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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]

Salmo caspius Kessler, 1877 is one of the most commercially important species of Salmonidae in the southern basin of the Caspian Sea. The occurrence of its wild populations has undergone sever reduction during the last years. In spite of the yearly restocking activity, still no progress on the recovery of its wild population has been observed. Hence, the present study was done in order to assess the efficiency of the current restocking activity in the southern Caspian basin in term of genetic diversity. DNA extracts of 32 S. caspius from four different groups were screened using 62621 genome-wide single nucleotide polymorphisms (SNP). The overal genetic diversity and Fst values were 0.18 and 0.08, respectively. Considering the observed admixture pattern and the positive values for inbreeding coeficient it seems that S. caspius suffers from its small effective population size. In order to obtain the maximum performance, alonside with expanding the size of brood stocks, rehabilitation of the habitats and spawning rivers of this nationally endangered species is of great importance. [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]

Potato is considered a key component of the global food system and plays a vital role in strengthening world food security. A major constraint to potato production worldwide is the Potato Virus Y (PVY), belonging to the genus Potyvirus in the family of Potyviridae. Selective breeding of potato with resistance to PVY pathogens remains the best method to limit the impact of viral infections. Understanding the genetic diversity and population structure of potato germplasm is important for breeders to improve new cultivars for the sustainable use of genetic materials in potato breeding to PVY pathogens. While, genetic diversity improvement in modern potato breeding is facing increasingly narrow genetic basis and the decline of the genetic diversity. In this research, we performed genotyping-by-sequencing (GBS)-based diversity analysis on 10 commercial potato cultivars and weighted gene co-expression network analysis (WGCNA) to identify candidate genes related to PVY-resistance. WGCNA is a system biology technique that uses the WGCNA R software package to describe the correlation patterns between genes in multiple samples. In terms of consumption, these cultivars are a high rate among Iranian people. Using population structure analysis, the 10 cultivars were clustered into three groups based on the 118343 single nucleotide polymorphisms (SNPs) generated by GBS. Read depth ranged between 5 and 18. The average data size and Q30 of the reads were 145.98 Mb and 93.63%, respectively. Based on the WGCNA and gene expression analysis, the StDUF538, StGTF3C5, and StTMEM161A genes were associated with PVY resistance in the potato genome. Further, these three hub genes were significantly involved in defense mechanism where the StTMEM161A was involved in the regulation of alkalization apoplast, the StDUF538 was activated in the chloroplast degradation program, and the StGTF3C5 regulated the proteins increase related to defense in the PVY infected cells. In addition, in the genetic improvement programs, these hub genes can be used as genetic markers for screening commercial cultivars for PVY resistance. Our survey demonstrated that the combination of GBS-based genetic diversity germplasm analysis and WGCNA can assist breeders to select cultivars resistant to PVY as well as help design proper crossing schemes in potato breeding. [ABSTRACT FROM AUTHOR]

Iran is one of the origins of some Salicornia species. Nevertheless, comprehensive research has not been conducted on genetic potential, distribution, selection of populations, and the economic utilization of Salicornia in Iran. In the current study, Salicornia was collected based on the previous data available for 26 different geographical locations of provinces in Iran. We examined Salicornia plants' universality DNA barcodes, including rbcL, matK, trnH-psbA, and ITS, and their species identification abilities and identified six species groups. Subsequently, accurate modeling of distributed areas was provided with MAXENT and highlighted the valuable information on the diversity of specific geographical regions, conservation status of existing species, prioritization of conservation areas, and selection of Agro-Ecological areas. Together, this type of integrative study will provide useful information for managing and utilizing Salicornia genetic resources in Iran. [ABSTRACT FROM AUTHOR]

In our ongoing project, which focuses on the introgression of Booroola/FecB gene and the myostatin (MSTN) gene into purebred Moghani sheep, we assessed the performance of second-generation Moghani crossbreds such as second crossbreds (F2) and initial backcross generation (BC1). These crossbreds were generated through different mating systems, including in-breeding, outcrossing, first paternal backcrossing (PBC1), and first maternal backcrossing (MBC1). Notably, F2 strains exhibited lean tail, woolly fleece and a higher percentage of white coat color compared to BC1. The impact of mating systems and birth types on pre-weaning survival rates was found to be statistically significant (P < 0.0001), with singleton offspring resulting from paternal backcross showing a particularly substantial effect. The F2 crossbred lambs carrying the Booroola gene did not show a statistically significant difference in survivability compared to those carrying the MSTN gene, implying the Booroola prolificacy gene had no significant impact on survival outcomes. However, the occurrence of multiple births had a significant negative impact on lamb survival (P < 0.0001). The PBC1 sheep strains, specifically Texel Tamlet ram strains carrying the MSTN mutation, exhibited superior growth rates compared to others (P < 0.05). Interestingly, the MSTN mutation in the homozygous variant genotype significantly impacts growth rate before weaning compared to other genotypes and pure Moghani sheep (P < 0.05). In conclusion, this study objectively underscores the pivotal role of genetic factors, specifically through strategic mating systems like paternal backcrossing, in enhancing desired traits and growth rates in Moghani sheep, thereby contributing valuable insights to the field of sheep breeding programs. [ABSTRACT FROM AUTHOR]

