaling, cell proliferation, xylem differentiation, cell elongation, secondary cell wall deposition, programmed cell death, and reactive oxygen species (ROS) scavenging showed significant differential expression during the graft union developmental process. In addition, we found that the content of auxin, cytokinin, and gibberellin were accumulated at the graft unions during the grafting process. These results will aid in our understanding of successful grafting in the future.

RNA-Seq Analysis of Developing Pecan (Carya illinoinensis) Embryos Reveals Parallel Expression Patterns among Allergen and Lipid Metabolism Genes

The pecan nut is a nutrient-rich part of a healthy diet full of beneficial fatty acids and antioxidants, but can also cause allergic reactions in people suffering from food allergy to the nuts. The transcriptome of a developing pecan nut was characterized to identify the gene expression occurring during the process of nut development and to highlight those genes involved in fatty acid metabolism and those that commonly act as food allergens. Pecan samples were collected at several time points during the embryo development process including the water, gel, dough, and mature nut stages. Library preparation and sequencing were performed using Illumina-based mRNA HiSeq with RNA from four time points during the growing season during August and September 2012. Sequence analysis with Trinotate software following the Trinity protocol identified 133,000 unigenes with 52,267 named transcripts and 45,882 annotated genes. A total of 27,312 genes were defined by GO annotation. Gene expression clustering analysis identified 12 different gene expression profiles, each containing a number of genes. Three pecan seed storage proteins that commonly act as allergens, Car i 1, Car i 2, and Car i 4, were significantly up-regulated during the time course. Up-regulated fatty acid metabolism genes that were identified included acyl-[ACP] desaturase and omega-6 desaturase genes involved in oleic and linoleic acid metabolism. Notably, a few of the up-regulated acyl-[ACP] desaturase and omega-6 desaturase genes that were identified have expression patterns similar to the allergen genes based upon gene expression clustering and qPCR analysis. These findings suggest the possibility of coordinated accumulation of lipids and allergens during pecan nut embryogenesis.

Toxic and essential elements in five tree nuts from Hangzhou market, China

In this study, a total of 35 tree nut samples of walnut, pecan, pine seed, hickory nut and torreya were obtained from 5 farm product markets in Hangzhou, China, and investigated for essential (Cr, Mn, Fe, Mo, Cu, Zn, Se and Sr) and toxic (Al, As, Cd and Pb) elements by inductively coupled plasma-mass spectroscopy. Mean elemental concentrations of different tree nuts were in the following ranges: Cr 0.26-0.78 mg kg^-1, Mn 42.1-174 mg kg^-1, Fe 33.7-43.9 mg kg^-1, Mo 0.11-0.48 mg kg^-1, Cu 10.3-17.6 mg kg^-1, Zn 21.6-56.1 mg kg^-1, Se 0.015-0.051 mg kg^-1, Al 1.44-37.6 mg kg^-1, As 0.0062-0.047 mg kg^-1, Cd 0.016-0.18 mg kg^-1 and Pb 0.0069-0.029 mg kg^-1. The estimated provisional tolerable daily intake of Al, As, Cd and Pb was much lower than the provisional tolerable daily intake.

Nickel affects xylem Sap RNase a and converts RNase A to a urease

BACKGROUND

Nickel (Ni) is an essential micronutrient; however, its metabolic or physiological functions in plants and animals are largely uncharacterized. The ribonucleases (RNase, e.g., RNase A) are a large family of hydrolases found in one form or many forms facilitating nitrogen (N) cycling. It is currently unknown how either a deficiency or excess of Ni influences the functionality of ribonucleases, like RNase A. This is especially true for perennial crops possessing relatively high Ni requirements.

RESULTS

We report that the 'rising' xylem sap of pecan [Carya illinoinensis (Wangenh.) K. Koch, a long-lived tree] at bud break contains a 14 kDa RNase A (aka, RNase 1), which amount has a 33% greater in Ni-deficient as in Ni-sufficient trees when exposed to Ni ions exhibits ureolytic activity. The homologous 13.4 kDa bovine pancreatic RNase A likewise exhibits ureolytic activity upon exposure to Ni ions. Ni therefore affects enzymatic function of a typically non-metalloenzyme, such as it transforms to an enzyme capable of hydrolyzing a linear amide; thus, converting an endonuclease esterase into a urease.

