Journal of Genetic Resources
Volume:9 Issue: 1, Winter -Spring 2023

The grain yield of cowpea across the producing countries falls below expectation due to diverse production constraints. Hence, it seems that broadening its genetic base for sustainable yield improvement and tolerance to environmental stresses in the context of global climate change is necessary. Therefore, the objectives of the present study is to evaluate the genetic differences and correlation of characters in F2 hybrids of cowpea and their parent lines. The present study was performed in the field during the rainy season. The obtained data were subjected to various statistical analyses. The hybrids and the parents exhibited significant variation for all the traits studied, including the seed yield. High variability among the offspring and parents suggests better chances of producing the desired recombinants in the successive generation. Emergence ranged between 53.04% in offspring of IT98K-555-1 × IT98K-205-8 and 73.68% in IT98K-555-1. Parents exhibited higher main branches (4.72 and 4.80). IT98K-555-1 was superior for most traits, including the seed yield per plant (288.64 g). However, IT98K-205-8 flowered first at day 45 while IT98K-555-1 flowered last at day 56. Traits such as emergence percentage, days to first flowering, pods/plant, and seed yield/plant exhibiting a combination of high broad-sense and narrow-sense heritability (˃ 60%) and high genetic advance as a percent of the mean (˃ 20%) indicated that they were under genetic control and responsive to the improvement. Traits such as plant height, seeds/pod, pods/plant, and seeds/plant with a high positive genotypic correlation (r ≥ 0.99) to seed yield/plant could be considered the core selection indices in cowpea improvement programs. Nonetheless, further studies into F3 and later generations are required to exploit the relationships between the high yields, seed coat color, and drought tolerance among the cowpea hybrids.

The main storage form of phosphorus is phytate (Myo-inositol Hexakisphosphate) in legume crops, such as clover and alfalfa, which are of high importance in terms of nutrition for humans and animals. In animals, due to a lack of phytase enzymes in their intestines, it is not possible to break the phytic acid (a nutritional constituent). Hence, phytic acid acts as an anti-nutritional chelating agent for various metal ions like Ca, Mg, Fe, Zn, etc., so it reduces the nutritive quality of food. Since phytase is an important enzyme in the food/feed industry, the objective of this study is to isolate phytase-producing bacteria cells to analyze phytate molecules. The present study was conducted in the laboratory of the Sana Institute of Higher Education. In this study, 8 soil samples of alfalfa and clover fields located in Isfahan (Khomeini Shahr and Morche Khort Regions) were collected and several bacteria isolates were separated using differential media. To examine the phytase activity, the isolated bacteria on the specific media fortified with phytate were cultivated and positive phytate bacteria were identified using morphological traits, biochemical tests, and 16srRNA sequencing determination. The data obtained from quantitative properties showed that two isolates of B1 and D1 have 17 and 20 mm size of zone diameters, respectively. Based on morphological properties, the B1 bacteria showed a big size of the colony, with a bump hanging in the margin surrounding the colony and white pigment, which was gram-positive. However, the D1 sample indicated a small colony size, with a wavy margin, smooth bump, and creamy pigment which was gram-positive. By biochemical recognition test, among all bacteria cells, two bacteria colonies were distinguished concerning the phytase activity and were recognized as Bacillus sp. In addition, the 16srRNA sequencing analysis showed that one strain belongs to Bacillus paralicheniformis (95%) and the other one is related to Bacillus endophyticus (95%), both of which are found in soil usually.

The plant Camelina sativa (L.), a member of the Brassicaceae family, is an ancient oilseed crop. Due to its adaptation to vast areas of the world and its unique oil composition and properties, it is useful for the production of biofuels, jet fuel, bio-based products, feed, and food. The present study was performed to investigate the morphological and agro-physiological characteristics of this plant through Factor Analysis (FA). For this purpose, 136 doubled haploid line genotypes were assessed in the form of a randomized complete block design with three replications in the research field of Razi University, Kermanshah, Iran. FA, based on the principal component analysis method and varimax rotation, showed that two important factors make up about 74.97% of the total variety of characters. The Eigen values of these two factors were 9.76 and 3.72, respectively. The first and second factors assigned 53.99 and 20.98 percent, respectively, of the total variation. Factor 1, which was called the biological performance, included the seed yield, number of pods per plant, number of pods per main branch plant, number of pods per lateral branch, biological yield per five plants, plant height with roots, root weight, shoots weight, pod straw weight, number of lateral branches, length of lateral branch and length of the main branch. Factor 2, which was called the seed characteristics, covered seed length, seed perimeter, seed area, the weight of 1000 seeds, and the number of seeds in the pod. Using FA, two sets of traits were identified and named in Camelina. The traits in one category that affected the attributes of the other category were selected to be studied to help Camelina breed more precisely. Entering more traits and performing FA increased the accuracy of the categories.

