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Pecan ( Carya illinoinensis ) is an economically important nut crop known for its genetic diversity and adaptability to various climates. Understanding the growth variability, phenological traits, and population structure of pecan populations is crucial for breeding programs and conservation. In this study, plant growth and phenological traits were evaluated over three consecutive seasons (2015–2017) for 550 genotypes from 26 provenances. Significant variations in plant height, stem diameter, and budbreak were observed among provenances, with Southern provenances exhibiting faster growth and earlier budbreak compared to Northern provenances. Population structure analysis using SNP markers revealed eight distinct subpopulations, reflecting genetic differentiation among provenances. Notably, Southern Mexico collections formed two separate clusters, while Western collections, such as 'Allen 3', 'Allen 4', and 'Riverside', were distinguished from others. 'Burkett' and 'Apache' were grouped together due to their shared maternal parentage. Principal component analysis and phylogenetic tree analysis further supported subpopulation differentiation. Genetic differentiation among the 26 populations was evident, with six clusters highly in agreement with the subpopulations identified by STRUCTURE and fastSTRUCTURE. Principal components analysis (PCA) revealed distinct groups, corresponding to subpopulations identified by genetic analysis. Discriminant analysis of PCA (DAPC) based on provenance origin further supported the genetic structure, with clear separation of provenances into distinct clusters. These findings provide valuable insights into the genetic diversity and growth patterns of pecan populations. Understanding the genetic basis of phenological traits and population structure is essential for selecting superior cultivars adapted to diverse environments. The identified subpopulations can guide breeding efforts to develop resilient rootstocks and contribute to the sustainable management of pecan genetic resources. Overall, this study enhances our understanding of pecan genetic diversity and informs conservation and breeding strategies for the long-term viability of pecan cultivation.

Background Expansins (EXPs) are important components of the plant cell wall. They are involved in plant growth and development and diverse environmental stress responses by promoting cell-wall loosening and cell enlargement. Although EXPs have been characterized in many plant species, little is known about the EXPs in Carya illinoinensis . Methods The CiEXP gene family was systematically analyzed using bioinformatics. RNA-seq data (both from our study and public databases) and qRT-PCR were employed to analyze the expression patterns of the CiEXP family in different tissues, under biotic and abiotic stress, and in persistent versus abscised fruit. Results In this study, a total of 39 EXP genes unevenly distributed on 14 chromosomes were identified in the C. illinoinensis genome, which were classified into four subfamilies (27 CiEXPAs, 3 CiEXPBs, 2 CiEXLAs, and 7 CiEXLBs), and the motif and gene structures were consistent with this subfamily classification. Thirty-six pairs of duplicated genes were identified, suggesting that gene duplication may have contributed to the expansion of the EXP gene family. Collinearity analysis provided further phylogenetic insights into the EXP gene family. Cis -acting element analysis revealed that the promoter regions of the CiEXPs gene were associated with hormone-responsive, plant growth and development, and stress-responsive, particularly ABA response element (ABRE) and MeJA-responsive element. The expression results showed that most CiEXPs exhibited tissue-specific expression patterns, and some CiEXPs were highly responsive to abiotic and biotic stresses. Additionally, most CiEXPA genes, CiEXPB1/2 , and CiEXLA2 were up-regulated in persistent fruit. Conclusions Our study findings enhance the understanding of the CiEXP gene family and facilitate the selection of suitable candidate genes for further study, which lays a foundation for future investigations into the functional roles of specific CiEXPs .

Khakiweed is a perennial broadleaf weed that is difficult to control because of its multiple means of reproduction, vigorous growth, and deep taproot. Khakiweed reduces the performance of pasture, pecan, and turf areas by choking out desirable grass and legume species. Because information on the effectiveness of contact and residual herbicides for control in pecan and pasture areas is limited, greenhouse studies were conducted to determine the effect of application timing, mode of action, and rate on khakiweed control. Preemergence and postemergence herbicides were applied to mature khakiweed plants at 0.25X, 0.5X, 1X, or 2X the label recommended rate for general broadleaf control. Biomass was collected 3 wk after application. Plants regrew from roots in the greenhouse until a second biomass harvest was collected at 6 wk after treatment (WAT). Metsulfuron-methyl, indaziflam, or pendimethalin was applied preemergence to the soil surface. All rates of preemergence herbicides provided high-efficacy control of regrowth (>85%) compared to the nontreated control. The efficacies of postemergence-applied metsulfuron-methyl, metsulfuron-methyl + nicosulfuron, indaziflam, aminopyralid + florpyrauxifen-benzyl, 2,4-D amine, and 2,4-D amine + florpyrauxifen-benzyl were also examined. All postemergence herbicide treatments exhibited control compared to the nontreated plants at both sample timings (3 and 6 WAT) and increased with herbicide application rate. No herbicide provided high-efficacy control during the initial postspray period (0 to 3 WAT). During the regrowth period (3 to 6 WAT), metsulfuron-methyl alone and in combination gave >85% control of khakiweed biomass, indicating that the sulfonylurea herbicides used in this study are well suited to controlling khakiweed. Nomenclature: Aminopyralid; florpyrauxifen-benzyl; indaziflam; metsulfuron-methyl; nicosulfuron; pendimethalin; 2,4-D; khakiweed, Alternanthera pungens Kunth; pecan, Carya illinoinensis (Wangenh.) K. Koch

