فهرست مطالب

Genetic Resources - Volume:7 Issue: 1, Winter-Spring 2021

Journal of Genetic Resources
Volume:7 Issue: 1, Winter-Spring 2021

  • تاریخ انتشار: 1400/02/08
  • تعداد عناوین: 12
  • Hao Lu, Alireza Asem, Yue Han, Muhan Li, Weidong Li *, Pei Zheng Wang Pages 1-14

    Coral Symbiodiniaceae and bacteria maintain a symbiotic relationship that is essential for coral survival. The symbiotic communities component in the polyps host could affect coral resistance and the ability to recover from stress. In this study, we increased the cultured range temperature (26 ± 1 ℃) of Sarcophyton trocheliophorum and Euphyllia ancora at 32 ℃ for 12 hours, and then amplified the ITS2 sequence of Symbiodinium and the bacterial 16S rRNA sequence in the sample, respectively to compare Symbiodiniaceae and bacteria diversity and abundance with normal culture temperature. The results showed that there was no change in the dominant species of Symbiodinium in these two corals in the heat treatment group, but the diversity of Symbiodinium in the two corals was significantly different. On the other hand, after thermal treatment, the endophytic bacteria of S. trocheliophorum represented more aerobic bacteria Delfitia, while the E. ancora was infected with more pathogenic endosymbiotic bacteria. This difference observation can be attributed to the different tolerance of corals.

    Keywords: Coral, Bacterial, Communities, Symbiodinium, ITS2 rDNA, 16s rRNA
  • Taghi Ghassemi Khademi *, Seyed Massoud Madjdzadeh, Rasoul Khosravi, Asadollah Asadi Pages 15-28

    Molecular data are powerful tools to resolve taxonomic problems. Each gene in each taxon shows a degree of variation through which we can understand phylogenetic relationships among different taxa. In this survey, the phylogenetic relationships within the tribe Bovini were reevaluated using 24 mitogenomes and cytochrome b (cytb), cytochrome c oxidase subunit 1 (cox1), 16S ribosomal RNA (16S rRNA), and NADH dehydrogenase subunit I (ND1) mitochondrial markers. We used all the gene sequences of extinct, domesticated, and wild species within the tribe Bovini. The phylogenetic trees were reconstructed using the maximum likelihood (ML) method. Based on the mitogenomes, the average base composition of mtDNA sequences was 27.1% T, 26% C, 33.5% A, and 13.4% G, showing a strong AT bias (60.6%). Our results revealed that the genus bison is not an independent taxon in the taxonomic rank of the genus and it is completely a paraphyletic taxon. Saola (Pseudoryx nghetinhensis) showed a sister relationship with other species belonging to the subtribe Bovina and it might be better to place this species within the subtribe Bovina. Also, in the mentioned subtribe, we distinguished three distinct monophyletic groups. In all of the phylogenetic trees, the subtribe Bubalina was a monophyletic taxon, and Syncerus caffer had a sister group relationship with other species belonging to the genus Bubalus. The obtained data should be taken into consideration in future conservation efforts for this tribe.

    Keywords: Bovini, Genes, Molecular assessment, mtDNA, phylogeny
  • Akram Rajabi Mazaher, Seied Mehdi Miri *, Abdollah Mohammadi Pages 29-35

