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Almond (Prunus dulcis Miller) is a major commodity with the highest nut production in the world. A core collection is of the utmost importance for fruit tree breeding programs from a managerial and economic perspective. In current study, an almond germplasm panel consisting of 228 genotypes was subjected to a comprehensive analysis for two years, which included 20 morphological and pomological traits. A curated ensemble of 28 almond genotypes or cultivars was precisely selected by applying stringent parameters through the use of the Power Core software, ultimately leading to the establishment of the novel almond core collection. It is noteworthy that this collection effectively contained 9.2% of quantitative traits and 3.5% of qualitative traits. In addition, variance difference (VD%) and mean difference (MD%) computations of quantitative and qualitative traits yielded values of 97.43% and 10.18%, respectively, thus indicating a profound degree of genetic variation in core collection. Moreover, the Shannon diversity index (H) pertinent to categorical traits demonstrated a substantial augmentation across all seven phenotypic factors. Cluster analysis indicated the core collection accessons were equally distributed among two distinct population groups. Furthermore, oil content measurement showed Ooil content ranged from 44.61% in genotype 151 to 62.72% in genotype C1, while fatty acid ranged from 60.20% in genotype K49 to 80.57% in Avizj, thereby indicating a metabolic variation in core collection germplasm. These results may provide valuable references and be conductive to the germplasm collection strategy, which may facilitate the improvement of almond in future breeding programs. [ABSTRACT FROM AUTHOR]

Preserving genetic diversity is pivotal for enhancing genetic improvement and facilitating adaptive responses to selection. This study focuses on identifying key genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs), while exploring the genomic evolutionary connectedness among seven Iranian horses representing five indigenous breeds: Caspian, Turkemen, DareShuri, Kurdish, and Asil. Using whole-genome resequencing, we generated 2.7 Gb of sequence data, with raw reads ranging from 1.2 Gb for Caspian horses to 0.38 Gb for Turkoman horses. Post-filtering, approximately 1.9 Gb of reads remained, with ~ 1.5 Gb successfully mapped to the horse reference genome (EquCab3.0), achieving mapping rates between 76.4% (Caspian) and 98.35% (Turkoman). We identified 2,909,816 SNPs in Caspian horses, constituting around 0.1% of the genome. Notably, 71% of these SNPs were situated in intergenic regions, while 8.5 and 6.8% were located upstream and downstream, respectively. A comparative analysis of SNPs between Iranian and non-Iranian horse breeds showed that Caspian horses had the lowest number of shared SNPs with Turkoman horses. Instead, they showed a closer genetic relationship with DareShuri, Quarter, Arabian, Standardbred, and Asil breeds. Hierarchical clustering highlighted Caspian horses as a distinct cluster, underscoring their distinctive genomic signature. Caspian horses exhibit a unique genetic profile marked by an enrichment of private mutations in neurological genes, influencing sensory perception and awareness. This distinct genetic makeup shapes mating preferences and signifies a separate evolutionary trajectory. Additionally, significant non-synonymous single nucleotide polymorphisms (nsSNPs) in reproductive genes offer intervention opportunities for managing Caspian horses. These findings reveal the population genetic structure of Iranian horse breeds, contributing to the advancement of knowledge in areas such as conservation, performance traits, climate adaptation, reproduction, and resistance to diseases in equine science. [ABSTRACT FROM AUTHOR]

The application of nanomaterials is a promising tool to achieve more efficient in vitro propagation. This study evaluated the effectiveness of rice husk derived biogenic silica nanoparticles (SiO2 NPs) and zinc oxide nanoparticles (ZnO NPs) on the growth and proliferation of in vitro cultures of quince rootstock 'QA'. In vitro cultures were exposed to six levels of SiO2 NPs (0, 1, 5, 25, 50, 100 mg L− 1) and seven levels of ZnO NPs (0, 0.5, 1, 2.5, 5, 25, 50 mg L− 1). Proliferation and growth rate were determined in plantlets recovered from ZnO NPs and SiO2 NPs-treatments and controls that were grown under in vitro conditions for 35 days. The results showed in vitro shoots of quince rootstock QA treated with SiO2 NPs at a concentration of 1 mgL− 1 had the highest number of axillary shoots (2.46). Also quince rootstock QA plantlets regenerated from ZnO NPs-treatments showed the highest shoot length and the number of leaves at a concentration of 2.5 mg L− 1 (6.86 and 14.26, respectively). This research demonstrated the use of 1 mg L− 1 of SiO2 NPs and 2.5 mg L− 1 of ZnO NPs in the tissue culture medium may improve proliferation and growth rate in quince rootstock 'QA' explants. [ABSTRACT FROM AUTHOR]