Salt stress severely limits the growth and ornamental value of pecan (Carya illinoinensis) in salinized regions, yet the transcriptional mechanisms underlying its stress adaptation remain unclear. In this study, a comprehensive genomic analysis of the GRAS transcription factor family identified 58 CiGRAS genes in pecan. These genes were classified into 11 subfamilies and showed conserved motifs and gene structures, with variation in promoter cis-elements suggesting diverse regulatory functions. Chromosomal distribution and duplication analysis indicated that whole-genome and dispersed duplication events were the main drivers of CiGRAS expansion. Transcriptome data revealed tissue-specific expression and strong responsiveness to salt and other stresses. Under 0.6% NaCl treatment, several CiGRAS genes were significantly upregulated, especially at 48 h. Gene co-expression analysis further highlighted GRAS-enriched modules associated with redox regulation and stress signaling. qRT-PCR validation confirmed time-specific induction of seven CiGRAS genes under salt stress. These findings provide insights into the evolutionary dynamics and stress-related roles of CiGRAS genes and offer candidate regulators for improving pecan salt tolerance in ecological greening and landscape applications.

The pecan (Carya illinoinensis) industry in South Africa is growing rapidly, and it is becoming increasingly crucial to understand the risks posed to pecans by fungal pathogens. Black spots on leaves, shoots, and nuts in shucks caused by Alternaria species have been observed since 2014 in the Hartswater region of the Northern Cape Province of South Africa. Species of Alternaria include some of the most ubiquitous plant pathogens on earth. The aim of this study was to use molecular techniques to identify the causative agents of Alternaria black spot and seedling wilt isolated from major South African pecan-production areas. Symptomatic and non-symptomatic pecan plant organs (leaves, shoots, and nuts-in-shucks) were collected from pecan orchards, representing the six major production regions in South Africa. Thirty Alternaria isolates were retrieved from the sampled tissues using Potato Dextrose Agar (PDA) culture media and molecular identification was conducted. The phylogeny of multi-locus DNA sequences of Gapdh, Rpb2, Tef1, and Alt a 1 genes revealed that the isolates were all members of Alternaria alternata sensu stricto, forming part of the Alternaria alternata species complex. The virulence of six A. alternata isolates were tested on detached nuts of Wichita and Ukulinga cultivars, respectively, as well as detached leaves of Wichita. The A. alternata isolates were also evaluated for their ability to cause seedling wilt in Wichita. The results differed significantly between wounded and unwounded nuts of both cultivars, but not between the cultivars. Similarly, the disease lesions on the wounded detached leaves were significantly different in size from the unwounded leaves. The seedling tests confirmed that A. alternata is pathogenic and that A. alternata causes black spot disease and seedling wilt of pecans. This study is one of the first documentations of Alternaria black spot disease of pecan trees and its widespread occurrence in South Africa.

Calcium-dependent protein kinases (CDPKs) are crucial for plant development and stress responses. In this study, we performed a comprehensive genomic analysis of the CDPK gene family in pecan (Carya illinoinensis) and evaluated their potential roles in salt stress responses. A total of 31 CiCDPK genes were identified and classified into four subgroups through phylogenetic analysis. Structural and promoter analyses revealed conserved motifs and regulatory elements linked to stress responses. Gene duplication analysis showed that WGD and DSD events were primary drivers of CiCDPK expansion, shaped by purifying selection. GO and KEGG annotations highlighted roles in kinase activity, calcium binding, and signal transduction, while interaction networks suggested involvement in ROS regulation and ATP-dependent phosphorylation. Tissue-specific expression patterns indicated distinct roles of CiCDPKs, with CiCDPK20 and CiCDPK31 predominantly expressed in male flowers and seeds, respectively. Transcriptome data showed that CiCDPKs exhibited distinct responses to abiotic and biotic stress, highlighting their functional specialization under various conditions. qRT-PCR analysis further confirmed the involvement of 16 CiCDPKs in salt stress adaptation, supporting their critical roles in signal transduction pathways during salinity stress. This study provides insights into CiCDPK functions, offering potential applications in breeding pecan varieties with enhanced salt tolerance.