Highlights • Variation analysis of Prunus scoparia by molecular marker. Abstract Evaluation of spatial and non-spatial distribution is of great importance for protection of plant's genetic resources. Prunus scoparia , a wild almond species, is an important economically and ecologically food resource plant in Iran with specific characteristics such as self-compatibility, resistant to drought and fungus, bitterness as well as small nuts. This wild species can provide an enlarged gene pool and may be considered as a valuable germplasm source for breeding the cultivated almond. In this study, the conservation planning and genetic variation of 158 Prunus scoparia accessions was investigated with the aid of 36 SSR markers to reveal genetic distinctness and structure. The molecular markers studied showed quite high level of genetic diversity on the basis of N a = 6.47, H o = 0.603 and H e = 0.737. The result of Neighbor net analysis was not in parallel with STRUCTURE data as classified samples into two and 12 main groups, respectively. On the other hand, the results of GENELAND analysis ensured the population classification and the genetic relatedness between populations from STRUCTURE analysis due to use of geographical data. All samples were grouped based on their geographical location. Moreover, utilization of GIS data accompanied by appropriate number of SSR markers could provide the possibility of prioritizing of distribution regions in natural and unnatural environments. The species distribution modeling would also help gain comprehensive information on conservation strategies of this wild almond species. [ABSTRACT FROM AUTHOR]

Pomegranate has been considered a medicinal plant due to its rich nutrients and bioactive compounds. Since environmental conditions affect the amount and composition of metabolites, selecting suitable locations for cultivation would be vital to achieve optimal production. In this study, data on the diversity of targeted metabolites and morphological traits of 152 Iranian pomegranate genotypes were collected and combined in order to establish the first core collection. The multivariate analyses were conducted including principal component analysis (PCA), and cluster analysis. In addition, the current and future geographical distribution of pomegranate in Iran was predicted to identify suitable locations using the MaxEnt model. The results showed high diversity in the studied morphological and metabolic traits. The PCA results indicated that FFS, NFT, JA, and AA are the most important traits in discriminating the studied genotypes. A constructed core collection using maximization strategy consisted of 20 genotypes and accounted for 13.16% of the entire collection. Shannon-Weaver diversity index of a core collection was similar or greater than the entire collection. Evaluation of the core collection using four parameters of MD, VD, CR, and VR also indicated the maintenance of the genetic diversity of the original set. According to the MaxEnt model, altitude, average temperature of coldest quarter, and isothertmality were the key factors for the distribution of pomegranate. The most suitable areas for pomegranate cultivation were also determined which were located in arid and semi-arid regions of Iran. The geographic distribution of pomegranate in the future showed that the main provinces of pomegranate cultivation would be less affected by climatic conditions by the middle of the century. The results of this study provide valuable information for selection of elite genotypes to develop the breeding programs to obtain the cultivars with the highest levels of metabolic compounds for pharmaceutical purposes, as well as identification of the most suitable agro-ecological zones for orchard establishment. [ABSTRACT FROM AUTHOR]

Highlights: [•] SSR and AFLP markers are powerful techniques for genotyping Prunus rootstock. [•] Iranian Prunus rootstock is of great genetic variability. [•] Neighbor-Net and Bayesian methods can be used for more precise clustering analysis. [Copyright &y& Elsevier]

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]

