https://pgr.lu.ac.ir/ Plant Genetic Research en daily 1 Mon, 22 Dec 2025 00:00:00 +0330 Mon, 22 Dec 2025 00:00:00 +0330 https://pgr.lu.ac.ir/article_734963.html In this study, the WOX gene family in sesame (Sesamum indicum L.) was comprehensively analyzed. A total of 36 SiWOX genes were identified in the sesame genome, distributed asymmetrically across the chromosomes, with the highest density observed on lincage groups (chromosomes) 1 and 2. The physicochemical characterization revealed that the WOX proteins ranged in length from 175 to 853 amino acids, with molecular weights between 20.11 and 93.62 kDa, and aliphatic indices ranging from 50 to 92.55. The isoelectric point (pI) values varied between 4.99 and 9.56, while the negative GRAVY values indicated the hydrophilic nature of the proteins. Subcellular localization prediction suggested that most proteins were localized in the nucleus, although some were also found in the chloroplast, cytoplasm, mitochondria, and plasma membrane. Phylogenetic analysis of SiWOX and AtWOX genes classified them into four main groups. Promoter analysis revealed 61 cis-regulatory elements associated with light, hormone, and stress-responsive pathways. Gene structure analysis showed variation in the number of exons and introns, and the presence of a conserved homeodomain in all proteins confirmed their role in DNA binding. Expression profiling of SiWOX9, SiWOX16, and SiWOX36 in two genotypes, Sardari and Dashtestan, showed that Sardari exhibited a more stress response, particularly through the significant upregulation of SiWOX16 after 48 hours. In contrast, the expression of these genes in Dashtestan was reduced or fluctuated slightly. Further RNA sequencing research is needed to identify candidate genes for breeding stress-tolerant cultivars and to support future functional studies and genome-assisted breeding. https://pgr.lu.ac.ir/article_734961.html Wheat is a vital food crop; however, its production is continuously threatened by abiotic stresses, particularly salinity stress. Understanding the molecular mechanisms through which wheat responds to salinity stress is essential for the development of salt-tolerant varieties. Given the significant role of the NAC and WRKY transcription factor families in stress responses, the expression levels of three key genes from these families—TaWRKY10, TaWRKY53, NAC2, and P5CS—were evaluated in the cultivars Kalateh, Baharan Gonbad, and N9108. In addition, total chlorophyll content and the cellular oxidation index were assessed in this study. The experiment was conducted as a split-plot arrangement within a randomized complete block design with four replications. Salinity treatment was applied through irrigation water after plant emergence and establishment (Zadoks growth stage 34). Sampling for gene expression and biochemical trait analysis was performed at the stem elongation stage. Gene expression levels were analyzed using qRT-PCR technology. Analysis of variance revealed that the interaction effect of salinity stress × cultivar was significant at the 1% level for chlorophyll a content and malondialdehyde content, and at the 5% level for chlorophyll b content. Gene expression analysis showed that TaWRKY10 exhibited the highest expression (1.5-fold increase compared to the control) under 9 dS/m salinity treatment in the Kalateh cultivar. NAC2 showed a 15-fold increase in expression compared to the control under 12 dS/m salinity treatment in the Kalateh cultivar. The P5CS gene also displayed an increasing trend under salinity stress with rising salinity levels, with the highest expression (16.34-fold increase compared to the control) observed in the Kalateh cultivar under 12 dS/m salinity treatment. The gene expression results indicated that increasing salinity levels significantly induced stress-responsive genes, including TaWRKY10, NAC2, and P5CS, particularly in the Kalateh cultivar, highlighting their key role in salinity tolerance mechanisms. The marked upregulation of these genes, especially under higher salinity levels, suggests that they may serve as suitable molecular markers in breeding programs aimed at selecting salt-tolerant wheat cultivars. https://pgr.lu.ac.ir/article_734964.html In order to understand the genetic structure of the agronomic traits related to grain yield, seven spring bread wheat cultivars including Shavour, Talaei, Khalil, Baharan, Taktaz, Araz and Arman were planted in a crossing block and direct diallel crosses were performed among the seven cultivars to produce F1 generation. The progenies of the crosses with their parents were evaluated based on a randomized complete block design (RCBD) with three replications at Gorgan agricultural research station in 2023-2024 cropping season. The results showed a significant difference among the genotypes for all the studied traits. Estimation of genetic parameters using Heiman's method showed that the values of dominance variance were significantly greater than that of the additive variance for grain