Root system architecture (RSA) is critical for improving nutrient and water uptake and maintaining crop yield under both optimal and drought conditions. The meristematic zone of root tips is ideal for studying RSA, because of its high mitotic rate. miRNAs are important post-transcriptional regulators and play a crucial role in plant response to drought stress. To decipher the changes in miRNA expression patterns under drought stress, sequencing of small RNAs in the meristematic root tips of the highly tolerant genotypes Azucena and the susceptible IR64 was performed. Prediction of target genes of differentially expressed miRNAs (DEMs) in drought-stressed Azucena compared with normal conditions revealed that these genes mainly encode aquaporin, AP2, DELLA protein, ERF, and OsIAA18-auxin responsive. Most of these genes are involved in the regulation of response to stress, meristem growth, ethylene-activated signaling pathway, post-transcriptional regulation, and lipid metabolism. Whereas, the predicted target genes in IR64 under the same conditions were mainly involved in controlling carbohydrate biosynthesis, lignin catabolism, primary metabolic processes, cell death, and RNAi. This result shows that IR64 promotes thickening of cell walls to cope with stress, while lateral root system expansion and root length are used as a strategy to cope with drought stress in Azucena. Azucena-specific down-regulation of miR164-NAC5, miR1857-MADX-box5, miR1861-EXP1, and miR169-NF-YA may be the main reason for root elongation, root system development, and stress adaptation of this genotype. Moreover, miR528 and miR398, which serve as hub regulators, and target redox-related enzymes such as SOD and peroxidase (POX) to control cellular homeostasis in response to drought stress, were down-regulated in Azucena. Furthermore, our histochemical assay also confirmed the fact that the cell wall thickness of the root tips was increased in the drought-sensitive IR64 for insulation purposes to cope with stress. However, this may substantially reduce its ability to extend roots to obtain water from deeper soil layers. Our results shed light on drought-related miRNA regulatory networks as well as important miRNAs that have the potential to further improve drought tolerance in rice. [ABSTRACT FROM AUTHOR]

Background: Plant organelles are highly motile where their movement is significant for fast distribution of material around the cell, facilitation of the plant's ability to respond to abiotic and biotic signals, and for appropriate growth. Abiotic and biotic stresses are among the major factors limiting crop yields, and biological membranes are the first target of these stresses. Plants utilize adaptive mechanisms namely myosin to repair injured membranes following exposure to abiotic and biotic stresses. Objective: Due to the economic importance and cultivation of potato grown under abiotic and biotic stress prone areas, identification and characterization of myosin family members in potato were performed in the present research. Methods: To identify the myosin genes in potato, we performed genome-wide analysis of myosin genes in the S. tuberosum genome using the phytozome. All putative sequences were approved with the interproscan. Bioinformatics analysis was conducted using phylogenetic tree, gene structure, cis-regulatory elements, protein–protein interaction, and gene expression. Result: The majority of the cell machinery contain actin cytoskeleton and myosins, where motility of organelles are dependent on them. Homology-based analysis was applied to determine seven myosin genes in the potato genome. The members of myosin could be categorized into two groups (XI and VIII). Some of myosin proteins were sub-cellularly located in the nucleus containing 71.5% of myosin proteins and other myosin proteins were localized in the mitochondria, plasma-membrane, and cytoplasm. Determination of co-expressed network, promoter analysis, and gene structure were also performed and gene expression pattern of each gene was surveyed. Number of introns in the gene family members varied from 1 to 39. Gene expression analysis demonstrated that StMyoXI-B and StMyoVIII-2 had the highest transcripts, induced by biotic and abiotic stresses in all three tissues of stem, root, and leaves, respectively. Overall, different cis-elements including abiotic and biotic responsive, hormonal responsive, light responsive, defense responsive elements were found in the myosin promoter sequences. Among the cis-elements, the MYB, G-box, ABRE, JA, and SA contributed the most in the plant growth and development, and in response to abiotic and biotic stress conditions. Conclusion: Our results showed that myosin genes can be utilized in breeding programs and genetic engineering of plants with the aim of increasing tolerance to abiotic and biotic stresses, especially to viral stresses such as PVY, PVX, PVA, PVS, high light, drought, cold and heat. [ABSTRACT FROM AUTHOR]