    The somatic chromosome numbers and karyotype features of seven populations representing three species of Stachys L. (Lamiaceae), which are naturally distributed across Iran, were described. The results confirm the presence of different basic chromosome numbers including x = 15 and 17 within the genus. All the studied taxa were diploid and the chromosome counts of two species including S. benthamiana and S. setifera (2n = 34) are reported for the first time, while the chromosome number of S. byzantina (2n = 30) is confirmed. The chromosomes in the studied taxa of Stachys were generally small, as the longest chromosome length was detected on S. setifera (18713) (2.26 μm), whereas S. setifera (23354) demonstrated the shortest length (1.46 μm). The karyotypes were symmetrical composing of metacentric chromosomes as indicated by their mean arm ratio (AR) that ranged between 1.11 in S. setifera (23354) and 1.29 in S. byzantina (37985), so it was classified as class 1A according to Stebbins’ categories. Based on the values of total form percentage (TF%, 47.1%), Arano index of karyotype asymmetry (AsK%, 52.5%), symmetry index (S%, 94.0%) and differences of range relative length (DRL, 0.36), S. setifera (23354) had the most inter-and intra-chromosomal symmetric karyotype. Also, S. byzantina (37985) had the most inter-and intra-chromosomal asymmetric karyotype based on the values of TF% (42.0%), AsK% (56.1%), and relative length of chromosome (RL%, 6.6%). The results of cluster analysis based on chromosomal parameters divided the taxa into two main groups using the Ward method. Group I included taxa with x = 17 and group II contained S. byzantina (x = 15).

    Keywords: Asymmetry index, Chromosome numbers, Karyotype, Stachys
  • Dabasa Wario *, Yosef Tadesse, Shashi Bhushan Singh Yadav Pages 36-48

    This study was conducted in two districts of Borena zone (Ethiopia), with the objectives to characterize phenotypically the indigenous chicken types in the study sites. The study involved both qualitative and quantitative types of research. A total of 480 chickens (144 male and 336 female) aged more than 6 months for the quantitative study were considered in this study. Descriptive statistics, frequency procedures, general linear model, univariate and multivariate analysis were used with SAS 9.1.3 to analyze the data. SPSS package was used to analyze qualitative data. Qualitative traits such as plumage color, comb type, shank color, eye, earlobe color, and skin color were used for the study. Quantitative traits included: body weight and linear morphometric measurements such as shank length, body length, wattle length, wingspan, chest circumference, comb width, and comb length. The result of this study revealed that white, red, and brown plumage color was dominated in the study area. The local chickens possessed variants in shank color, skin color, comb type, and eye color. White shanks, white skin, single combs, and red earlobe color were predominately seen across both the study districts. The mean body weights of indigenous male and female chickens were 1.623± 0.229 kg and 1.313 ± 0.81 kg, respectively. Large comb, wattle, and long legs were observed in the study areas. Generally, morphological and morphometric variations were observed between and within the indigenous chicken populations, which suggests that there is an opportunity for genetic improvement through selection.

    Keywords: Borena zone, Characterization, Morphological trait, Morphometric traits, Multivariate, Plumage, Scavenging, Univariate
  • Maryam Zali Benekohal, Parinaz Ghadam *, Sara Gharavi, Ahya Abdi Ali, Firoozeh Piroozmand Pages 49-58

    P. aeruginosa is an opportunistic bacterium that produces a capsule-like polysaccharide called alginate in response to various stimuli. The mucoid strain of Pseudomonas aeruginosa produces alginate which is an exopolysaccharide and is involved in the pathogenicity and persistence of these bacteria in infections. The alginate lyase gene is required for alginate synthesis. The enzyme can also degrade this polymer. This enzyme has a polymorphism in different bacteria even in one species and finding an enzyme with tremendous characters is very important. In this study, alginate lyase from P. aeruginosa strain 293 which was previously isolated from the sputum, and the encoding gene was characterized, and thermal and pH stability, as well as the substrate specificity of the partially purified alginate lyase, were determined. The amount of 70% activity of the enzyme was maintained after incubation at 80 ˚C for 6 hrs and 50% activity retained after incubation in alkaline and acidic pH. Moreover, it showed activity towards guluronic acid blocks, mannuronic acid blocks, and alginate blocks with both of them. Due to the unique properties of the alginate lyase that are useful in medicinal, and industrial applications, the gene encoding the enzyme was expressed in pET-28a (+)/E. coli BL21 (DE3) system to produce 371 -amino acid alginate lyase protein, the molecular weight of which was estimated by Sodium Dodecyl Sulfate- Polyacrylamide gel electrophoresis to be about 40 kDa. Bioinformatic analysis of P. aeruginosa strain 293 algL gene revealed that G225A point mutation can improve its thermostability. Therefore, the P. aeruginosa 293 alginate lyase is proposed as an appropriate candidate for the evaluation of potential therapeutic and industrial applications.