yield, biological yield, 100-kernel weight, number of grains per spike, number of spikelets per spike, spike weight and grain weight per spike. Conversely, the values of additive variance were significantly greater than that of the dominance variance for peduncle length. Also. there was a small difference between the values of dominance and additive variance for the plant height and spike length triats. For biological yield, 100-kernel weight, number of grains per spike and number of spikelets per spike, the proportion of dominant alleles and was greater than the recessive alleles, whereas the proportion of dominant and recessive alleles was equal in the other traits. High broad-sense heritability in grain yield and biological yield and number of grains per spike and their smallish narrow-sense heritability showed a greater share of the dominance effect in controlling these traits. The results of graphical analysis showed that grain yield, biological yield, number of grains per spike, number of spikelets per spike, spike weight and grain weight per spike were controlled with overdominance gene action, 100-kernel weight was controlled with complete dominance gene action and other traits were controlled with incomplete dominance gene action. The study of the distribution of parents around the regression line showed that Shavour, Khalil and Talaei cultivars carried the most dominant genes, whereas Araz and Taktaz cultivars carried the most recessive genes in controlling grain yield and biological yield. These findings suggest that crossing these cultivars could lead to the production of hybrids with improved performance. https://pgr.lu.ac.ir/article_734965.html Throughout evolution, plants have developed complex molecular mechanisms to cope with biotic and abiotic stresses, many of which are driven by the reprogramming of gene expression. Multiple genetic factors regulate the molecular responses of plants to unfavorable environmental conditions, among which long non-coding RNAs (lncRNAs) play a significant role. LncRNAs play a pivotal role in regulating gene expression, epigenetic modifications, and signaling pathways, significantly contributing to responses against both biotic and abiotic stresses. In this study, for the first time, the identification, functional determination, and expression analysis of LncRNAs in lentil (Lens culinaris L.) under salt stress conditions were investigated. LncRNAs were identified using the lentil transcriptome reference, which was generated by assembling RNA sequencing data from the leaf and root tissues of lentil under both stress and control conditions. After filtering protein-coding sequences, several lncRNA sequences were identified using PLncPRO software. The relative expression levels of the identified sequences were measured, and the co-expression network with differentially expressed genes (DEGs) was constructed. To validate the RNA-seq data, the expression of selected lncRNAs was analyzed by qRT-PCR. The processing and refinement of the expression profile of lentil under salt stress resulted in the identification of 7677 lncRNA sequences, with 722 sequences being identified for the first time in lentil. Gene expression analysis revealed that 90 sequences in leaf tissue and 48 in root tissue showed increased expression under salt stress. Functional analysis of the co-expressed genes indicated that these genes were involved in biological processes such as translation, ion transport, and stress response. Metabolic pathway enrichment analysis identified 18 significant pathways, including S-adenosyl-L-methionine cycle, abscisic acid biosynthesis, and cytosolic glycolysis. The qRT-PCR validation confirmed the correlation of RNA-seq and qRT-PCR results with a 95% correlation coefficient. In conclusion, the results of this study revealed that the identified lncRNAs play a significant role in regulating key genes involved in essential metabolic pathways in lentil's molecular response to salt stress. Identifying and analyzing these lncRNAs in lentil can provide a better understanding of the molecular mechanisms underlying these stress responses. Investigating the interactions of these identified RNAs with other regulatory molecules, such as ABA and protein-coding genes, could contribute to the development of breeding strategies aimed at improving lentil’s tolerance to both biotic and abiotic stresses. https://pgr.lu.ac.ir/article_734966.html Stevia rebaudiana Bert. is a medicinal plant widely utilized as a source of natural sweeteners. Its sweetening potency is attributed to steviol glycosides, diterpenoid compounds present in the leaves. Similar to other plant secondary metabolites, production of steviol glycosides can be modulated by biotic and abiotic elicitors. Among biotic elicitors, the fungus Serendipita indica has been shown to positively influence steviol glycoside production. In the present study, the effect of S. indica symbiosis on the relative expression patterns of key early biosynthetic pathway genes