Abstract: A set of twelve simple sequence repeat markers was used to evaluate the genetic background of 738 pomegranate (Punica granatum L.) accessions, which belonged to the Iranian National Pomegranate Collection, from 23 provinces of Iran. Genetic diversity among the accessions was analysed using several variability parameters. Forty-three alleles were detected with a mean of 3.59 alleles per locus. The highest levels of polymorphism were found for the locus ABRII-MP26. The mean values of expected heterozygosity and polymorphic information content were 0.521 and 0.458, respectively. Neighbour-Net analysis based on uncorrected P distances and a model-based method separated the accessions into 8 main groups and several subgroups, with a tendency to cluster by geographical origin. From the simple sequence repeat analysis, it can be concluded that the genetic base of the Iranian National Pomegranate Collection is broad enough to ensure future progress in breeding programmes and these markers are effective tools for conducting genetic diversity studies in pomegranate and developing strategies for germplasm management. [Copyright &y& Elsevier]

* Premise of the study: Twelve novel polymorphic microsatellite loci were developed and characterized from a repeat-enriched genomic library of Crocus sativus to study population and conservation genetics of this economically and medically important species. * Methods and Results: The microsatellite loci were isolated using a modified Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) method. The average number of alleles per locus was 2.6. The observed and expected heterozygosities varied from 0.07 to 0.92 and 0.1 to 0.58, respectively. Polymorphic information content value ranged from 0.09 to 0.55 with an average of 0.34. Four out of twelve loci showed significant departures from Hardy--Weinberg equilibrium. * Conclusions: The microsatellite markers reported here will be useful for evaluating genetic diversity and will likely serve as an ideal resource for use in marker-assisted breeding programs, germplasm analysis, and varietal identification. [ABSTRACT FROM AUTHOR]

Sheep is a major contributor to global food production among livestock and one of the great sources of red meat for human consumption. Several QTL and numerous genes with major and minor effects have been identified in association with the muscle characteristics in sheep breeds worldwide. Understanding the genetic background of growth and carcass‐related traits in sheep is a major factor in increasing muscle growth, muscle hypertrophy and, eventually, meat production. This review concisely shows how major signaling pathways control skeletal muscle growth. Herein we aimed to discuss and summarize different research findings on genomic regions related to carcass traits and meat production in sheep. Several causative mutations with major effects on different muscle‐related traits have been reported in various sheep breeds. A general overview of the studies on main candidate genes showed that some alleles have major phenotypic effects in different breeds with commercial and farm level usability. However, numerous genes with minor effects were also reported regarding the polygenic nature of muscle‐related traits. The knowledge of the candidate genes involved in growth traits and their effects provides valuable information for breeding and selection of muscularity traits. [ABSTRACT FROM AUTHOR]

Background: The cuticular wax serves as a primary barrier that protects plants from environmental stresses. The Eceriferum (CER) gene family is associated with wax production and stress resistance. Results: In a genome-wide identification study, a total of 52 members of the CER family were discovered in four Gossypium species: G. arboreum, G. barbadense, G. raimondii, and G. hirsutum. There were variations in the physicochemical characteristics of the Gossypium CER (GCER) proteins. Evolutionary analysis classified the identified GCERs into five groups, with purifying selection emerging as the primary evolutionary force. Gene structure analysis revealed that the number of conserved motifs ranged from 1 to 15, and the number of exons varied from 3 to 13. Closely related GCERs exhibited similar conserved motifs and gene structures. Analyses of chromosomal positions, selection pressure, and collinearity revealed numerous fragment duplications in the GCER genes. Additionally, nine putative ghr-miRNAs targeting seven G. hirsutum CER (GhCER) genes were identified. Among them, three miRNAs, including ghr-miR394, ghr-miR414d, and ghr-miR414f, targeted GhCER09A, representing the most targeted gene. The prediction of transcription factors (TFs) and the visualization of the regulatory TF network revealed interactions with GhCER genes involving ERF, MYB, Dof, bHLH, and bZIP. Analysis of cis-regulatory elements suggests potential associations between the CER gene family of cotton and responses to abiotic stress, light, and other biological processes. Enrichment analysis demonstrated a robust correlation between GhCER genes and pathways associated with cutin biosynthesis, fatty acid biosynthesis, wax production, and stress response. Localization analysis showed that most GCER proteins are localized in the plasma membrane. Transcriptome and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) expression assessments demonstrated that several GhCER genes, including GhCER15D, GhCER04A, GhCER06A, and GhCER12D, exhibited elevated expression levels in response to water deficiency stress compared to control conditions. The functional identification through virus-induced gene silencing (VIGS) highlighted the pivotal role of the GhCER04A gene in enhancing drought resistance by promoting increased tissue water retention. Conclusions: This investigation not only provides valuable evidence but also offers novel insights that contribute to a deeper understanding of the roles of GhCER genes in cotton, their role in adaptation to drought and other abiotic stress and their potential applications for cotton improvement. [ABSTRACT FROM AUTHOR]