Trigonella foenum-graecum is widely distributed worldwide and grown under a wide range of climatic conditions. The current research was conducted to study the effects of the environmental variables on yield related traits and metabolite contents of 50 different Persian fenugreeks at various geographical locations. Accordingly, multivariate statistical techniques including canonical correspondence analysis (CCA), hierarchical clustering on principal components, and partial least squares regression (PLSR) were applied to determine important proxy variables and establish a relevant model to predict bioactive compounds in fenugreeks. The interrelation of clustered groups emphasized the importance of functional groups of bioactive compounds and several yield related traits. The CCA indicated that two climatic variables of temperature and solar irradiation contributed prominently to 4-hydroxyisoleucine accumulation. The predicted model based on PLSR revealed climatic variables such as temperature, solar, and rain. The precursor of isoleucine was the predictive power for 4-hydroxyisoleucine accumulation while seed weight predicted trigonelline content. The current study's findings may provide helpful information for the breeding strategies of this multipurpose crop. [ABSTRACT FROM AUTHOR]

Persian walnut (Juglans regia L.) is an economically important species of edible nuts. In the present study, northwest regions of Iran were explored to find the spring frost resistant Persian walnut genotypes. Pomological traits related to the fruits of selected genotypes and physiochemical properties were measured and analyzed. Moreover, an optimized model using supervised machine learning models to predict the tolerant and sensitive genotypes based on pomological and physiochemical traits was developed. In the current study, we identified 24 superior genotypes with ideal values. Nut weight in our identified genotypes varied from 5.26 to 20.6 g, kernel weight ranged from 0.35 to 8.42 g, and kernel percentage varied from 6.65 to 73.83%. Significant positive correlation was observed between nut dimensions and kernel percentage. Results showed that the tolerant genotypes had significant lower injury index than sensitive genotypes. In comparison to the sensitive genotypes, higher levels of proline, protein and lower level of H2O2 content were measured in cold-tolerant genotypes. Moreover, water content had significant correlation with proline, malonyldialdehyde, H2O2, and relative electrolyte leakage. The best performances of the model based on pomological and physiochemical traits gained when the tree was induced by the decision tree with Information Gain ratio and decision tree with Information Gain criteria, respectiveley. In conclusion, identified genotypes can be cultivated in frost occurrence regions or can be used for germplasm conservation programs. Moreover, the optimized machine learning-based model presented here opens a new avenue for future studies in this field. [ABSTRACT FROM AUTHOR]

Background: The Plant U-box (PUB), ubiquitin ligase gene, has a highly conserved domain in potato. However, little information is available about U-box genes in potato (Solanum tuberosum). In this study, 62 U-box genes were detected in the potato genome using bioinformatics methods. Further, motif analysis, gene structure, gene expression, TFBS, and synteny analysis were performed on the U-box genes. Results: Based on in silico analysis, most of StU-boxs included a U-box domain; however, some of them lacked harbored domain the ARM, Pkinase_Tyr, and other domains. Based on their phylogenetic relationships, the StU-box family members were categorized into four classes. Analysis of transcription factor binding sites (TFBS) in the promoter region of StU-box genes revealed that StU-box genes had the highest and the lowest number of TFBS in MYB and CSD, respectively. Moreover, based on in silico and gene expression data, variable frequencies of TFBS in StU-box genes could indicate that these genes control different developmental stages and are involved in complex regulatory mechanisms. The number of exons in U-box genes ranged from one to sixteen. For most U-box genes, the exon–intron compositions and conserved motifs composition in most proteins in each group were similar. The intron–exon patterns and the composition of conserved motifs validated the U-box genes phylogenetic classification. Based on the results of genome distribution, StU-box genes were distributed unevenly on the 12 S. tuberosum chromosomes. The results showed that gene duplication may possess a significant role in genome expansion of S. tuberosum. Furthermore, genome evolution of S. tuberosum was surveyed using identification of orthologous and paralogous. We identified 40 orthologous gene pairs between S. tuberosum with Solanum lycopersicum, Oryza sativa, Triticum aestivum, Gossypium hirsutum, Zea maize, Coriaria mytifolia, and Arabidopsis thaliana as well as eight duplicated genes (paralogous) in S. tuberosum. StU-box 51 gene is one of the important gene among other StU-boxes in S. tuberosum under drought stress which was expressed in tuber and leaf under drought stress. Furthermore, StU-box 51 gene has the highest expression levels in four tissue-specific (stem, root, leaf, and tuber) in potato as well as it had the highest number of TFBS in promoter region. Based on our results, StU-box 51 can introduce to researcher to utilize in breeding program and genetic engineering in potato. Conclusions: The results of this survey will be useful for further investigation of the probable role and molecular mechanisms of U-box genes in response to different stresses. [ABSTRACT FROM AUTHOR]