of steviol glycosides, including Dxs, Cms, Mcs, Hds, Hdr, and Ggdps was investigated. Following fungal inoculation and confirmation of root colonization, samples were collected from treated plants. After RNA extraction and cDNA synthesis, transcript levels of the target genes were assessed using quantitative real-time PCR (qRT-PCR) with three biological and three technical replicates. The results demonstrated that symbiotic association with S. indica significantly up-regulated the expression of all examined genes. The highest up-regulation expression was observed for Ggdps gene, suggesting that it can be considered as a candidate gene for metabolic engineering aimed at enhancing steviol glycoside biosynthesis. https://pgr.lu.ac.ir/article_734967.html In recent years, leaf drying disorder has emerged as a major threat to date palm (Phoenix dactylifera L.) production in Iran’s arid and semi-arid regions. Despite its economic significance, the molecular mechanisms underlying this condition remain poorly understood. This study aimed to investigate the expression patterns of seven key stress-responsive genes (OSCA1, FERONIA, FLS2, CERK1, HKT, UVR8, and COLD) in three date palm cultivars (Estamaran, Barhi, and Hallawi) exhibiting contrasting phenotypes: with and without leaf drying symptoms. Our results reveal a two-phase molecular defense strategy in tolerant cultivars (Estamaran and Hallawi). Under non-stress conditions, these cultivars exhibited significantly higher basal expression of OSCA1, FLS2, and HTK, suggesting a state of "pre-emptive defense priming" that likely enhances readiness against osmotic and salinity stresses. Conversely, upon symptom development, tolerant cultivars showed marked upregulation of FERONIA and CERK1, indicating an intelligent, pathogen-responsive immune activation, potentially against fungal agents implicated in the disorder. In contrast, the susceptible cultivar (Barhi) displayed dysregulated expression: elevated UVR8 and COLD1 levels correlated with accelerated leaf senescence and water loss, while reduced OSCA1 and HTK expression was associated with impaired ion homeostasis. Collectively, our findings demonstrate that tolerance to leaf drying is not governed by a single gene but by a coordinated, multi-stage defense system involving both pre-stress preparedness and stress-responsive immunity. These results provide a foundational framework for developing molecular markers and cultivar-specific breeding strategies to mitigate this emerging threat in date palm cultivation. https://pgr.lu.ac.ir/article_734968.html Antimicrobial peptides (AMPs) are a diverse group of low-molecular-weight bioactive molecules that serve as the primary defense line of the innate immune system against infections in all multicellular organisms. In plants, these peptides exhibit high biodiversity and belong to several families, being produced both constitutive and inducible in response to environmental stresses. Knottin antimicrobial peptides are a class of peptides found in plants, animals, and insects which are cysteine-rich peptides. This study aimed to identify and characterize some Knottin antimicrobial peptides from white mustard (Sinapis alba L.). In this research, the gene sequences of seven Knottin antimicrobial peptides from white mustard were predicted and identified using bioinformatics and laboratory techniques. Initially, bioinformatics methods were used to predict the encoding sequences of the target peptides from the transcriptome of white mustard. Subsequently, these encoding sequences were isolated and identified using polymerase chain reaction (PCR). The PCR products were sequenced and analyzed using various bioinformatics tools. The physicochemical properties of the seven identified Knottin peptides from white mustard were predicted, with molecular weights ranging from 9.92 to 11.05 kDa, isoelectric pH values from 4.46 to 7.89, instability index from 38.06 to 63.9, aliphatic index from 62.36 to 81.82, and GRAVY values ranging from -0.249 to 0.18. It was also found that the Knottin peptides of white mustard contain four intramolecular disulfide bonds formed by eight conserved cysteine residues, contributing to their unique structure and stability. Additionally, bioinformatics analysis revealed that all the identified Knottin peptides in white mustard have potentially antimicrobial activities. Given that plants produce a wide range of antimicrobial peptides, and considering that purification methods can be complex, costly, and time-consuming, these peptides can be identified, designed, and chemically synthesized or produced recombinantly using bioinformatics tools and after validation through further experiments, could be a promising therapeutic potential to develop as new antimicrobial agents against drug-resistant pathogens. https://pgr.lu.ac.ir/article_734969.html This aimed to assess genetic diversity, evaluate quantitative and qualitative traits, and identify superior sugar beet genotypes in two different climatic