In this study, a comparative analysis of the vertebral column and the caudal skeleton of 245 specimens of 10 Aphanius and three Aphaniops species was conducted based on X-ray imaging, and interspecific variation of these characters was examined. The vertebral bending index showed that straight and almost straight vertebral columns were more common in Aphaniops than in the Aphanius species. The numbers of abdominal and caudal vertebrae, principal caudal fin rays, and principal rays supported by the hypural plate were significantly lower in Aphaniops than in Aphanius species. Those species of Aphanius which were found in higher latitudes or altitudes had more vertebrae than the remaining Aphanius species and all members of Aphaniops, revealing the role of environmental factors. The number of preural (PU) vertebrae and the width of neural and haemal spines of preural vertebrae 2-4 were significantly higher in Aphaniops than in the Aphanius species. The conspicuous variations detected among localities of A. arakensis highlight the importance of more profound studies on the diversity of this species. In the genus Aphaniops, 17% of specimens showed a straight epural bone and 83% showed a sinu soidal bone. In comparison, Aphanius species showed that 91% and 7% of specimens displayed straight and sinuous shape epural bone, respectively. Such intra-species polymorphism of the epural character state was first reported for Aphaniid species. Hence, the previously proposed synapomorphy for the genus Aphaniops based on sinu soidal epural bones may need further investigation.

RNA interference is a cellular process for regulating gene expression by double-stranded RNA (dsRNA). In the past two decades, this cellular process has been used as a tool for the temporary knockdown of gene expression to study gene function in reverse genetics studies. In this regard, double-stranded RNA has been made in various ways and used to knock down the corresponding gene. In the past decade, the potential of the technique for insect pest management has become clear although the costs associated with the production of dsRNA are not reasonable and affordable for such use. Even on the laboratory scale, making the dsRNA for RNAi experiments using dsRNA production kits is not affordable for most researchers and laboratories. Therefore, researchers are focused on ways to make the production of dsRNA more affordable. The conventional method of carrying out RNAi experiments uses a vector called pL4440 and a host strain of E. coli called HT115 (DE3) to make dsRNA. This method which is called bacterium-mediated RNAi (bmRNAi) has been used successfully for the knockdown of many genes in Caenorhabditis elegans. However, the number of studies that used this technique so far in insects is limited to a few major insect orders, namely Coleoptera, Lepidoptera, Diptera, and Hymenoptera. In this review, the bmRNAi technique is discussed in detail and the studies successfully conducted using this technique are introduced.

The chitinase enzymes are known to play an important role in the plant defense system against phytopathogenic fungi. The effect of chimeric chitinase, which is chitinase-42 with a chitin-binding domain (ChBD), was previously analyzed in the T0 generation of the transgenic canola. In this research, three homozygous lines (pGFC3, pGFC13, and pGFC26) containing a single copy of the transgene (chimeric chitinases) on the two homologous chromosomes were selected in the T2 generation using a kanamycin-resistant marker (NPTII gene). The selected homozygous plants in T2 generation were induced by chitin as an elicitor in the greenhouse. The results of the semi-quantitative RT-PCR, chitinase enzyme activity, and growth inhibition of phytopathogenic fungi demonstrated that the synthetic inducible promoter of transgenic plants was induced by chitin. The results of chitinase activity of extracted protein from all transgenic lines containing inducible promoters showed a 3.2-5.8-fold increase in chitinase activity compared to non-induced plants. The antifungal activity of the inducibly expressed chitinase was examined on Sclerotinia sclerotiorum and Rhizoctonia solani. The results showed that fungal growth inhibition increased via elicitor treatment of the inducible promoter, 82% for S. sclerotiorum and 62% for R. solani, respectively. The result of light microscopic observation demonstrated morphological changes in hyphae and that the expressed enzyme can lyse the mycelial cell walls of R. solani. Moreover, resistance to S. sclerotiorum in the intact leaves of transgenic plants (T2) was confirmed using bioassay analysis. Based on these results, it seems that the synthetic inducible promoter containing F cis-acting element driving chimeric chitinase is suitable for increasing the resistance of the canola transgenic plant when attacked by phytopathogenic fungi.