CONCLUSIONS

We conclude that Ni potentially affects the level and activity of RNase A present in the spring xylem sap of pecan trees, and probably in other crops, it has the same influence. The catalytic property of RNase A appears to shift from a nuclease to a urease relying on Ni exposure. This is suggestive that RNase A might possess novel metabolic functionality regarding N-metabolism in perennial plants. The ability of Ni to convert the activity of plant and animal RNase A from that of a ribonuclease to a urease indicates a possible unrecognized beneficial metabolic function of Ni in organisms, while also identifying a potential detrimental effect of excessive Ni on N related metabolic activity if there is sufficient disruption of Ni homeostasis.

Interaction of Concurrent Populations of Meloidogyne partityla and Mesocriconema xenoplax on Pecan

The effect of the interaction between Meloidogyne partityla and Mesocriconema xenoplax on nematode reproduction and vegetative growth of Carya illinoinensis 'Desirable' pecan was studied in field microplots. Meloidogyne partityla suppressed reproduction of M. xenoplax, whereas the presence of M. xenoplax did not affect the population density of M. partityla second-stage juveniles in soil. Above-ground tree growth, as measured by trunk diameter 32 months following inoculation, was reduced in the presence of M. partityla alone or in combination with M. xenoplax as compared with the uninoculated control trees. The interaction between M. partityla and M. xenoplax was significant for dry root weight 37 months after inoculation. Results indicate that the presence of the two nematode species together caused a greater reduction in root growth than M. xenoplax alone, but not when compared to M. partityla alone. Mouse-ear symptom severity in pecan leaves was increased in the presence of M. partityla compared with M. xenoplax and the uninoculated control. Infection with M. partityla increased severity of mouse-ear symptoms expressed by foliage. The greater negative impact of M. partityla on vegetative growth of pecan seedlings in field microplots indicates that it is likely a more detrimental pathogen to pecan than is M. xenoplax and is likely an economic pest of pecan.

Identification and quantitation of asparagine and citrulline using high-performance liquid chromatography (HPLC)

High-performance liquid chromatography (HPLC) analysis was used for identification of two problematic ureides, asparagine and citrulline. We report here a technique that takes advantage of the predictable delay in retention time of the co-asparagine/citrulline peak to enable both qualitative and quantitative analysis of asparagine and citrulline using the Platinum EPS reverse-phase C18 column (Alltech Associates). Asparagine alone is eluted earlier than citrulline alone, but when both of them are present in biological samples they may co-elute. HPLC retention times for asparagine and citrulline were influenced by other ureides in the mixture. We found that at various asparagines and citrulline ratios [= 3:1, 1:1, and 1:3; corresponding to 75:25, 50:50, and 25:75 (microMol ml(-1)/microMol ml(-1))], the resulting peak exhibited different retention times. Adjustment of ureide ratios as internal standards enables peak identification and quantification. Both chemicals were quantified in xylem sap samples of pecan [Carya illinoinensis (Wangenh.) K. Koch] trees. Analysis revealed that tree nickel nutrition status affects relative concentrations of Urea Cycle intermediates, asparagine and citrulline, present in sap. Consequently, we concluded that the HPLC methods are presented to enable qualitative and quantitative analysis of these metabolically important ureides.

Entomopathogenic Nematodes and Bacteria Applications for Control of the Pecan Root-Knot Nematode, Meloidogyne partityla, in the Greenhouse

Meloidogyne partityla is a parasite of pecan and walnut. Our objective was to determine interactions between the entomopathogenic nematode-bacterium complex and M. partityla. Specifically, we investigated suppressive effects of Steinernema feltiae (strain SN) and S. riobrave (strain 7-12) applied as infective juveniles and in infected host insects, as well as application of S. feltiae's bacterial symbiont Xenorhabdus bovienii on M. partityla. In two separate greenhouse trials, the treatments were applied to pecan seedlings that were simultaneously infested with M. partityla eggs; controls received only water and M. partityla eggs. Additionally, all treatment applications were re-applied (without M. partityla eggs) two months later. Four months after initial treatment, plants were assessed for number of galls per root system, number of egg masses per root system, number of eggs per root system, number of eggs per egg mass, number of eggs per gram dry root weight, dry shoot weight, and final population density of M. partityla second-stage juveniles (J2). In the first trial, the number of egg masses per plant was lower in the S. riobrave-infected host treatment than in the control (by approximately 18%). In the second trial, dry root weight was higher in the S. feltiae-infected host treatment than in the control (approximately 80% increase). No other treatment effects were detected. The marginal and inconsistent effects observed in our experiments indicate that the treatments we applied are not sufficient for controlling M. partityla.