environments (Fasa and Gonbad). A set of yield, and industrial quality-related traits, including root yield, white sugar yield, molasses sugar percentage, root alkalinity, α-amino nitrogen, sodium content, and potassium content, were measured and analyzed. The results of this study showed that most traits exhibited high heritability and substantial genetic advance, enabling effective selection at early stages of breeding. Multivariate analyses, including genotype × trait biplot and cluster analysis, revealed the genetic structure of the population. In the biplot diagram, yield and quality traits such as root yield, white sugar yield, and white sugar content showed positive and significant correlations, and genotypes 6, 7, 14, and 19 were positioned along these vectors and were identified as superior genotypes. In contrast, traits such as root alkalinity, sodium content, and molasses sugar percentage showed negative correlations with desirable sugar traits, and genotypes located near these vectors were evaluated as undesirable. Cluster analysis in both environments resulted in the formation of three distinct clusters. Genotypes in the third cluster in Fasa and the first cluster in Gonbad exhabited higher mean values for yield and quality traits and were identified as valuable genetic resources. These findings indicate that multi-trait approaches and targeted genotype selection across diverse climatic conditions can effectively enhance sugar beet improvement. https://pgr.lu.ac.ir/article_734962.html Terminal drought stress severely constrains wheat production in arid and semi-arid regions such as Iran, where yield stability is heavily reliant on unpredictable spring precipitation. The CONSTANS-Like (COL) gene family integrates light signals and circadian rhythms to regulate flowering time and is also involved in abiotic stress adaptation. This study investigated the physiological and transcriptional responses of eight COL gene family members to terminal drought stress in the flag leaf tissue of a synthetic hexaploid wheat line, in comparison to the commercial cultivar Pishgam. A split plot experiment was performed under field conditions the fram of a randomized complete block design with three replications. Two The main factor was irrigation regimes (well-watered and drought-stressed) and two genotypes were located in subplots. The synthetic line maintained higher levels of photosynthetic pigments and exhibited enhanced activity of key antioxidant enzymes, particularly superoxide dismutase (SOD) and peroxidase (POD), under both conditions. Under well-watered conditions, all homeologous groups showed higher transcript abundance in the synthetic line, correlating with its accelerated growth and early flowering phenotype. Under drought stress, one homeologous group was downregulated in both genotypes, whereas the other two were significantly upregulated, with markedly stronger induction in the synthetic line. This expression pattern suggests their involvement in promoting early maturity and desiccation escape mechanisms. The coordinated enhancement of antioxidant defense and selective upregulation of specific COL genes indicates a synergistic interaction between oxidative stress mitigation and developmental acceleration under drought conditions. Collectively, these findings indicate that superior tolerance to late drought of the artificial wheat line is associated with stable photosynthetic performance and a distinct COL gene expression profile, making this line a suitable candidate for cultivation in areas with late-season drought stress. https://pgr.lu.ac.ir/article_734970.html Lentil (Lens Culinaris) is one of the most important sources of protein worldwide and most widely consumed. This plant has high nutritional value among legumes. The present study was conducted to estimate broad-seanse heritability and to perform clustering of lentil genotypes using multivariate statistical approaches. Genotypes were evaluated in a randomized complete block design with three replications at Sarab-Changai Research Station, Lorestan Agricultural and Natural Resources Research and Education Centre, Khorramabad, Iran. Traits were recorded for each genotype and raw data were analyzed using Statistical experimental design model and multivariate statistical methods. Analysis of variance indicated significant differences between genotypes in most of traits. The highest heritability estimates were observed for total dry matter per plant, number of two-seeded pods, and number of seeds per pod. Based on the results of most multivariate analyses, genotype G5 was identified as the superior genotype, whereas genotype G6 was consistently classified as the weakest. The Superior Genotype Index (SIIG) was used for the final ranking of the 15 lentil genotypes. Overall, the results indicate that genotype G5, which showed high heritability for key yield-related traits, is the most promising genotype and has strong potential for use in future breeding and subsequent research programs.