Recurrent spontaneous abortion (RSA) is one of the causes of infertility following fetus creation. This can lead to the reduction of the fertility rate in various populations. Collagens’ structure, their ratios to each other, and their connections to various receptors are some of the key players in successful fetus implantation. Among them, COL12A1 has a special role because of its very high expression in the uterus. Also, the CD44 protein as a cell adhesion molecule which is a receptor for some of the collagens plays a significant role in RSA. The aim of the study is to investigate the association of CD44-rs13347 and CoL12A1-rs970547 with RSA in a case-control base, and the impacts of COL12A1-rs970547 on protein structure. To genotype single nucleotide polymorphisms (SNPs) of the genes, the PCR-RFLP method was performed on the 124 RSA and 124 control samples. The results were analyzed by the binary-logistic regression method (p-value≤0.05). The SNPs’ effect on the proteins’ structure was analyzed by PSIPRED, HOPE, LOMET, and chimera-USF. Proteins signaling pathway and physical interaction between COL12A1 and CD44 were investigated by KEGG-pathway and GeneMANIA, respectively. Results showed that TT (P= 0.032) genotype of CD44-rs13347 increased the risk of RSA while the CT (P= 0.027) genotype of CD44-rs13347, TT (P= 0.044) genotype, and T (P= 0.019) mutant allele of COL12A1-rs970547 decreased the risk of RSA. Moreover, 3D structures investigation indicated that COL12A1-rs970547 may affect the structure of COL12A1 and its interaction with Integrins. The analysis of the signaling pathway and proteins’ physical interaction network also revealed the interaction of COL12A1 and CD44 with MMP2 and MMP9. On this base, we recommend that T allele of COL12A1-rs970547 has a protective feature against RSA, especially in homozygous form by improving their interaction with Integrins and probably MMPs, too. On the other hand, the CD44-rs13347 probably has an indirect influence on the attachment of the fetus to the extracellular matrix by affecting the MMPs and finally leading to a greater risk of RSA.

Human T-cell leukemia virus (HTLV) is a member of the retroviridae family that can be transmitted through infected lymphocytes, sex, blood transfusion, and organ transplantation as well as from mother to child by breastfeeding. It is estimated that nearly 15-20 million people have been infected with the virus worldwide. HTLV can cause malignant diseases such as adult T-cell leukemia (ATL), inflammatory diseases such as uveitis, HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), alveolitis, and infectious dermatitis. Iran is considered to be the country most infected with HTLV in Asia, after Japan. This study aimed to evaluate the serological prevalence of HTLV 1/2 infection in blood donors and thalassemia major and hemophilic patients in Rafsanjan and Jiroft cities of Kerman province. Sera were collected from 100 blood donors, 60 thalassemia major patients, and six hemophilic patients and tested for the presence of HTLV1/2 specific antibody using enzyme-linked immunosorbent assay (ELISA) and confirmed with Western blot and (real-time reverse transcription polymerase chain reaction) qRT-PCR techniques. The results of the ELISA test for Rafsanjan and Jiroft blood donors, as well as thalassemia and hemophilic patients in Rafsanjan, were negative but among thalassemia major patients of Jiroft, there was one positive case.  The results of Western blot and qRT-PCR tests were also positive. The number of provirus copies was, 3140750 per ml of the sample. Based on the findings of this study, the Kerman province is important in terms of the spread of the HTLV virus. According to the identification of infection in thalassemia patients in this province, it is recommended to investigate the incidence of this infection in other high-risk populations in this region.

Finding novel antimicrobials to treat drug-resistant Psudomonas aeruginosa is a major health challenge. In this study, ZnO nanoparticles functionalized by Thiosemicarbazone nanoparticles (ZnO@Glu-TSC NPs) were synthesized and the effect of the NPs alone and in combination with thymol on the expression of biofilm and efflux pump genes in P. aeruginosa was investigated. Physicochemical features of the ZnO@Glu-TSC NPs were evaluated by FT-IR, XRD, EDS-mapping, and SEM and TEM imaging. The inhibitory effect of ZnO@Glu-TSC NPs and thymol, alone and in combination, were determined by broth microdilution method, and quantitative PCR was used to evaluate the expression of the pelA, pslA, algD, mexA, mexB, and mexX genes. The synthesized NPs were almost spherical, without impurities, and in a size range of 20 to 60 nm. Simultaneous treatment of P. aeruginosa with ZnO@Glu-TSC and thymol had a significantly stronger inhibitory effect (MIC: 3.12-25.5 µg/mL) than either agent alone. The relative expression of the pelA, pslA, and algD genes in P. aeruginosa strains treated with ZnO@Glu-TSC+thymol was reduced by 0.44, 0.43, and 0.46 folds, respectively. Furthermore, the expression of mexA, mexB, and mexX genes decreased in P. aeruginosa strains treated with ZnO@Glu-TSC+thymol (0.42, 0.45, and 0.41 folds, respectively). Also, it was found that the combination of ZnO@Glu-TSC and thymol could synergically reduce the expression of the mentioned genes in comparison with either agent alone. This study showed that ZnO@Glu-TSC NPs and thymol synergically inhibited biofilm maturation and efflux pump systems in P. aeruginosa strains and could be considered a novel antibacterial candidate against P. aeruginosa strains.