Recycling Potential and Fitness of Steinernematid Nematodes Cultured in Curculio caryae and Galleria mellonella

The recycling potential of entomopathogenic nematodes in the pecan weevil, Curculio caryae, following inundative applications is an important factor in considering whether nematodes could be incorporated into a C. caryae management strategy. Our objective was to determine the recycling potential and fitness of Steinernema carpocapsae and S. riobrave cultured in C. caryae. To estimate fitness and quality, we reared nematodes in larvae of C. caryae and in the commonly used standard host, the greater wax moth, Galleria mellonella. Nematode lipid content, infectivity (power to invade), virulence (power to kill), and reproductive capacity (yield per insect) in C. caryae larvae were compared with G. mellonella data. Lipid content was higher in S. carpocapsae cultured in C. caryae than in G. mellonella, but S. riobrave lipid content was not affected by host source. Host source did not affect subsequent infectivity or virulence to C. caryae (P > 0.05) but did affect reproductive capacity (P < 0.0001). Both nematode species produced more progeny in C. caryae when they were first cultured in G. mellonella than when they were first passed through C. caryae. In terms of potential to recycle under field conditions, we predict that nematodes resulting from one round of recycling in C. caryae larvae would be equally capable of infecting and killing more weevils, but the potential to continue recycling in C. caryae would diminish over time due to reduced reproduction in that host.

Survey of crop losses in response to phytoparasitic nematodes in the United States for 1994

Previous reports of crop losses to plant-parasitic nematodes have relied on published results of survey data based on certain commodities, including tobacco, peanuts, cotton, and soybean. Reports on crop-loss assessment by land-grant universities and many commodity groups generally are no longer available, with the exception of the University of Georgia, the Beltwide Cotton Conference, and selected groups concerned with soybean. The Society of Nematologists Extension Committee contacted extension personnel in 49 U.S. states for information on estimated crop losses caused by plant-parasitic nematodes in major crops for the year 1994. Included in this paper are survey results from 35 states on various crops including corn, cotton, soybean, peanut, wheat, rice, sugarcane, sorghum, tobacco, numerous vegetable crops, fruit and nut crops, and golf greens. The data are reported systematically by state and include the estimated loss, hectarage of production, source of information, nematode species or taxon when available, and crop value. The major genera of phytoparasitic nematodes reported to cause crop losses were Heterodera, Hoplolaimus, Meloidogyne, Pratylenchus, Rotylenchulus, and Xiphinema.

Meloidogyne partityla on Pecan Isozyme Phenotypes and Other Host

Meloidogyne sp. from five pecan (Carya illinoensis) orchards in Texas were distinctive in host range and iszoyme profiles from common species of Meloidogyne but were morphologically congruent with Meloidogyne partityla Kleynhans, a species previously known only in South Africa. In addition to pecan, species of walnut (Juglans hindsii and J. regia) and hickory (C. ovata) also were hosts. No reproduction was observed on 15 other plant species from nine families, including several common hosts of other Meloidogyne spp. Three esterase phenotypes and two malate dehydrogenase phenotypes of M. partityla were identified by polyacrylamide gel electrophoresis. Each of these isozyme phenotypes was distinct from those of the more common species M. arenaria, M. hapla, M. incognita, and M. javanica.

Society of Nematologists Extension Committee. Bibliography of U.S. Extension and Extension-related Publications on Nematodes

A listing was compiled of hematology publications available through the Cooperative Extension Service and similar organizations in the United States. It provides a convenient reference to current articles addressing many of the more applied aspects of plant nematology and nematode management.