Using ITS1-based metabarcoding, we investigated the structure of the soil fungal communities in the central and peripheral zones of a 25-hectare pecan nut ( ) orchard located in the arid region of Coahuila, Mexico. While environmental conditions such as soil moisture and temperature varied between zones, physicochemical soil properties (pH, organic carbon, total carbon, organic matter, electrical conductivity, and zinc) remained homogeneous. A total of 4,443 fungal OTUs were detected at 97% similarity. Alpha diversity indices did not differ significantly between zones. The fungal community was dominated by the phyla Ascomycota and Basidiomycota, with Pezizomycetes, Dothideomycetes, and Agaricomycetes as dominant classes. No statistically significant differences in beta diversity or community composition were found between zones (PERMANOVA p = 0.662). Redundancy analysis also revealed no clear clustering by zone, though localized differences were observed. Our findings suggest that agronomic management in this system promotes environmental homogeneity, leading to relatively uniform fungal communities. This exploratory study highlights the need for future research incorporating comparisons with adjacent natural ecosystems to better assess spatial patterns and potential edge effects in agroecosystems.

Plant R2R3-MYBs comprise one of the largest transcription factor families; however, few R2R3-MYB genes in pecan have been functionally analyzed due to the limited genome information and potential functional redundancy caused by gene duplication. In this study, 153 R2R3-MYB genes were identified and subjected to comparative phylogenetic analysis with four other plant species. Then, the pecan R2R3-MYB gene family was divided into different clades, which were also supported by gene structure and motif composition results. Fifty-two duplication events including 77 R2R3-MYB genes were identified in this gene family, and Ka/Ks values showed that all of the duplication events were under the influence of negative selection. Expression levels of pecan R2R3-MYB genes during the graft union formation process were further investigated using RNA-seq with four different timepoints after grafting, namely, 0, 8, 15 and 30 d. Sixty-four differentially expressed R2R3-MYB genes were identified and showed different expression patterns after grafting. Co-expression networks were further constructed to discover the relationships between these genes. The co-expression networks contained 57 nodes (R2R3-MYB genes) and 219 edges (co-expression gene pairs) and CIL1528S0032 contained the maximum number of edges. Fifteen genes contained more than 10 edges; the majority of these were up-regulated during graft union formation and verified by qRT-PCR. This study provides a foundation for functional analysis to investigate the roles that R2R3-MYBs play in graft union formation in pecan and identify the key candidate genes.

In order to determine the appropriate harvesting period of Carya illinoinensis planted in Nanjing city of China, this study analyzed the phenotypic characteristics and inclusions, including single fruit quality, fruit transverse and vertical diameter, kernel rate, water content, color, respiratory strength, crude fat, soluble sugar, soluble protein, and total phenols, of two cultivars ‘Pawnee’ and ‘Wichita’ during September and October, respectively. Results showed that the respiration intensity and IAD values of pecan fruits decreased as the harvest date was delayed. ‘Pawnee’ fruits exhibited the highest seed kernel fullness, ∆E value, fruit transverse diameter, shape index, kernel yield, crude fat, and total phenolic content in late September and early October, while the quality of ‘Wichita’ fruits reached its peak in late October. The appropriate harvest period is conducive to the material accumulation of Carya illinoinensis, which is of great practical significance for improving the commodity value of pecans. The optimal harvesting period for ‘Pawnee’ in Nanjing is from the end of September to the beginning of October, and the optimal harvesting period for ‘Wichita’ is from mid- to late-October to the end of October.

Pecan ( Carya illinoinensis ) cultivars adapted to Missouri produce small to medium sized nuts regarded as having light-colored, high-quality kernels, and good flavor. Improved grafted orchards are an important component of Missouri’s pecan industry. As of the 2022 US Department of Agriculture, National Agricultural Statistics Service Agricultural Census, there are 2524 improved and 7194 native pecan acres in the state. In the northern production regions, like Missouri, pecan orchards are often lower input (pesticide, pruning, nonirrigated) and can be produced organically or within agroforestry systems, and nuts are commonly sold directly to consumers. Cultivar selection has an outsized impact on an orchard’s long-term production and profit potential. Long-term evaluations provide growers with valuable insight when considering adoption of new cultivars. In 1996, eight pecan cultivars commonly grown in Missouri were grafted onto ‘Colby’ seedling rootstock and established in three complete randomized blocks for long-term evaluation at the University of Missouri’s Horticulture and Agroforestry Research Farm in New Franklin, MO, USA. Evaluations included total yield per tree (kg), nut quality, pecan scab rating on leaves and nuts, and diameter at breast height each year from 2019–21 with an additional year of total nut yield per tree taken in 2024. Mean per tree nut yields ranged from 4.5 to 40.4 kg in 2019, 0.1 to 14.9 kg in 2020, 7.8 to 78.7 kg in 2021, and 0.0 to 23.6 kg in 2024. Mean in-shell weight ranged from 4.7 to 7.3 g in 2019, 3.7 to 7.1 in 2020 g, and 4.2 to 7.5 g in 2021. ‘Kanza’ stands out as a high-yielding cultivar with medium sized nuts and good kernel quality recommended to central Missouri growers.