    Keywords: Alginase, AlgL, computational study, pH stability, thermostability
  • Farshad Mohammadzadeh Gharegheshlagh, Arman Mahmoudi Otaghvari *, Habib Zare, Tahereh A. Aghajanzadeh Pages 59-71

    Bryophytes are small, non-vascular, and non-flowering plants. Neckera complanata (Hedw.) Huebener and Neckera crispa Hedew.are one of the most prominent species in the Hyrcanian wetland found in glossy pale or yellowish-green patches. There is no evidence for morphometry and isoenzymes biochemical markers (Peroxidase/Superoxide dismutase) works on this genus in Iran. The purpose of this study is to investigate the differences and similarities among Neckera complanata and Neckera crispa moss populations in the north of Iran using morphometry and isoenzymes biochemical markers (Peroxidase / Superoxide dismutase). For this purpose, 18 populations from three provinces including Golestan, Mazandaran, and Guilan were collected at the same altitudes in autumn 2017. The results of morphometry were shown leaf length and leaf apex width/length were the most effective traits for the separation of populations. The results of the morphometry method and the results of isozyme banding patterns were the same, although very minor differences were observed. The largest diversity of Shannon (H́) belongs to the population of Neckera crispa from Hezarjarib while other populations have low genetic diversity. Because of the destruction of many habitats in the northern provinces of Iran and the increase in pollution in these areas, it can be said as a general result that perhaps the reason for low genetic diversity in Neckera complanata and Neckera crispa populations is the gradual extinction of these two species.

    Keywords: Mosses, Neckera, Peroxidase, Superoxide dismutase, Numerical Taxonomy
  • Somayyeh Makhtoum, Hossein Sabouri *, Abdollatif Gholizadeh, Leila Ahangar, Mahnaz Katouzi Pages 72-86

    Chlorophyll fluorescence is one of the very useful techniques in plant physiology because of the ease with which the user can gain detailed information on the state of photosystem II (PSII) at a relatively low cost. Detection of quantitative traits loci related to chlorophyll fluorescence have a major role in understanding the genetic mechanisms of photosynthesis. In the present research, to mapping, the genome regions controlling chlorophyll fluorescence traits, barley (Hordeum vulgare L) from 106 F8 recombinant inbred lines caused by crossing two cultivars of Badia × Kavir was used and these lines were cultured in a complementary randomized design with two replications. Traits studied include ABS/CSo, TRo/CSo, DIo/CSo, ABS/CSm, DIo/CSm, psi (Eo), TRo/RC, REo/RC, ABS/RC, DIo/RC, Area, Fv/Fm, Sm. Linkage maps were prepared using 152 SSR polymorphic markers, 72 ISSR, 7 IRAP, 29 CAAT, 27 Scot, and 15 iPBS alleles. Molecular markers were assigned on 7 chromosomes of barley. The linkage map covered 999.2 cM of the barley genome and the average distance between two flanking markers was 3.387 cM. Three major QTLs were identified for Area, psi (Eo), and Dio/Rc on Chromosome 6 between ISSR31-1-Bmag0867 in position 62 Centimorgan that explained 17.2%, 31.5%, and 15.9%, respectively. Also, another colocation was detected for ABS/CSo, TRo/CSo, ABS/CSm, and DIo/CSm QTLs on chromosome 6 in position 72 Centimorgan. The results obtained in the present research provide valuable information on the genetic basis of the Chlorophyll fluorescence parameters that can be used in the barley breeding program, including marker-assisted selection.