Alfalfa, as a fodder plant in Hamedan, is attacked by alfalfa leaf weevil (Hypera postica Gell.). In this study, 76 alfalfa populations in the germplasm of Bu-Ali Sina University farm were investigated randomly. Traits SPAD, number of larvae, percentage of damage, height of the plant in the time of damage and harvest, percentage of dry matter, and traits of the dry and fresh yield of forage were studied in this research. The results showed that there is a correlation between the number of larvae trait and damage percentage (r = 0.733**), SPAD and damage percentage (r = 0.292*), forage yield and plant height at the time of damage (r = 0.512**), dry fodder yield and plant height at the time of damage (r = 0.314**), the yield of wet and dry fodder (r = 0.754), the percentage of dry matter with the yield of fodder (r = 0.316**), and the dry yield of fodder with the percentage of dry matter (r= 0.332**). Step-by-step regression for the wet yield of fodder as a function variable showed that traits of the dry yield of fodder, percentage of dry matter, and plant height in the damage stage were entered into the model, respectively, and justified the most changes in fodder performance with a cumulative explanation coefficient of 93.53%, while other studied traits had no significant effect on the model.  According to the entered traits (forage dry yield traits, dry matter percentage, and plant height in the damage stage) in the regression model, path analysis was done to determine causal relationships affecting. Path analysis of traits under study on wet forage yield revealed that it had the most direct and indirect effects on dry forage yield and matter percentage, respectively. This result was confirmed by the high correlation between wet fodder yield and dry fodder yield.

Cervical cancer is one of the most common malignancies and one of the main death causes among females all over the world. The discovery of tumor-related genes is crucial for understanding tumor biology and developing preventative and therapeutic strategies. However, genes included in the tumorigenesis of cervical cancer cells are still unclear. Due to its high prevalence and mortality, understating its pathogenesis and biomarker detection is necessary. The purpose of this study was to recognize potential biomarkers related to cervical cancer and analyze their prognostic significance. The present research used the level 3 mRNA expression data and clinical data of cervical cancer from The Cancer Genome Atlas database to identify differentially expressed genes followed by gene ontology. Weighted co-expression Network Analysis was used to construct scale-free gene co-expression networks. In the co-expression network, the hub module and hub genes were identified. The significant modules associated with T, N, M, and FIGO staging in the network were subsequently screened. Next, overlapping genes between significant gene modules and DEGs were screened. CALML5, TERT, PNPLA3, CHRDL1, C7, LEFTY2, and PCP4 were identified as hub genes. Survival analysis was performed to identify the association between these genes and survival using the GEPIA database. Survival analysis showed that PCP4 was slightly less expressed in patients with primary solid tumors than normal, and related to poor prognosis in cervical cancer. These results show that these hub genes, especially PCP4, may be a potential diagnostic biomarker for cervical cancer and provide a new perspective on the pathogenesis of cervical cancer.

Considering the importance of Caspian Sea sturgeon conservation according to CITES rules, finding effective and efficient methods for tracing and identifying sturgeon species are necessary. Residual DNA detection in fish ponds can be used as a model for tracing fish environmental DNA (eDNA) in rivers and seas. This method of DNA detection is non-invasive and advantageous for the conservation of critically endangered sturgeons. Sampling was done from the water of the Persian sturgeon fish pond and fixed with precipitation premix solution (ethanol and acetate sodium). DNA was extracted from fixed water, and fine tissue of two sturgeon species in the Caspian Sea, Sterlet, and Siberian sturgeon. The positive specificity of primers was checked by conventional PCR for sturgeons with fine tissue DNA samples. The linear relationship between the threshold cycle (ct) value and the Persian Sturgeon DNA concentration was measured by the Mini-Barcoding quantitative real-time PCR. DNA samples of fish ponds generated a curve that could not be produced in negative control and irrelevant (non-sturgeon) genomic DNA.  Although residual DNA of Persian sturgeons was detected in fish pond water at picogram level through the quantitative method, molecular diagnosis with this method can confirm only the existence of sturgeon species (in general) in fish ponds. In identifying residual DNA in the picogram level of the Persian sturgeon fish pond, SYBER Green real-time PCR method can be an acceptable method for barcoding with high efficiency compared to other methods such as conventional PCR method and non-invasive which is advantageous for the conservation of critically endangered sturgeons.