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Background Calcium (Ca 2+ ) serves as a ubiquitous second messenger and plays a pivotal role in signal transduction. Calcineurin B-like proteins (CBLs) are plant-specific Ca 2+ sensors that interact with CBL-interacting protein kinases (CIPKs) to transmit Ca 2+ signals. CBL-CIPK complexes have been reported to play pivotal roles in plant development and response to drought stress; however, limited information is available about the CBL and CIPK genes in pecan, an important nut crop. Results In the present study, a total of 9 CBL and 30 CIPK genes were identified from the pecan genome and divided into four and five clades based on phylogeny, respectively. Gene structure and distribution of conserved sequence motif analysis suggested that family members in the same clade commonly exhibited similar exon-intron structures and motif compositions. The segmental duplication events contributed largely to the expansion of pecan CBL and CIPK gene families, and Ka / Ks values revealed that all of them experienced strong negative selection. Phylogenetic analysis of CIPK proteins from 14 plant species revealed that CIPKs in the intron-poor clade originated in seed plants. Tissue-specific expression profiles of CiCBLs and CiCIPKs were analysed, presenting functional diversity. Expression profiles derived from RNA-Seq revealed distinct expression patterns of CiCBLs and CiCIPKs under drought treatment in pecan. Moreover, coexpression network analysis helped to elucidate the relationships between these genes and identify potential candidates for the regulation of drought response, which were verified by qRT–PCR analysis. Conclusions The characterization and analysis of CBL and CIPK genes in pecan genome could provide a basis for further functional analysis of CiCBLs and CiCIPKs in the drought stress response of pecan.

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 NH 4   + / NO 3   − 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 NH 4   + / NO 3   − 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.

Large amounts of residues are generated in pecan cultivation processes. Biochar is an environmentally friendly way to utilize residues but attempts to prepare and apply biochar with pecan residues are rare. In this study, six types of biochars were produced from pecan branches, trunks, roots, nutshells, husks, and leaves under pyrolysis, and their physicochemical properties were compared to assess their application perspective in environmental and agricultural fields. The yields of six pecan biochars were 32.1%–45.9%, with the highest yield for husk biochar (HB) (45.9%). Among the pecan biochars, trunk biochar (TB) and root biochar (RB) had much larger specific surface areas. Branch biochar (BB), TB, and RB presented tubular structures with elliptical pores, while nutshell biochar (NSB), HB, and leaf biochar (LB) appeared flaky or as clustered structures with relatively rougher outer surfaces and irregular pores. The functional group types of pecan biochars were generally similar, but the intensities of the peak near 2900 cm−1 in BB were obviously higher than those of the other biochars. RB and LB contained significantly more ash and volatile than those of the other pecan biochars, with the highest fixed carbon content being found in NSB (70.1%). All of the pecan biochars were alkaline (7.90–9.87), and HB, LB, and NSB had significantly higher pH values than those of the other biochars. Elemental analysis indicated that RB, NSB, and LB had higher carbon levels (more than 70%) with lower O/C ratios (no more than 0.2). HB possessed a relatively high content of nitrogen, potassium, magnesium; the phosphorus content was highest in NSB; LB had the highest calcium content. The results of principal component analysis showed that BB, LB, and NSB were clustered in the same quadrant with relatively close relationships. The results of this study can guide the utilization of pecan wastes and their application as biochar in different fields.

Endophytic fungi establish mutualistic relationships with host plants and can promote the growth and development of plants. In this study, the endophytic fungus JRF11 was isolated from Carya illinoinensis. Sequence analysis of the internal transcribed spacer (ITS) region and 18S rRNA gene combined with colonial and conidial morphology identified JRF11 as a Paraphaosphaeria strain. Plant–fungus interaction assays revealed that JRF11 showed significant growth-promoting effects on plants. In particular, JRF11 significantly increased the root biomass and soluble sugar content of plants. Furthermore, transcriptome analysis demonstrated that JRF11 treatment reprogrammed a variety of genes involved in plant mitogen-activated protein kinase (MAPK) signaling and starch and sucrose metabolism pathways through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Our research indicates that beneficial endophytic fungi are able to interact with plants and exhibit outstanding plant growth-promoting activities.

Biochar and beneficial microorganisms have been widely used in ecological agriculture. However, the impact of biochar loaded with microbes (BM) on plant growth remains to be understood. In this study, BM was produced by incubating pecan biochar with the bacterial strain N33, and the effects of BM on pecan growth and the microbial community in the rhizosphere were explored. BM application significantly enhanced the biomass and height of pecan plants. Meanwhile, BM treatment improved nutrient uptake in plants and significantly increased the chlorophyll, soluble sugars, and soluble proteins of plants. Furthermore, BM treatment improved the soil texture and environment. Finally, BM application substantially enhanced the diversity of soil fungi and bacteria as well as the relative abundances of the phyla Firmicutes and Chloroflexi, and families Bacillaceae and Paenibacillaceae, as shown by high-throughput sequencing. Together, this study clarified the growth-promotive effects of BM on pecan plants and suggested an alternative to synthetic fertilizers in their production.

