Journal of Genetic Resources
Volume:10 Issue: 2, Summer-Autumn 2024

Tyrosinases are essential enzymes with diverse applications, such as breaking down phenolic compounds and producing melanin. Actinobacteria are one of the most notable tyrosinase producers. This study investigated tyrosinase-producing actinobacterial strains and evaluated enzyme activity in different sources of L-tyrosine. Twenty strains were isolated from the soil of Langar, Kerman, Iran, with characteristics of actinobacteria (gram-positive filamentous or rod-shaped bacteria and powdery consistency colonies that stick firmly to agar surface). All strains were cultured in a medium with L-tyrosine to assess tyrosinase production. The best tyrosinase-producing strain was selected based on dark-colored colony formation. Also, enzyme activity was evaluated in the four mediums with different L-tyrosine sources (Tyrosine, Glucose-Yeast-Peptone (GYP), Soybean, and Peanut). On the other, the pigment produced by actinobacteria was investigated for significant properties such as Sun Protection Factor (SPF) and antioxidant activity. The results showed that the HM24 strain is the best strain for producing tyrosinase. The results showed that the HM24 strain was the best tyrosinase-producing strain, and the most enzyme activity was in the peanut medium as well as in the soybean meal substrate. According to the 16S rRNA sequencing, the HM24 strain belonged to the genus Microbacterium with 99.97% identity. The pigment produced by HM24 demonstrated an SPF of 134.36 and a 69% DPPH reduction, which indicated strong antioxidant activity. These findings underscore the significant potential of actinobacterial strains in various industrial applications. Considering the production of tyrosinase enzyme by strain HM24, its ability to efficiently utilize natural L-tyrosine sources, and the biological properties of the resulting pigment, this strain holds significant potential for applications in various industrial processes.

In this study, the experiment was carried out in a completely randomized design to discover the diversity among 300 Ali Kazemi rice populations from three provinces (ten populations) in the north of Iran using SPSS, Past, Graph Pad, and Excel software. The studies were conducted based on 30 morphological traits. Quantitative traits, like panicle traits, grain length, 100-grain weight, and number of spikelets, demonstrated high variation between populations. Cluster and ordination analyses were performed on morphological characters. The cluster analysis made it possible to divide the Ali Kazemi rice into three sub-clusters of different geographical regions, showing this local variety’s adaptability to the environment. Of the three populations, Guilan appeared to be more variable than the Qazvin and Zanjan, as variability was observed among populations for some characters, such as awn length, number of spikelets, blade length, and panicle traits between populations. GLN01 had the highest average plant height (1185.60 mm). The populations of Guilan also had the longest leaf blade and stem length. The highest value for grain size was also recorded from the Guilan populations. For the ten Ali Kazemi rice populations, the ordinal analysis revealed the traits that cause the greatest variation between populations. Highly significant correlations were found between awn length and traits such as grain length (r= 0.395), panicle length (r= 0.477), panicle weight (r= 0.349), and 100-grain weight (r= 0.440). The highest correlation was between the number of spikelets and some traits, such as plant height, leaf length, culm outer diameter, number of tillers, and panicle traits, indicating that a selection advantage for panicle traits occurs mainly for quantitative traits. Overall, the data collected in the present study could have valuable implications for improving Ali Kazemi rice cultivars in farmers' fields.

The transition of the shoot apical meristem from vegetative to reproductive phases is a critical stage in the plant life cycle. In contrast, the success of reproduction depends on the flowering initiation timing. One of the key repressors of flowering is the gene FLOWERING LOCUS C (FLC), which is important for determining flowering time. The present study, therefore, aimed to identify and investigate the expression patterns of Lepidium sativum genes, considering FLC. Specific primers were designed for the RT-PCR assays, amplifying a 361-nucleotide fragment of the LsFLC gene, recorded in the NCBI database under the accession number GenBank: KT582105.1. The sequenced fragment encoded for a deduced protein sequence of 120 amino acids. The expression of LsFLC in different plant organs was analyzed at various phenological stages, namely two days (early stage of vegetative development), 13 days (early vegetative stage), 28 days (vegetative maturity or transition stage), and during reproductive development stages, which fall on 33 days (early reproductive stage) and 34 days (flowering stage). Results showed that LsFLC expression levels were very high in the root and relatively high in leaves and stems, whereas no expression was allowed in flowers. Indeed, the mRNA levels were much higher during the vegetative phase compared to the transition to flowering, therefore agreeing with the known role of FLC as a promoter of vegetative growth and an inhibitor of flowering. Phylogenetic analysis showed that the LsFLC gene has a close relationship with Brassicaceae members, in particular with the highest homology with Arabidopsis lyrata. The current study has contributed to the knowledge of the functions of LsFLC proteins during the phenology of L. sativum and could contribute to strategies developed for improving this species in desirable traits.

