فهرست مطالب

Genetic Resources - Volume:5 Issue:2, 2019
  • Volume:5 Issue:2, 2019
  • تاریخ انتشار: 1398/04/10
  • تعداد عناوین: 9
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  • Kiarash Jamshidi Goharrizi, Farzane Amirmahani *, Foad Fatehi, Maryam Nazari, Sayyed Saeed Moosavi Pages 72-82
    Through the exponential development in the specification of sequences and structures of proteins by genome sequencing and structural genomics approaches, there is a growing demand for valid bioinformatics methods to define these proteins function. In this study, our objective is to identify the function of unknown proteins from UCB-1 pistachio rootstock and specify their classification using bioinformatics tools. In previous research, we recognized 5 HPs in proteomic profile of the University of California at Berkeley I pistachio rootstock leaf under salinity stress. Two of them had 2.95 and 2.29-fold up-regulation under salinity stress. In this study, the probable function and characterization of these HPs were recognized using different statistical methods and programs. According to our analyses, these HPs have similarities with reverse transcriptase enzyme as well as helicase enzyme and some responsive proteins to salt stress. These observations suggest a close relationship between the overexpression of these enzymes and plant responses to salinity stress. These stress-responsive proteins could provide a novel plant defense strategy in response to salinity.
    Keywords: Hypothetical protein, UCB-1 pistachio rootstock, Response to salinity, Reverse transcriptase enzyme
  • Reemana Fatema, Jamilur Rahman *, Habibul Shozib, Mohammad Nazrul, Kaniz Fatima Pages 83-96
    Considering the crucial focus on plant developments as high yielding, protein, and disease-resistant varieties, in this study, the genetic diversity and nutritional traits of available kidney bean germplasms found in Bangladesh have been evaluated based on seventeen quantitative and six nutritional traits. Analysis of genotypic, phenotypic variance and covariance showed that higher environmental influence was found in 1000-seed weight and seed yield/plant than other characters. High heritability was observed in dry weight (94.59%), leaf area (96.83%), days to 5 leaves stage (88.80%), number of leaves (87.38%) and number of pods per plant (87.32%), while high genetic advance was found in leaf area (59.46), 1000-seed weight (52.80), seed yield/plant (39.89). The genotypes were grouped in four clusters by diversity (D2) analysis where clusters I and III consisted of seven and one genotypes, respectively. Furthermore, highest inter and intracluster distance was found between Cluster I and Cluster III (23.742) and cluster IV (0.900) respectively. Principle component analysis revealed that days to 5- leaves stage, days to 1st flowering and days to 50% flowering were major characters contributing towards genetic diversity (74.8%) in Kidney bean. Analysis of nutritional traits showed that the germplasms of Sylhet region contained more carbohydrate (60.24-64.03%), fiber (2.08-2.46%) and ash (2.31-2.95%), whereas the germplasms of Bandarbanhad had more protein content (23.05-23.11%) than the released varieties used as control. In addition, the genotypes of the Sylhet region e.g. G6 (2.68t/ha), G5 (2.56 t/ha) and G4 (2.49 t/ha) showed maximum seed yield/ha. The results suggest that the germplasms of Sylhet and Bandarban could serve as valuable genetic resources to breed high yielding and super quality Kidney bean varieties.
    Keywords: Diversity, Heritability, Nutrient components, Kidney bean
  • Fatemeh Eskandari, Mohammad Ali Ebrahimi, Hamid Reza Naseri, Nasim Zarinpanjeh * Pages 97-103
    Ghar-e-Dagh (Nitraria schoberi) is a native perennial plant profoundly resistant to salinity and drought. This plant, having a well-developed deep rooting system can act as sand dunes stabilization agent and also, due to its special alkaloids may perform a very significant role in pharmaceutical industries. Considering the importance of genetic engineering as a novel method to generate genetic variation in practicing precise and purposeful breeding of plants in terms of increasing their resistance against biotic and abiotic stresses and also, to increase the production of specific secondary metabolites, the present investigation was performed as a prerequisite of any transformation. In this research, the issues of pre-culture time, co-culture time, acetosyringone and kanamycin concentrations were investigated. The results obtained suggest that the interaction of pre-culture and co-culture times and also, acetosyringone concentration is significant at 1% probability level. The mean comparisons also showed that the maximum transformation rate was gained in 48 hours pre-culture time, at 100 µM acetosyringone density and 72 hours co-culture. The ultimate confirmation of β- glucuronidase (GUS) gene presence in transgenic plants was performed by performing polymerase chain reaction (PCR) and reverse transcription PCR (RT-PCR) and histochemical assay. The method presented here can be used for further genetic engineering purposes of N. schoberi.
    Keywords: Nitraria schoberi, Agrobacterium, Acetosyringone, Pre-culture, Co-culture
  • Aniseh Noroozipoor, Mahnaz Aghdasi *, Hamid Reza Sadeghipour Pages 104-117
    Trehalose is a non-reducing sugar that plays an important role in plant growth and development. To study the role of trehalose on lipid metabolism and gluconeogenesis, Arabidopsis thaliana wild type (WT) and TreF (a line expressing trehalase) were grown on ½ MS medium with or without 100 mM sucrose and or trehalose in light or continuous darkness. In dark, trehalose leads skotomorphogenesis in WT seedlings and inhibits hypocotyl elongation without altering root growth. Then, a knock out mutant of icl (defective in isocitrate lyase/ICL) was identified in the SALK T-DNA insertion line, yet plants of this line were not altered with regard to growth on MS medium supplemented with or without trehalose in light condition, compared to WT. But the hypocotyl length of icl seedling was shorter than WT when grown on trehalose in darkness. The current data revealed that trehalose feeding altered seedling establishment in both WT and icl mutant. ICL enzyme activity measurement showed that the patterns of changes were similar in all treatments. Meanwhile, trehalose feeding reduced icl gene expression and enzyme activity. Trehalose fed seedlings demonstrated a high accumulation of total lipids in darkness. Also fatty acids level was higher in seedlings grown in darkness, compared with the light condition. Therefore, trehalose may inhibit lipid utilization by suppressing icl gene expression and enzyme activity and thus restrict the supply of carbon sources to the growing seedling. These observations confirm that trehalose regulates plant metabolism in both light and dark.
    Keywords: Darkness, Gluconeogenesis, Growth, icl mutant, Light, Trehalose
  • Fatemeh Aghighiravan, Majid Shokrpour *, Vahideh Nazeri, Mohammad Reza Naghavi Pages 118-129
    DNA barcoding is a simple method for the identification of any species using a short genetic sequence from a standard genome section. The present study aimed at examining the nuclear and chloroplast diversity as well as the phylogenetic relationships of eight species of saffron including four spring-flowering and five autumn-flowering species from different parts of Iran, using the nuclear barcode and chloroplast genes to specify their evolutionary pathway and to examine their genetic affinity. First, PCR was performed using the primers designed based on the chloroplast barcodes of matK, trnL, and rbcL, and nuclear barcode of ITS. Then, the PCR products were purified and sequenced. The results of the phylogenetic tree indicated that the examined saffron species of Iran were separated from each other based on the sequences of ITS, matK, and trnL barcodes. In the rbcL barcode, the relationships of a number of species remained unresolved, and this genetic region could not appropriately discriminate the species. The ITS barcode was introduced as the best barcode due to its discriminatory power, a high number of SNPs, and its comprehensiveness in most species. Moreover, the matK and trnL barcodes were identified as complementary barcodes. The use of the four genetic regions in comparison with their individual use has caused these species to be well separated. Overall, the obtained phylogram showed that the cultivated species were more similar to C. pallasii subsp. haussknechtii species.
    Keywords: Saffron, Wild species, PCR, Cluster Analysis, DNA marker
  • Shadi Riki, Mohammad Ali Sabokkhiz, Toktam Hajar, Madjid Momeni Moghaddam * Pages 130-135