Pecan (Carya illinoinensis [Wangenh]. K. Koch) germplasm resources are abundant, yet the characteristics of each cultivar at the seedling stage remain insufficiently understood. This study systematically evaluated the growth parameters, photosynthetic traits, and anatomical structures of one-year-old grafted seedlings from five pecan cultivars: “Pawnee”, “Mandan”, “Nacono”, “Caddo”, and “Creek”. Principal component analysis (PCA) was employed to comprehensively assess 56 indicators. The results indicated that, in terms of vegetative growth, leaf area and biomass of “Nacono” and “Creek” were significantly greater than those of “Pawnee” (p < 0.05). “Mandan” ranked second. Additionally, the seedling quality index of “Creek” was markedly superior to all other cultivars (p < 0.05). Anatomically, “Pawnee” exhibited greater leaf thickness, more highly differentiated palisade tissue, and the development of the main vein. By contrast, “Mandan” displayed larger branch radius, cortex thickness, and pith radius, accompanied by finer vessels and large but sparsely distributed stomata (p < 0.05). Regarding photosynthetic performance, “Mandan” accumulated the highest concentrations of photosynthetic pigments and achieved the greatest photosynthetic efficiency, significantly outperforming the remaining cultivars (p < 0.05). The PCA-based comprehensive evaluation revealed that “Mandan” outperformed the other cultivars in seedling growth, making it the most suitable for promotion, followed by “Creek”, “Nacono”, “Caddo”, and “Pawnee”. This research offers a theoretical foundation for the breeding, promotion, and application of superior pecan cultivars.

Background Pecan ( Carya illinoinensis ) is an important woody oilseed tree species, known for its nuts rich in healthy oil. However, the molecular mechanisms and functions of key genes involved in lipid biosynthesis during pecan seed development remain poorly understood. Results In this study, the oil content of mature seeds from the ‘Nacono’ and ‘Creek’ cultivars was 70.22% and 58.39%, respectively. Untargeted lipidomics identified five major classes of lipid molecules, with the highest proportions of glycerophospholipids and glycerolipids. These lipids contained five distinct fatty acids, with linolenic and lignoceric acids being the most abundant. cDNA libraries were constructed for seeds at 110, 124, 138, and 152 days after flowering (DAF) in both cultivars. A total of 25,099 differentially expressed genes (DEGs) were identified, including 1,695 transcription factor (TF) genes classified into 67 families. Based on transcriptome data, 15 TF genes exhibiting significant trends in fragments per kilobase of transcript per million mapped reads (FPKM) were selected for qRT-PCR validation, and the expression patterns were consistent with the transcriptome analysis. As the DAF increased, the expression levels of CiPaw16G032200-bHLH , CiPaw07G014900-bHLH , and CiPaw06G056900-C2H2 were continuously down-regulated, while CiPaw15G075200-C2H2 was up-regulated, suggesting that these genes may play crucial roles in lipid accumulation during pecan seed development. Conclusions This study presentes a comprehensive analysis of lipid accumulation and transcriptional regulation during pecan seed development. The results reveal the molecular and biochemical mechanisms governing lipid deposition and offer valuable insights for the genetic enhancement of oil yield in this economically important species.

Pecan is an important oilseed tree species valued for its nutrient-rich nuts. WRKY and VQ proteins play crucial roles in plant growth, development, and stress response. However, few WRKY and VQ genes in pecan have been functionally analyzed due to functional redundancy caused by gene duplication. In this study, 89 CiWRKYs and 47 CiVQs were identified in pecan genome, which were unevenly distributed across chromosomes. Gene structure and conserved motif analyses revealed high diversity among members. Duplication analysis indicated that segmental duplication was the major factor of family expansion of CiWRKY and CiVQ. Ka/Ks ratios revealed that most duplicated gene pairs underwent purifying selection. Promoter analysis identified numerous cis-acting elements associated with light response, hormone regulation, and abiotic stress, implying their potential regulatory roles in development and stress response. Expression data across six tissues demonstrated tissue-specific patterns, with several genes highly expressed in flowers and roots. Transcriptome analysis revealed that 63 CiWRKY and 27 CiVQ genes were significantly upregulated under drought stress. qRT-PCR validation confirmed that CiPaw.10G165200 and CiPaw.04G072500 were highly induced by salt treatment, with expression levels increasing over 100-fold at 8 d. Moreover, CiPaw.10G165200 was also highly expressed under ABA treatment, which indicated it might play a key role in the response to abiotic stresses. Our results provide valuable insights into the evolutionary patterns and functional roles of WRKY and VQ genes in pecan and lay a foundation for improving stress tolerance and molecular breeding in this economically important nut tree.

Pecan seed oil is a valuable source of essential fatty acids and various bioactive compounds; however, the functions of microRNAs and their targets in oil biosynthesis during seed development are still unknown. Here, we found that the oil content increased rapidly in the three early stages in three cultivars, and that oleic acid was the predominant fatty acid component in the mature pecan embryos. We identified, analyzed, and validated the expression levels of miRNAs related to seed development and oil biosynthesis, as well as their potential target genes, using small RNA sequencing data from three stages (120, 135, and 150 days after flowering). During the seed development process, 365 known and 321 novel miRNAs were discovered. In total, 91 known and 181 novel miRNAs were found to be differentially expressed, and 633 target genes were further investigated. The expression trend analysis revealed that the 91 known miRNAs were classified into eight groups, approximately two-thirds of which were up-regulated, whereas most novel miRNAs were down-regulated. The qRT–PCR and degradome sequencing data were used to identify five miRNA- target pairs. Overall, our study provides valuable insights into the molecular regulation of oil biosynthesis in pecan seeds.

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.