Oriental beech (Fagus orientalis) is distributed from Turkey to northern Iran. It is one of the most economically important tree species in this natural distribution range and has been exploited for a long time in the Hyrcanian forest. This study compared genetic variation between adult individuals and recent cohorts of 1–3-year-old seedlings using 14 SSR primers in four pure stands of F. orientalis with over 90% canopy cover. The results showed that the expected heterozygosity (He) varied from 0.83 to 0.92 (mean value 0.88), and a significant difference was detected between the expected and observed heterozygosity. In total, 75 private alleles were detected; of these, 56 were rare and had a frequency below 0.05. Pairwise Fst values indicated that seedlings were more similar to each other than to mature trees in the same population. It was found that the populations in each pair (mature trees-seedlings) differed (global average D = 0.35). The average percentage of migrants in the population was 8.83% and varied from 6.64% to 13.41%. The genetic differentiation within the same stands, the genetic differences between adults and seedlings were also significant in some populations, and contemporary gene flow drastically decreased in the next generation. Therefore, the transfer of genetic variation between tree generations is currently strongly affected by anthropogenic influence, at least in the studied beech populations, leading to the high vulnerability of Oriental beech populations to future climate changes.

Biological nitrogen fixation is a process by which atmospheric nitrogen could be converted to the bioavailable nitrogen forms for plants. Among plants, legumes have the ability to fix nitrogen through symbiotic interaction with a specific group of bacteria called rhizobia. Because of this interaction, organs named nodules form on the plant roots. Nodule organogenesis on plant roots begins with the perception of Nod factor by plant root cells. Downstream of Nod factor perception, activation of transcription factor (TF) signaling cascade in root tissue take place. This results in the formation of structure named infection thread and initiation of cell division in root cortex and finally formation of functional nodules. Due to the importance of biological nitrogen fixation to improve soil fertility, the molecular mechanism of nodule development is studied extensively. Here in order to identify new possible regulators that affect the formation of nodules during symbiosis in Medicago truncatula, the most significant symbiotic related TFs including MtIPD3, MtNSP1, MtNSP2, MtNIN, MtERN1, MtERN2, and MtERN3 were studied. Analyzing co-expressed genes with Phytozome database and examining interaction networks with STRING database have indicated potential new regulators involved in nodule development. According to our data, there is a high physical interaction score between IPD3 with some splicing factors and cell cycle proteins. This shows that IPD3 through interaction with these proteins could be involved in regulation of gene expression and cell cycle. Besides, we found a possible cytokinin transport gene ABCG38 and showed the activation of its expression in nodules compared to root. Moreover, we showed that auxin response factor Medtr2g043250 could be direct target of NIN transcription factor. Our results on potential regulators of nodule organogenesis will pave the way for additional researches.

Tomato is one of the most cultivated vegetable crops worldwide, with a global production of over one hundred and thirty million tons. Its multi-purpose uses range from being consumed in various forms, including salads, pastes, sauces, and soups, to its culinary and antioxidant properties. Assessment of variability among genetic materials is essential for maintaining and utilizing genetic resources. A fundamental requirement for the effective use of these genetic materials in breeding and crop improvement is a thorough analysis of the genetic variability and structure of the accessions. This study aims to assess the genetic diversity of tomato accessions in the Nigeria gene bank using Simple Sequence Repeat (SSR) markers. DNA was extracted from fifty tomato accessions using the CTAB protocol. The DNA was quantified using a Nanodrop Spectrophotometer and quality-checked on 1%w/v agarose. High-quality DNA was then used for amplification with five polymorphic SSR markers. The total number of alleles was 23, with a mean of 3.20. The polymorphic information content (PIC) values ranged from 0.35 (ODT4) to 0.50 (ODT1), with a mean value of 0.43, while the gene diversity ranged from 0.45 to 0.57, with a mean value of 0.51. The cluster analysis based on the Unweighted Pair-Group Method using Arithmetic Means (UPGMA) grouped the accessions into two major clusters, each with two subclusters. The first major cluster comprised two subclusters of three and thirty tomato accessions, respectively, while the second major cluster had one and sixteen tomato accessions in its subclusters. The results showed that SSR markers were successfully used to discriminate among the tomato accessions based on the PIC and genetic diversity values, hence promoting their use for future crop improvement and contributing to food security.