Background: The mechanisms underlying rice root responses to drought during the early developmental stages are yet unknown. Results: This study aimed to determine metabolic differences in IR64, a shallow-rooting, drought-susceptible genotype, and Azucena, a drought-tolerant and deep-rooting genotype under drought stress. The morphological evaluation revealed that Azucena might evade water stress by increasing the lateral root system growth, the root surface area, and length to access water. At the same time, IR64 may rely mainly on cell wall thickening to tolerate stress. Furthermore, significant differences were observed in 49 metabolites in IR64 and 80 metabolites in Azucena, for which most metabolites were implicated in secondary metabolism, amino acid metabolism, nucleotide acid metabolism and sugar and sugar alcohol metabolism. Among these metabolites, a significant positive correlation was found between allantoin, galactaric acid, gluconic acid, glucose, and drought tolerance. These metabolites may serve as markers of drought tolerance in genotype screening programs. Based on corresponding biological pathways analysis of the differentially abundant metabolites (DAMs), biosynthesis of alkaloid-derivatives of the shikimate pathway, fatty acid biosynthesis, purine metabolism, TCA cycle and amino acid biosynthesis were the most statistically enriched biological pathway in Azucena in drought response. However, in IR64, the differentially abundant metabolites of starch and sucrose metabolism were the most statistically enriched biological pathways. Conclusion: Metabolic marker candidates for drought tolerance were identified in both genotypes. Thus, these markers that were experimentally determined in distinct metabolic pathways can be used for the development or selection of drought-tolerant rice genotypes. [ABSTRACT FROM AUTHOR]

The hydrangea (Hydrangea macrophylla (Thunb). Ser.), an ornamental plant, has good marketing potential and is known for its capacity to change the colour of its inflorescence depending on the pH of the cultivation media. The molecular mechanisms causing these changes are still uncertain. In the present study, transcriptome and targeted metabolic profiling were used to identify molecular changes in the RNAome of hydrangea plants cultured at two different pH levels. De novo assembly yielded 186,477 unigenes. Transcriptomic datasets provided a comprehensive and systemic overview of the dynamic networks of the gene expression underlying flower colour formation in hydrangeas. Weighted analyses of gene co-expression network identified candidate genes and hub genes from the modules linked closely to the hyper accumulation of Al3+ during different stages of flower development. F3′5′H, ANS, FLS, CHS, UA3GT, CHI, DFR, and F3H were enhanced significantly in the modules. In addition, MYB, bHLH, PAL6, PAL9, and WD40 were identified as hub genes. Thus, a hypothesis elucidating the colour change in the flowers of Al3+-treated plants was established. This study identified many potential key regulators of flower pigmentation, providing novel insights into the molecular networks in hydrangea flowers. [ABSTRACT FROM AUTHOR]

Objective: Seed germination is an important process that determines the beginning of the seed plant life cycle. However, the mechanism underlying seed germination in barley remains unclear. To understand the molecular mechanism of seed germination in barley, WGCNA analysis was used to detect the hub and responsive genes and to reveal the expression of the genes on seed germination. WGCNA is a valuable tool for studying the correlation between genes, identifying modules with high correlation, and identifying Hub genes in different modules. Materials and methods: Raw microarray data related to the germination stage were obtained from the GEO microarray database for 0h, 3h, 9h, 18h, 33h, and 71h after the germination stage. Then, weighted gene coexpression network analysis (WGCNA) was utilized for the detection of co-expressed network genes. In the present study, a barley cultivar, Mahtab, was utilized to show expression patterns after 9h, 18h, and 71h after the germination stage. A total number of 4137 differentially expressed genes (DEG) were identified, with some genes showing higher expression in Mahtab and three genes verified by qRT-PCR. Results: Most of these DEGs were involved in metabolic processes, cellular processes, glycolysis, and response to a stimulus. Hub gene in MEbrown was alpha/beta-Hydrolases superfamily protein, MEpurple was U-box domain-containing protein 4, and MEdarkgrey was B3 domain-containing transcription factor ABI3 which were positively correlated with germinated seeds. The results showed a microarray database and candidate genes for further study of barley at germination stages. In addition, DEGs were divided into three modules by WGCNA. In this study, gene modules associated with seed germination during barley seed germination were identified. Transcription factor and alpha/beta-hydrolase played an important role at the germination stage. Also, gene modules and hub genes at 9h, 18h, and 71h after germination were detected. As there is a lack of information on the seed germination requirements of barley, this research was conducted to study seed germination mechanisms as well as evaluation of hub genes to study molecular mechanism of seed germination in barley. Conclusions: The results of the present study provide new insights into the molecular mechanism underlying barley seed germination. Based on the network analysis, transcription factors (TFs) and ubiquitin proteins were involved in germination. Most of the genes related to each module were related to proteins involved in carbohydrate metabolism, glycolysis, and protein degradation. Our gene expression results can serve as molecular markers in barley cultivars during seed germination. These findings can be suitable for molecular-assisted selection and breeding of fast-germinating barley genotypes. [ABSTRACT FROM AUTHOR]