    Keywords: Barley, Hordeum vulgare L, Chlorophyll fluorescence, Molecular markers, QTL
  • Mohammad Sanei, Azim Ghasemnezhad *, Alireza Sadeghi Mahounak, Mohammad Masoumi, Khalil Ghorbani Pages 87-105

    Recently, the beneficial effects of the plants' secondary compounds for the treatment and improvement of diseases have been strongly interested. This study was conducted in a completely randomized design with three replications in the Paveh and Ormanat region of Kermanshah province. For this purpose, after studying the flora of the region, 10 high-widespread families (Apiaceae, Boraginaceae, Lamiaceae, Rosaceae, Solanaceae, Polygonaceae, Fabaceae, Brassicaceae, Liliaceae, and Asteraceae) were selected. In each case, three plant species with three replications were identified and randomly collected during flowering from April to September. Antioxidant potentials of the samples were evaluated by four methods of DPPH, FRAP, ABTS, and TAC. Results of analysis of variance showed significant differences between measured traits in plant species as well as plant family with 99% confidence. Among the studied plants, Pimpinella kotschyana Boiss. from Apiaceae, Bellevalia dichroa Hausskn. from Liliaceae, Muscari neglectum Guss, from Liliaceae showed the highest antioxidant activities using different methods. Results also showed that among the studied plant families, Liliaceae, Rosaceae, Brassicaceae, and Asteraceae showed considerable antioxidant potential and could be noticed in future research.

    Keywords: ABTS, DPPH, FRAP, Kermanshah, Kurdistan, Phenols, TAC
  • Fereshteh Morteza, Sevil Nematollahi *, Davoud Koolivand Pages 106-115

    Cucurbit crops belonging to the family Cucurbitaceae are one the most important horticultural crops worldwide and cultivated widely in Iran. To aim detection and phylogenetic analysis of potyvirus members, during 2015-2016, 215 leaf samples from cucumber, melon, watermelon, and squash symptomatic with deforming and reduction in leaf size, blistering, mild and severe mosaic, fruit deformation, and stunting were collected from 10 major cucurbits-growing locations in West Azerbaijan province. Following mechanical inoculation of Cucurbita pepo as an indicator plant with symptomatic cucurbit crop extracts, a variety of symptoms developed on the plants. Then, total RNA extracted from 70 symptomatic leaf samples, and partial RNA-dependent RNA polymerase (NIb) (350 bp) was amplified using universal primer pairs (NIb2F/NIb3R) by reverse transcription-polymerase chain reaction (RT-PCR). The infection by potyviruses in 38.75% of the samples was confirmed based on the result. The five PCR products belonging to different hosts at the expected size (350bp) were sequenced. One sample (Ir-Na: MH491979) was determined to be infected by the Watermelon mosaic virus (WMV) whereas four samples (Ir-Ma:MH491979, Ir-Ng:MH491980, Ir-Pi:MH491981, and Ir-Ur:MH491982) infected by Zucchini yellow mosaic virus (ZYMV). In the phylogenetic analysis based on Maximum-likelihood, three ZYMV isolates (Ir-Ng, Ir-Pi, and Ir-Ur) were placed in subgroup I whereas one isolate (Ir-Ma) was placed in subgroup II belonging to group A. Also, WMV isolate (Ir- Na) was placed in CL phylogroup.

    Keywords: Detection, Universal primer, WMV, ZYMV
  • Shiva Shiehbeiki, Mostafa Motallebi *, Mohammad Zamani, Esmat Jourabchi Pages 116-124

    Defensins are a superfamily of antimicrobial peptides that can inhibit the growth of a broad spectrum of fungi. To evaluate the antifungal activity of Tfgd2 gene of Trigonella foenum graecum, the coding region of this gene in the cDNA form was subcloned in the expression vector pET26b (+) and the construct was designated as pETSH1. The obtained construct expressing the recombinant protein with a hexahistidine tag at the C-terminal end transformed into the E. coli BL21 (DE3). Taguchi test applied for optimizing the protein expression and the expressed protein TFGD2 confirmed by SDS-PAGE and western blotting. The recombinant TFGD2 protein was purified using affinity chromatography with a Ni-NTA column. In vitro assay indicated a broad spectrum of antifungal activity of purified expressed recombinant TFGD2 against different fungal phytopathogens, such as Fusarium oxysporum, Rhizoctonia solani, Sclerotinia sclerotiorum, Alternaria solani, and Verticillium dahliae.