Viral diseases affect quince plant productivity and fruit quality. This study evaluated the effectiveness of droplet-vitrification cryotherapy and thermotherapy methods in the eradication of apple chlorotic leaf spot virus (ACLSV) and apple stem grooving virus (ASGV) from virus-infected in vitro cultures of quince rootstock 'QA' and cultivar 'Neyshabour'. In vitro cultures infected with ACLSV and ASGV were thermo-treated at 38 °C for 0, 7, 10, and 15 days followed by apical shoot tip isolation. In the cryotherapy procedure, shoot tips were incubated on preculture medium and then exposed to plant vitrification solution 2 for 30 min at 0 °C prior to liquid nitrogen (LN) exposure. Shoot tips were warmed in unloading solution and placed on recovered medium. The frequency of virus eradication was determined using RT-PCR in plantlets recovered from thermo-and cryo-treatments and controls that were grown under in vitro conditions for 4 months. Droplet-vitrification cryotherapy and thermotherapy resulted in high frequencies of ACLSV and ASGV eradication from in vitro cultures of quince. The results showed that increasing the duration of thermotherapy significantly increased virus eradication. In vitro shoots of quince rootstock 'QA' and cultivar 'Neyshabour' heat-treated for 10 days were 64% and 67% free of ACLSV and 55% and 33% free of ASGV, respectively. All quince rootstock 'QA' plantlets regenerated from droplet-vitrification cryotherapy and RT-PCR assessed were free of ACLSV and 67% were free of ASGV. Cryotherapy and thermotherapy may be considered as promising methods for virus eradication programs in quince genotypes facilitating the production of healthy stock plants. [ABSTRACT FROM AUTHOR]

Soil salinity presents a serious threat to crop production. The relatively poor tolerance to this stress agent exhibited by conventional crops incentivizes the search for alternative producers of food and forage in salinity-affected environments. Halophytes belonging to the genus Salicornia L. have been suggested as being able to provide both forage and edible seed oil. Here, a set of 14 Salicornia europaea L. accessions was investigated for their ability to produce seed oil and forage in response to a range of salt concentrations (100, 300 and 600 mM NaCl) in the water used for irrigation. Seed of the accessions was collected from diverse sites close to saline rivers and the sea in Iran. Salinity was shown to have a major effect on biomass yield, and on seed oil yield and composition. The ratio of unsaturated to saturated fatty acids in the seed oil was remarkably high. Forage yield was highest when irrigated with 300 mM NaCl for most of the accessions, while a level of 600 mM NaCl suited the production of seed oil. [ABSTRACT FROM AUTHOR]

Descurainia sophia is a valuable medicinal plant in family of Brassicaceae. To determine the range of diversity amongst D. sophia in Iran, 32 naturally distributed plants belonging to six natural populations of the Iranian plateau were investigated by inter-simple sequence repeat (ISSR) markers. The average percentage of polymorphism produced by 12 ISSR primers was 86 %. The PIC values for primers ranged from 0.22 to 0.40 and Rp values ranged between 6.5 and 19.9. The relative genetic diversity of the populations was not high (Gst =0.32). However, the value of gene flow revealed by the ISSR marker was high (Nm = 1.03). UPGMA clustering method based on Jaccard similarity coefficient grouped the genotypes into two major clusters. Graph results from Neighbor-Net Network generated after a 1000 bootstrap test using Jaccard coefficient, and STRUCTURE analysis confirmed the UPGMA clustering. The first three PCAs represented 57.31 % of the total variation. The high levels of genetic diversity were observed within populations, which is useful in breeding and conservation programs. ISSR is found to be an eligible marker to study genetic diversity of D. sophia. [ABSTRACT FROM AUTHOR]

