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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.

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.

Ion transporters are essential for plant growth and development, and play key roles not only in acquisition/ transportation of essential ions from the surrounding and within the plant but also in boosting and regulating the important cellular and physiological processes like signaling, protection from attacks, keeping osmotic homeostasis and conferring stress adaptations. Being sessile in nature, plants frequently face climatic changes and challenging environmental conditions, which significantly hamper their growth, development and crop yields. These transporters have been studied for their role in metabolic-molecular pathways that are used by plants to confer tolerance for such abiotic stresses. This review highlights the current understanding and developments and futuristic perspectives on major plant ion transporters and families, their importance in plants, especially in sensing and adaptive mechanisms against abiotic stresses. Current approaches used to identify and characterize ion transporters including computational tools in constructing signaling networks, for improving our understanding of the behavior of transporters under abiotic stress, have been presented. A perspective discussion has been presented on potential exploration of plant ion-transporters for engineering abiotic stress tolerance in crops via important approaches like transcriptional activators-like effectors, microRNAs, marker assisted breeding and CRISPR-Cas9 based genome editing for ensuring sustainable crop production. The current review holds significance and novelty and provides the reader a comprehensive and updated account on major ion transporters in plants, their roles and tools currently in use for their characterization and their exploration for engineering crops for improved abiotic stress tolerance.

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.

Nitrogen (N) is a major limiting factor for plant growth and crop production. The use of N fertilizer in forestry production is increasing each year, but the loss is substantial. Mastering the regulatory mechanisms of N uptake and transport is a key way to improve plant nitrogen use efficiency (NUE). However, this has rarely been studied in pecans. In this study, 10 AMT and 69 NRT gene family members were identified and systematically analyzed from the whole pecan genome using a bioinformatics approach, and the expression patterns of AMT and NRT genes and the uptake characteristics of NH4+ and NO3− in 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 gene duplication was the main reason for the amplification of the AMT and NRT gene families in pecan, both of which experienced purifying selection. Based on qRT-PCR results, CiAMTs were primarily expressed in roots, and CiNRTs were majorly expressed in leaves, which were consistent with the distribution of pecan NH4+ and NO3− concentrations in the organs. The expression levels of CiAMTs and CiNRTs were mainly significantly upregulated under N deficiency and T4 treatment. Meanwhile, T4 treatment significantly increased the NH4+, NO3−, and NO2− concentrations as well as the Vmax and Km values of NH4+ and NO3− in pecans, and Vmax/Km indicated that pecan seedlings preferred to absorb NH4+. In summary, considering the single N source of T5, we suggested that the NH4+/NO3− ratio of 75:25 was more beneficial to improve the NUE of pecan, thus increasing pecan yield, which provides a theoretical basis for promoting the scale development of pecan and provides a basis for further identification of the functions of AMT and NRT genes in the N uptake and transport process of pecan.

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.

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.