    Keywords: Antifungal activity, Defensin, SYTOX Green, TFGD2, Pathogenesis-related protein
  • Mohammad Khalaj Kondori *, Mina Khajehdehi, Zeinab Shaghaghi Torkdari Pages 125-132

    Alzheimer's disease (AD) is a multifactorial disorder that its progress and development are related to various genetic and environmental factors. The disease onset is affected by both genetic and environmental factors such as oxidative stress, inflammation, and mitochondrial dysfunction, and is remarkably related to age progress. Aluminum, a neurotoxic environmental factor, impairs memory performance and can cause neurodegenerative diseases such as AD. On the other hand, the regulatory RNA-binding product of Fragile X mental retardation (FMR1) gene exerts a translational inhibitory effect on the expression of amyloid precursor protein (APP), the main culprit in AD development. In the present study, we treated AlCl3-induced Alzheimer’s disease model rats with Frankincense and investigated its protective and therapeutic effects on the AlCl3-induced memory disturbance by behavioral and molecular assays. Also, Rivastigmine was used as a standard control. Morris Water Maze (MWM) was used to assay special memory working of the rats and quantitative real-time PCR (qRT-PCR) was applied to investigate the expression profile of the FMR1 gene in the hippocampus of the treated rats. MWM behavioral tests indicated that both Frankincense and Rivastigmine not only may prevent AlCl3-induced memory impairment but also may alleviate the memory declines induced by AlCl3 in the rats. Expression analysis showed significant upregulation of the FMR1 gene in response to both Frankincense and Rivastigmin treatments. Further, qRT-PCR results revealed that the AlCl3-induced downregulation of the FMR1 gene expression could significantly be reversed by both Frankincense and Rivastigmine, though Rivastigmine was more effective than Frankincense. In conclusion, our results highlighted that Frankincense might be effective both in the prevention and treatment of memory impairments, to some extent, by affecting the FMR1 gene expression.

    Keywords: Alzheimer's disease, Frankincense, Morris Water Maze, Rivastigmine
  • Abiola Ajayi *, Alaba Gbadamosi, Victor Olumekun, Idowu Omotuyi Pages 133-143

    Drought significantly reduces cowpea productivity. Information on genetic variation for differential expression of candidate genes for drought tolerance among cowpea genotypes, from which improvement plan could be drawn is limited in Nigeria. Variability of expression of the candidate gene NCED1 in cowpea was analyzed under different drought stress conditions. Primers based on NCED1 and P-Actin (used as an internal control) successfully amplified products from both stressed and unstressed accessions of cowpea. Contradictory responses were observed among drought-tolerant (mean STI > 0.57) and susceptible accessions (mean STI ˂ 0.57). NCED1 was significantly repressed by drought stress in all accessions, except in AC10, AC11, AC13 (tolerant accessions), and AC12 (susceptible accession). The results from stressed and unstressed conditions confirmed that the gene is expressed in both conditions. Biplot divided the accessions into four major groups, with most of the tolerant accessions in groups I and II, while most of the susceptible accessions occupied III and IV. Tolerant accessions such as AC22, AC15, AC23, AC13, AC10, AC11, and AC21 that combined higher plant height and dry root weight under drought stress with stress tolerance indices (STIs) possessed higher gene expression under both control and drought stress conditions. Therefore, positive correlations between the expression of the gene in both conditions and plant height under stress, on one hand, dry root weight under stress on the other hand, and the STIs confirm that its expression may be involved in drought tolerance of cowpea. Hence, the selection of cowpea based on higher levels of gene expression among accessions under both conditions may be effective for breeding drought-tolerant cowpea.

    Keywords: Drought stress, Cowpea, PCR products, Primers, Variability