Morphology and feature selection are key approaches to address several issues in fisheries science and stock management, such as the hypothesis of admixture of Caspian common carp (Cyprinus carpio) and farmed carp stocks in Iran. The present study was performed to investigate the population classification of common carp in the southern Caspian basin using data mining algorithms to find the most important characteristic(s) differing between Iranian and farmed common carp. A total of 74 individuals were collected from three locations within the southern Caspian basin and from one farm between November 2015 and April 2016. A dataset of 26 traditional morphometric (TMM) attributes and a dataset of 14 geometric landmark points were constructed and then subjected to various machine learning methods. In general, the machine learning methods had a higher prediction rate with TMM datasets. The highest decision tree accuracy of 77% was obtained by rule and decision tree parallel algorithms, and "head height on eye area" was selected as the best marker to distinguish between wild and farmed common carp. Various machine learning algorithms were evaluated, and we found that the linear discriminant was the best method, with 81.1% accuracy. The results obtained from this novel approach indicate that Darwin's domestication syndrome is observed in common carp. Moreover, they pave the way for automated detection of farmed fish, which will be most beneficial to detect escapees and improve restocking programs. [ABSTRACT FROM AUTHOR]

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]

Abstract: In this study, in order to know the variability for a rootstock breeding program genetic diversity and relationships among 55 Iranian almond genotypes and seven related Prunus species were investigated. Morphological and molecular analyses were used. Principal component analysis showed that three components explained 67.6% of the total morphological variation for the first year and 68.06% for the second year of the study. Leaf traits were predominant in the first component and contributed most of the total variation. Leaf length and width, as well as, leaf area were highly correlated with each other and correlated to vigor. Also a negative correlation was found between leaf length/width ratio and vigor. Ward''s method was used to construct cluster from morphological data which allocated individuals into their respective species. Out of 100 pre-screened RAPD primers, 16 with reproducible bands and maximum polymorphism were selected. Two-hundred and sixty bands were scored of which 250 of them were polymorphic. Average value of polymorphism per primer was 95.81% and maximum value for polymorphism (100%) was obtained from TIBMBA-14, TIBMBA-17, TIBMBB-05, TIBMBB-08, TIBMBD-09, and TIBMBD-10. On the other hand, the minimum value was obtained from TIBMBB-16 (86%). Primer TIBMBB-5 gave the maximum number of bands (25 fragments) and the minimum obtained from TIBMBE-18 (11 fragments). Genetic similarity based on Jaccard''s coefficient ranged from 0.28 to 0.79 with an average of 0.53. Molecular analysis revealed a high degree of separation among samples regarding their geographical origin. Correlation between two approaches was low (R =−0.38). High molecular and morphological variability indicated that this collection includes rich and valuable plant materials for almond rootstock breeding. [Copyright &y& Elsevier]