    Galectin-1 and superoxide dismutase are two known molecules in the wound healing process that induce such healing by different mechanisms in the wound site. Larval therapy is one of the methods use by Lucilia sericata fly larvae, nowadays returned to the list of therapeutic methods despite chronic diabetic ulcers and antibiotic resistance of bacteria. In this study, we aimed to evaluate the effect of larvae extract on fibroblast cells to determine its role in the levels of Galectin-1 and superoxide dismutase proteins in fibroblast cells. To determine proteomic changes, 3T3 fibroblast cells were treated with larval extract, 3T3 fibroblast cells were cultured and divided into two groups after appropriate density. The first group was considered as control and the second group was treated with larvae extract at a concentration of 12.5 μg/ml. After 24 hours, the two-dimensional gel electrophoresis method for protein level and real-time PCR for gene expression studies were used. In 2D gel testing, three spots were successfully identified including galectin-1, superoxide dismutase, and glyceraldehyde-3-phosphate dehydrogenase. The expression of these three proteins was significantly increased in the cells treated with larvae extract compared to the control cells. Also, the quantitative expression of these genes was confirmed by real-time PCR. Finally, it was found that the treatment of fibroblast cells with larvae extract increased expression of galectin-1, superoxide dismutase and glyceraldehyde-3-phosphate dehydrogenase, which their positive effect on wound healing is well known.