In an intracytoplasmic sperm injection (ICSI) procedure, sperm must be immobilized due to its manipulation; therefore, Polyvinylpyrrolidone (PVP) has been used for this purpose. Based on many studies, fertilization rates may be reduced by incubation of sperm in PVP as it changes sperm mitochondria, nucleus, and membrane structures. Since PVP is used widely in infertility centers, it is noteworthy to investigate the side effects of this agent. This study was designed to evaluate the effects of this component on chromatin quality with acridine orange (AO) staining, Malondialdehyde (MDA) levels, and BAX, BCL2, HSP70 (HSPA2), and SOD2 genes expression in different time intervals (0, 15, 30, and 60 minutes). In this research, 25 normal sperm specimens were applied after preparation with the swim-up method. Results showed that incubation of sperm in PVP for 15, 30, and 60 min significantly increased MDA levels and AO percentage rate compared to unexposed spermatozoa to PVP. Furthermore, the expression of BAX, BCL2, HSP70, and SOD2 genes were altered after incubation in a PVP medium at different time intervals. Incubation of sperm in PVP significantly increased the adverse effects after 15 min. Therefore, sperm should not be exposed to PVP for more than 15 minutes during the ICSI procedure. Altogether, results showed that incubation of sperm in a PVP medium during an ICSI procedure for more than 15 min may result in significant changes in the biological features of sperm. Therefore, expediting the ICSI procedure could mitigate the potential adverse effects of PVP on sperm parameters.

Numerous studies have recognized GSK3ß as a gene associated with susceptibility to schizophrenia (SZ), highlighting its essential function in neurodevelopment and its potential as a target for antipsychotic medications. In this study, we examined the connection between two polymorphisms of the GSK3ß gene, rs334558 and rs3755557, and their potential link to the risk of schizophrenia. We performed a case-control analysis to investigate this relationship within a population from southern Iran. DNA samples were isolated from 100 cases with schizophrenia and 100 normal controls. Then, we used a polymerase chain reaction (PCR) followed by the restriction fragment length polymorphism method (PCR-RFLP) to examine the GSK3ß SNPs (rs334558 and rs3755557) patterns. The frequency of genotypes, alleles, and the Hardy-Weinberg equilibrium were evaluated. Research has shown that individuals with the TA genotype and those with the combined TA+AA genotype at the rs3755557 (T/A) locus have a significantly higher risk of developing schizophrenia (OR= 2.94; 95% CI: 1.54-5.61, P= 0.0001) and (OR= 3.78; 95% CI: 2-7.13, P< 0.0001), respectively. Similarly, the GA genotype and the combination of GA+AA genotypes at the rs334558 (G/A) locus also notably increase the risk of schizophrenia, (OR= 6.62; 95% CI: 3.4-13; P< 0.001) and OR = 7.63; 95%CI: 3.95-14.7; P< 0.001), respectively. In this investigation, our findings have elucidated a substantial correlation between polymorphisms in the GSK3ß gene and the susceptibility to schizophrenia. The analysis indicated that variations in genotype frequencies between the control and the patient group could serve as a diagnostic criterion for schizophrenia. It is recommended that subsequent research involving larger sample sizes across diverse genetic populations be conducted to corroborate the current findings.

Lipases are the third category of widely used hydrolytic enzymes that catalyze the hydrolysis of triacylglycerols, glycerol, and free fatty acids. Actinobacteria, which are Gram-positive bacteria, have the largest genome size among bacteria and produce various secondary metabolites, including enzymes. This study aimed to isolate lipase-producing Actinobacteria strains from the Lut Desert in Iran. In this study, microbial samples isolated from the Lut Desert region of Iran in 2017-2018 were cultured on specific Actinobacteria growth media. These samples were activated and cultivated on Tween 80 agar plates for lipase production. After seven days of bacterial growth, the samples were assessed based on the transparent clear zone diameter around the colonies. The lipase activity was measured spectrophotometrically using para-nitrophenyl palmitate as the specific substrate, and the best lipase-producing strain was identified based on its 16S rRNA sequence. Among the six isolated Actinobacteria strains, three strains exhibited lipase production capability. Strain Ga7 had the largest clear zone with a diameter of 7 mm and lipase activity of 5.45×10 -7 µmol/min, making it the most promising potential lipase producer. Based on its 16S rRNA sequence, strain Ga7 belongs to the genus Streptomyces sp., with 99% similarity to Streptomyces indoligenes. This study highlights the significance of using bacteria as a microbial source for lipase production for future industrial and biotechnological applications. Based on the findings of this study, it was determined that the Ga7 strain, due to its bacterial genus and its isolation from the Gandom Beryan area of the Lut Desert as the hottest place on earth, can be a suitable candidate for lipase production in various industries. These findings emphasize the importance of studying microorganisms from extreme environments like the Lut Desert as rich sources for discovering and utilizing industrial enzymes.