Iran is a center of origin and diversity for walnuts (Juglans regia L.) with very good potential for breeding purposes. The rich germplasm available, creates an opportunity for study and selection of the diverse walnut genotypes. In this study, the population structure of 104 Persian walnut accessions was assessed using AFLP markers in combination with phenotypic variability of 17 and 18 qualitative and quantitative traits respetively. The primers E-TG/M-CAG, with high values of number of polymorphic bands, polymorphic information content, marker index and Shannon's diversity index, were the most effective in detecting genetic variation within the walnut germplasm. Multivariate analysis of variance indicated 93.98% of the genetic variability was between individuals, while 6.32% of variation was among populations. A relatively new technique, an advanced maximization strategy with a heuristic approach, was deployed to develop the core collection. Initially, three independent core collections (CC1–CC3) were created using phenotypic data and molecular markers. The three core collections (CC1–CC3) were then merged to generate a composite core collection (CC4). The mean difference percentage, variance difference percentage, variable rate of coefficient of variance percentage, coincidence rate of range percentage, Shannon's diversity index, and Nei's gene diversity were employed for comparative analysis. The CC4 with 46 accessions represented the complete range of phenotypic and genetic variability. This study is the first report describing development of a core collection in walnut using molecular marker data in combination with phenotypic values. The construction of core collection could facilitate the work for identification of genetic determinants of trait variability and aid effective utilization of diversity caused by outcrossing, in walnut breeding programs. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are small endogenous non-coding RNAs in eukaryotes which regulate the expression of numerous genes post-transcriptionally, thereby playing critical roles in cells and organismal development. The high-throughput sequencing technologies enable the effective detection and annotation of miRNAs. Several miRNA variants with heterogeneous ends, lengths, and sequences can be generated from a single miRNA locus. Discovery of these miRNA variants, also known as miRNA isoforms or isomiRs, has made our understanding of the cells' miRNome deeper than previously pictured. Despite their wide presence in multiple datasets, the different possible origins and true biological significance of isomiRs are yet to be uncovered. Several recent emerging studies suggest that isomiRs are biologically active and non-randomly formed. This review aims to provide a comprehensive insight into the origins and biological importance of isomiRs, highlighting the enormous complexity of miRNA regulatory networks which broadens our knowledge about the post-transcriptional gene regulation in plants. • miRNAs are known to regulate a wide range of key biological processes in plants • Several miRNA variants can be generated from a single miRNA locus • The origins and true biological significance of isomiRs are yet to be uncovered • studies suggest that isomiRs are biologically active and non-randomly formed • It broadens our knowledge about the post-transcriptional gene regulation in plants [ABSTRACT FROM AUTHOR]

• Plant response to stress requires a programmed change in gene/protein expression. • miRNAs play a central role in fine-tuning of gene expression. • The correlation between stress-induced proteome and miRNome are discussed. Environmental stresses, notably drought, soil salinity, extreme temperatures, nutrient deficiency and UV radiation, act both singly and in combination to reduce crop productivity. Plant survival depends on an ability to either tolerate or to avoid stress, so a variety of means have evolved to adjust the growth and development of plants in response to perturbations in their external environment. Plant response to environmental fluctuations requires a programmed change in gene/protein expression which necessitates a tight regulation. The required fine-tuning of gene expression is achieved at multiple levels, of which post-transcriptional regulation represents as one of the main regulatory routes in which microRNAs (miRNAs) play a central role. These short RNA sequences act to suppress their target genes either by inhibiting their translation or by degrading their transcript. The genes encoding miRNAs can themselves be responsive to external stresses. The extent to which stress-induced changes in the plant proteome are influenced by miRNA activity is uncertain, but the implementation of high throughput analytical technologies is beginning to reveal that miRNAs do contribute to the proteomic response to stress. The present review focuses on the impact on the crop plant proteome of stress-induced alterations to miRNome. A particular emphasis is placed on the need to experimentally validate predictions based on bioinformatic data. [ABSTRACT FROM AUTHOR]

• Population genetics of Capreolus capreolus (roe deer) in Iran was investigated. • Environmental factors impeding the gene flow for roe deer were determined. • Geographical distance does not have a significant relationship with genetic distance of roe deer. • Roe deer dispersal is strongly linked to forest cover. Habitat destruction and fragmentation are major factors in the destruction of genetic diversity and affect the movement behavior of the Roe deer population in the remaining habitats. Here, we study the population and landscape genetics of Capreolus capreolus (roe deer) in northern and northwestern Iran using twelve polymorphism microsatellite markers. From 111 total specimens, 63 had successful extraction (6 feces, 35 tissues, 9 bones, and 13 antlers). We considered 30 microsatellite polymorphic loci, of which only 12 were amplified for our further analysis. For genetic diversity analysis, the Weir-Cockerham method was applied to measure the inbreeding coefficient (FIS) and fixation index (FST) for each locus as well as for each population. For landscape genetics, the susceptibility patterns of genetic variations were assessed using three hypotheses including isolation by distance (IBD), isolation by environment (IBE), isolation by resistance (IBR), and individual landscape genetic analysis. A habitat suitability map as an indicator of landscape resistance was constructed from several species distribution models (SDMs) algorithms including Generalized Boosting Models (GBM), Maximum Entropy (Maxent), Random Forest (RF), Generalized Linear Model (GLM), Multivariate Adaptive Regression Splines (MARS) and artificial neural networks (ANN) and an ensemble model. Our estimated FIs index showed that the Golestan, Arasbaran, and Guilan populations had the highest and lowest genetic diversity among roe deer populations. According to the Fst criterion, our results showed that Golestan and East Azarbaijan (Arasbaran) had the highest and Mazandaran had the lowest genetic distance patterns. Our results do not suggest that there is high genetic differentiation for roe deer in the region, with high levels of gene flow between study areas. We found that geographic distance has no significant relationship with genetic distance and that there is no significant relationship between the ecological niche non-similarity matrix and the genetic distance matrix. The most influential factors affecting gene flow in roe deer were aspect and elevation variables. The analysis suggests that the landscape has no significant influence on the structuring of the studied population and shows little genetic differentiation. [ABSTRACT FROM AUTHOR]