The data that support the findings of this study are deposited at https://submit.ncbi.nlm.nih.gov/subs/sra/ and received submission code of SUB5704553." now reads: "All the data analyzed or generated during this study are included in this article. Correction to: I Scientific Reports i https://doi.org/10.1038/s41598-020-72895-7, published online 25 September 2020 The original version of this Article contained an error in the link in the Data Availability section where, "All the data analyzed or generated during this study are included in this article. [Extracted from the article]

Witches' broom disease of lime, caused by ' Candidatus Phytoplasma aurantifolia', is responsible for major losses of Mexican lime trees in Southern Iran, Oman and the United Arab Emirates. The causative phytoplasma is transmitted by the leafhopper, Hishimonus phycitis. We combined ecological niche modelling with environmental and genetic data for six populations of H. phycitis from Iran and one from Oman. The mitochondrial cytochrome c oxidase I (COI) gene and nine microsatellite DNA markers were used for the genetic analyses. Although the Oman population had specific haplotypes, the COI sequences were highly conserved among all populations studied. In contrast, the microsatellite data divided the populations from Iran and Oman into two separate clades. An analysis of molecular variance indicated a high level of variation within populations. The Mantel test showed no correlation between genetic and geographical distances. Gene flow values were small between the populations from Iran and north of Oman but significantly higher among the Iranian populations supporting the differentiation between Iran and Oman. In addition, we found that patterns of genetic divergence within Iranian populations were associated strongly with divergence in terms of their ecological niches. Data on six climatic variables, including elevation, were used to create ecological niche models. Our results suggest that the genetic differentiation of H. phycitis may be attributable to climatic conditions and/or geographical barriers. [ABSTRACT FROM AUTHOR]

In this study, we used 20 morphological traits (during two consecutive growing seasons) and 11 microsatellite markers to assess the morphological and molecular variability and structure of the almond ( Prunus dulcis (Mill.) D.A. Webb). Seventy one promising Iranian genotypes and three foreign reference cultivars (Ferragnes, Supernova, and Touno) were evaluated in this study. Kernel/shell ratio, kernel width/thickness ratio, softness of shell, nut weight, and kernel thickness were highly variable. Strong positive and, occasionally, negative correlations were detected among nut and kernel traits. Morphological traits were categorized by principle-components analysis (PCA) into 6 components which explained 88.1 % of the total variation. On the basis of the first two PCA axes, the 2-dimensional PCA plot grouped the samples according to their phenotypic characteristics. The results from molecular analyses (including a Bayesian clustering approach and a molecular phylogenetic network) did not correspond to morphological groupings. In this paper we report, for the first time, morphological and molecular variability and genetic structure of Iranian almond germplasm. Our results showed that model-based cluster analysis (using Structure software) was very appropriate for study of genetic relationships among almond accessions and can be used for study of the genetic structure of Prunus germplasm as well. [ABSTRACT FROM AUTHOR]

Alternate bearing (AB) refers to the tendency of trees to have an irregular crop load from 1 year (ON) to the next year (OFF). Despite its economic importance, it is not fully understood how gene networks and their related metabolic pathways may influence the irregular bearing in olive trees. To unravel molecular mechanisms of this phenomenon in olive (cv. Conservalia), the whole transcriptome of leaves and buds from ON and OFF-trees was sequenced using Illumina next generation sequencing approach. The results indicated that expressed transcripts were involved in metabolism of carbohydrates, polyamins, phytohormones and polyphenol oxidase (POD) related to antioxidant system. Expression of POD was increased in leaf samples of ON- versus OFF-trees. The expression pattern of the greater number of genes was changed more in buds than in leaves. Up-regulation of gene homologues to the majority of enzymes that were involved in photorespiration metabolism pathway in buds of ON-trees was remarkable that may support the hypotheses of an increase in photorespiratory metabolism in these samples. The results indicated changes in expression pattern of homologous to those taking part of abscisic acid and cytokinin synthesis which are connected to photorespiration. Our data did not confirm expression of homologue (s) to those of chlorogenic acid metabolism, which has been addressed earlier that have a probable role in biennial bearing in olive. Current findings provide new candidate genes for further functional analysis, gene cloning and exploring of molecular basses of AB in olive. [ABSTRACT FROM AUTHOR]