Plant stresses caused by phytopathogenic bacteria are categorized into biotic stresses. The study aimed to perform a meta-analysis of A. thaliana transcriptomic data in response to infection by P. syringae and P. syringae pv. maculicola. The gene expression and transcription factors (TFs) of A. thaliana infected by the bacteria were investigated using published RNA-Seq data. Also, critical factors, including hub genes, protein-protein interaction (PPI), and micro RNAs (miRNAs), were analyzed. A total number of 22 biological pathways were significantly enriched with up-/down-regulated differentially expressed genes (DEGs) in the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Also, 39 TFs of A. thaliana were altered during the bacterial infection. Moreover, 5034 DEGs were significantly different from non-stressed plants, of which 2291 and 2743 DEGs were up- and down-regulated, respectively. The expression of genes related to stress response, cellular process, metabolic process, and stimulus response was up-regulated in the bacteria-infected plant. In contrast, the down-regulation of genes involved in the cellular and biosynthesis processes was observed. Regarding molecular function, 412 genes associated with kinase, catalase, and oxidoreductase activities were up-regulated in the bacteria-infected plants, while down-regulation of hydrolase and transferase activity genes was observed. The PPI network showed 107 nodes and 189 edges. The most important hubs genes included MYC2, WRKY40, WRKY33, and other genes. Moreover, the total number of 41 miRNA families was determined during the A. thaliana-bacterium interaction. Infection of A. thaliana by P. syringae and P. syringae pv. maculicola induced the expression of some stress-responsive genes and pathways among which some defense-related hub genes were identified. The results provide a clearer understanding of the strategies applied to program defense pathways in bacterial infection of A. thaliana.

Cantharidin and cantharidin-related compounds (CRCs) are synthesized by Meloidae to defend against predators. Also, Cantharidin and CRCs are known as biopesticides. Because biopesticides are increasingly used to replace chemical pesticides in pest control, it is necessary to investigate the amount of cantharidin and CRCs (palasonin and palasoninimide) as known biopesticides. In this research, cantharidin content was determined in four species of Meloidae (Hycleus colligatus, Mylabris schrenki, Mylabris cincta, and Hycleus schah) which were abundant in Kerman province. Each species was divided into three groups including males, mated females, and virgin females. The results showed that Hycleus colligatus had the highest level of cantharidin (Mean± SE: 20.38± 0.49 µg/mg). The levels of cantharidin for Mylabris schrenki, Mylabris cincta, Hycleus schah were 12.44± 0.17, 5.24± 0.06, and 3.49± 0.03µg/mg, respectively. The level of cantharidin in mated females and virgin females in all species, had the highest and lowest levels, respectively. The results showed that only males can synthesize cantharidin and transfer it to females during mating. Mated females get this toxin from males during mating and use it for defending eggs from attacking predators and inducing feeding versions in predators exposed to the toxin. Also, in this research, palasonin and palasoninimide content were determined in these four species. Palasonin and palasoninimide were found in mated females but not in males indicating that CRCs do not have the same transfer pattern as cantharidin and thus unlike cantharidin, could not have been transferred from males to females. The study showed that in mated females of four species, the percentage of cantharidin was more than palasonin and palasoninimide.

Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum is one of the most destructive diseases of rapeseed (Brassica napus L.) globally. This study identifies key genes involved in the pathogenicity of S. sclerotiorum during rapeseed infection. It examines these genes' codon usage bias (CUB) to find the optimal codons effective in gene expression and the factors effective in the formation of CUB. Protein-protein interaction network was drawn and several hub genes were determined and ranked according to the CytoHubba tool among which the genes encoding nitrate reductase, beta-glucosidase, glucanase, PA14 domain-containing protein, carbohydrate-binding module family 1, and acyl-coenzyme A oxidase were found to be associated with the SSR induction. Gene ontology (GO) analysis showed that the genes related to the metabolism of organic substances, catalytic activity, and cellular anatomical entity had the highest count. Also, KEGG pathways analysis revealed 16 biological pathways modulated by S. sclerotiorum among which the genes associated with the metabolic pathways exhibited the highest count. CUB indices including CAI (codon adaptation index), ENC (effective number of codons), GC, GC3S (GC content in the third open position of the codon), and RSCU (relative synonymous codon usage) were determined and the results showed a significant positive correlation between GC and GC3S. Also, the possible effects of mutation pressure and natural selection in shaping CUB were determined. The mean ENC range from 42.4-56.65 indicating less orientation in codon usage. The range CAI was found to be 0.74-0.89 indicating the importance of genes in adapting to environmental stresses. The maximum RSCU was 1.76 for the CCA codon, which encodes the amino acid (aa) proline with a high preference for that codon compared to other synonymous codons of that aa. These results demonstrated that S. sclerotiorum modulates some genes involved in disease induction (e.g., cell wall-degrading enzymes, biosynthesis of secondary metabolites & metabolic pathways) to infect its host plant.