    Keywords: Galectin 1, Superoxide dismutase, Wound healing, Fibroblasts, Lucilia sericata
  • Mehrnaz Riasat *, Sara Sadeghian Pages 136-142
    Chromosome information is an important key for taxonomy, phylogeny and genetic in Trifolium plants. Thus, ten Trifolium species namely T. grandiflorum, T. resupinatum, T. dasyurum, T. campestre, T. tomentosum, T. hirtum, T. scabrum, T. lappaceum, T. stellatum, and T. repens were collected from their habitats in Fars province based on their morphological characteristics to investigate their karyotypes. To analyze the karyology of samples, the fresh grown root tips were used. Then α-bromonaphtaline, formaldehyde and chromium trioxide (1:1), 1N NaOH and hematoxylin were used for pre-treatment, fixative, hydrolyzer and chromosome staining agent, respectively. We found the three usual basic chromosome numbers in the genus as x=5, x=7 and x=8. Nine species were diploid and T. repense was only tetraploid species (2n=4x=32). The detailed correlation coefficient was estimated for all paired combinations of the karyotypic characteristics to investigate their inter-relationships. Duncan’s test applied to the chromosome morphometric traits showed a highly significant difference among all examined species belongs to different sections.
    Keywords: Chromosome, Karyology, Iran, Papilionaceae, Trifolium
  • Sadegh Rajabi, Romina Dastmalchi, Mohammad Hossein Dehghan, Ali Eftekharian, Elmira Aghazadeh, Sayyed Mohammad Hossein Ghaderian * Pages 143-148
    Hereditary hearing loss (HHL) comprises half of the congenital deafness which arises from genetic mutations. Mutations in the TJP2 gene, encoding tight junction protein 2, are one of the gene alterations in HHL resulting in an autosomal dominant nonsyndromic form of the disease. An 11-year-old male patient with clinically approved congenital hearing loss was referred to our laboratory. The molecular genetic analysis detected an atypical heterozygous variant -c.1012G > C, p.G338R in exon 5 of the TJP2 gene on chromosome 9 position 71836379 (GRch37). Segregation analysis for his parents has uncovered the same mutation in the patient’s mother, but without any deafness phenotype. This case report provided evidence to demonstrate for the first time the incomplete penetrance of this TJP2 mutation and proposed this mutation as a “likely pathogenic” variant in an Iranian pedigree.
    Keywords: Hereditary hearing loss, Missense mutation, Incomplete penetrance, TJP2
  • Raziyeh Abdilzadeh, Mansour Aliabadian *, Urban Olsson Pages 149-162

    The largest genus in the Sylviidae family is Sylvia, which is the archetype for warblers. It contains up to 28 species that are distributed in the Old World. Here, we study Iranian Sylvia using cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) mitochondrial markers to identify them and place them in a phylogenetic context using all available GenBank samples of sufficient length. Bayesian trees for both cytb and cox1 mitochondrial markers are compatible. Previous results suggesting that the Sylvia curruca complex is separated into two major clades with high support are corroborated, as our results show two main clades, one that includes Sylvia atricapilla and Sylvia borin plus Pseudoalcippe atriceps and Lioptilus nigricapillus, and the remainder of the Sylvia species in the other one. Our study did not support the geographical groups: The West-Mediterranean group, the Central-Mediterranean group, and the East-Mediterranean or the African-European species, the African-Asian species, and the Mediterranean species inferred on molecular evidenced by previous studies. Sylvia cantillans is divided into three clades, corroborating previous studies. All Iranian samples were conclusively identified to species level, and none of them give rise to any further taxonomic inquiry.

    Keywords: cox1, cytb, phylogeny, songbirds