The mature body size of sheep is a polygenic trait that is used as a main selection criterion for increasing meat production through genetic selection. The purpose of this study was to characterize polymorphisms of the follistatin gene (FST locus), which is known to regulate muscle hypertrophy by inhibiting both myostatin and activin. Using single-strand conformation polymorphism analysis (SSCP) and Sanger sequencing, we examined polymorphisms of the ovine FST gene (OAR_v.3.1; Chr 16, NC_019473.1) in Iranian Mehraban sheep (n = 100, seven-month-old male lambs) with records of body measurements, fat-tails, and head morphometry. Among the nine SSCP patterns A to I, we identified five single nucleotide polymorphisms (SNPs), including g.25632659 G>C, g.25632701 G>A, g.25633069 A>G, g.25633069 A>T, and g.25634085 G>C. The only amino acid-altering variant was g.25632659 G>C in exon 3 (p.216Thr > Ser). According to a subsequent statistical analysis, SSCP patterns A (g.25632659 G/C, g.25632701 G/G), B (g.25632659 C/C, g.25632701 G/A), C (g.25632659 C/C, g.25632701 A/A), D (homozygous reference; g.25633069 A/A), E (heterozygous; g.25633069 A/G) and F (homozygous variant; g.25633069 T/T) were significantly (P < 0.05) connected with body measurements. Furthermore, patterns A and B had significantly (P ≤ 0.05) longer forehead lengths than the lambs with the pattern C. Pattern I (homozygous variant; g.25634085 C/C) was significantly associated with an increased mouth width, and decreased eye length compared to patterns H (heterozygous; g.25634085 G/C) and G (homozygous reference; g.25634085 G/G). The findings of this study provide primary evidence of linking between the polymorphisms of the FST gene and body size in a small panel of Iranian Mehraban sheep population. • Five SNPs were found in the follistatin gene of Iranian Mehraban sheep, three of which were novel. • Polymorphisms in the follistatin gene linked to body measurements and head morphometrics in Mehraban sheep (n = 100). • Two novel variants, G and T, at g.25633069A in intron 3 show significant enhancing effect on girth circumference in this study. • No significant association was found between the polymorphisms of the follistatin gene and fat-tail traits in Mehraban sheep [ABSTRACT FROM AUTHOR]

Highlights • In a Persian walnut collection with 104 accessions, evaluation of phenotypic diversity showed that among studied genotypes or cultivars there were 53 days of differences in leafing date (from March, 5 to April, 27). Regarding nut and kernel weight and kernel percentage, there were 8.7 g (from 6.60 to 15.33 g), and 5.5 g (2.67–8.21 g) of difference in kernel weight in nut weight respectively. Kernel percent showed a variation of 35 % (from 35.39 to 71.09%). Nut production efficiencies among genotypes and cultivars varied from 0.20 to 11.39 nuts per centimeter square of tree trunk cross sectional area, and from 0.27 to 93.17 nut per meter square of tree scaffold cross area. • Factor analysis showed that in 18 evaluated walnut traits, there were 6 factors explaining together around 80% of the total variance. • Evaluation of traits in walnut primary collection with 104 accessions using the Maximization strategy showed a core subset with 26% of genotypes/cultivars. In this evaluation the variance difference was 38.37%, the mean difference was 9.88%, the coincidence rate was 95.05% and the variable rate was 120.28%. • The difference between the mean of the core and the original collection was non-significant except for the start of pollen shedding and beginning of the pistillate flowers receptivity. In addition, the"Coverage" analysis accounting for the number of variables captured in the core set with respect to the primary collection, showed the complete coverage (100%) of the different phenotypic variables considered in this study. Abstract Persian walnut (Juglans regia L.) is a very important nut crop with increasingly attention in the world. It was among the fruit tree species that has been propagated sexually, up to some decades ago. So, there were no or limited cultivars and the breeding works are usually new. In order to release new cultivars, a walnut improvement program started in Iran in 1980s. There was established a walnut collection, with selection of some superior genotypes from the orchards together with some introductions. As, the comprehensive characterization of germplasm is necessary in the breeding programs, in this study a collection of 104 Persian walnut accessions has been evaluated especially in order to create a core or breeding collection with reduced number of accessions and keeping maximum variability. To carry out this work, 18 walnut important traits were evaluated during 2014 and 2015 in the walnut collection of Horticultural Science Research Institute, Karaj, Iran. A wide variation was observed for several important characteristics such as leafing date (from March, 5 to April, 27), nut weight (6.60–15.33 g), kernel weight (2.67–8.21 g), and kernel percentage (35.39–71.09%). Significant correlations were observed between traits. Factor analysis showed that the six major factors affecting traits were explaining 79.9% of the total variance. The analysis, using maximization strategy through a heuristic algorithm, determined a core collection consisted of 27 accessions with similar variability respect to primary collection (mean difference percentage = 9.88% and coincidence rate of range = 95.05%). The parameters showed that this core includes 100% coverage of the primary diversity. According to result the F-test revealed no-significant differences for all traits. In this paper, for the first time, a walnut core collection was established from a primary collection. Conservation of this core collection could be more economic and better manageable for breeding purposes. [ABSTRACT FROM AUTHOR]

Date palm hooper is one of the most important pests on date palms with many highly diverged populations varied in damaging rate and preferring host cultivar. Current and potential geographic distribution of date palm hopper, Ommatissus lybicus (de Bergevin; Hemiptera: Tropiduchidae) in Iran was modeled using the Maxent procedure. Point sampling data sets included latitude, longitude, and altitude and were augmented with data on 19 bioclimatic variables retrieved from WorldClim dataset for use as predictor variables in Maxent. Maxent results demonstrated that northwest Sistan-Baluchestan, east, south and southeast Kerman, northeast and northwest Hormozgan and small districts of Bushehr provinces are hot spot habitats for O. lybicus in Iran. Jackknife analysis revealed that precipitation of warmest quarter was the most influential explanatory variable in determining distribution of O. lybiucs in Iran. Moreover, curve response and frequency distribution analyses revealed that annual mean temperature was the most predictive factor of the distribution of O. lybicus. Discontinuity in predicted hot spot habitats of O. lybicus was consistent with the genetic structure recorded for this species. Our study represents valuable information that can inform pest management strategies aimed at preventing population expansion and niche shift. [ABSTRACT FROM AUTHOR]

Study of genetic structure of Ommatissus lybicus de Bergevin revealed significant variation among the allopatric populations of this pest. High biological and behavioral variation suggest either that this is a highly variable pest species or a complex with a mix of cryptic species. The degree of reproductive isolation was tested by crossing experiments on four allopatric Iranian populations. These experiments were performed at 27 × 2 °C, 6565% RH, and a photoperiod of 14:10 (L: D) h. In addition, to examine the possible role of Wolbachia in accelerating speciation through reproductive isolation, a PCR-based Wolbachia detection and frequency assay was used. Intercross mating studies with four divergent populations demonstrated fecundity in all of the no-choice mating trials, while in some replicates of the interpopulation crossing treatments (Abu Musa × Tezerj and Bam × Tezerj), no adult insects were produced. These populations experienced repeated exposure to heavy pesticide applications, which may accelerate genetic divergence. Wolbachia was detected in specimens from two O. lybicus populations (Bushehr and Jahrom) with 100% infection rate. Results of no-choice mating trials supported reproductive isolation among O. lybicus populations, which may lead to rapid evolution and speciation. A comprehensive and ecofriendly management program with emphasis on judicious use of pesticides for O. lybicus management is recommended to reduce genetic diversification in this species. [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]

Pomegranate (Punica granatum L.) has been cultivated from ancient times for its economic, ornamental and medicinal properties globally. Here, we report the isolation and characterization of 12 polymorphic microsatellite markers from a repeat-enriched genomic library of Punica granatum L. The genetic diversity of these loci was assessed in 60 genotypes of Punica granatum L. All loci were variable: the number of polymorphic alleles per locus ranged from two to five (average 2.9). The observed and expected heterozygosities ranged from 0.15 to 0.87 and 0.29 to 0.65, respectively. The polymorphic information content ranged from 0.26 to 0.61 (average: 0.43). To the best of our knowledge, this is the first time that polymorphic microsatellite markers have been reported for P. granatum L. These new markers should allow studies of the population structure and genetic diversity of pomegranate to be performed in the future. [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]