@article{ author = {}, title = {Construction of high density linkage map in spring bread wheat recombinant inbred lines using genotyping by sequencing (GBS) method}, abstract ={High density linkage maps are essential for precise mapping of gene loci controlling quantitative traits. In the present study, a high density linkage map of spring wheat recombinant inbred lines population derived from a cross between Yecora Rojo and No. 49 was constructed using genotyping by sequencing (GBS) method. To identify single nucleotide polymorphisms (SNPs), sequencing of parents and recombinant inbred lines was carried out at three lanes of Illumina Hiseq 2500. In total, more than 36 thousand SNP were identified of which 804 SNPs were not aligned to any wheat chromosome. Among these SNPs, 3042, 3977 and 769 SNPs were belonged to A, B and D sub genomes, respectively. After removing SNPs with ≥20% missing data and minimum allele frequency ≤0.05 as well as loci segregating from 1:1 Mendelian ratio, in total 5831 polymorphic SNPs identified and assigned to 21 chromosomes of wheat. These markers spanned 3642.14 cM of the wheat genome with an average marker density of 0.62 (markers/cM).  }, Keywords = {Genotyping by Sequencing (GBS), Linkage map, Single Nucleotide Polymorphism, Wheat}, volume = {14}, Number = {4}, pages = {281-290}, publisher = {Genetics Society}, url = {http://mg.genetics.ir/article-1-130-en.html}, eprint = {http://mg.genetics.ir/article-1-130-en.pdf}, journal = {فصلنامه علمی ژنتیک نوین}, issn = {2008-4439}, eissn = {2008-4439}, year = {2020} } @article{ author = {Latifi, N. and HashemzadehSegherloo, I. and Sheikh, Y. and Ashrafzadeh, M. and Rahimi, R.}, title = {Genetic Barcoding of fishes in Chahnimeh-ha, Zabol, Iran}, abstract ={Due to drought during the recent years, the Hamoon wetland has become unstable and hence Chah-nimeh water reservoirs of Zabol (Sistan, Iran) have become increasingly important for aquatic life. Hence, it is necessary to identify biodiversity of fish in Chah-nimeh reservoirs to provide baseline data for management and conservation purposes. In order to identify and DNA barcode fish species in Chah-nimeh reservoirs, fish specimens were collected during 2017. Totally, 29 specimens belonging to Schizothorax zarudnyi, Carassius sp., Paracobitis rhadianaeus, Ctenopharingodon idella, Gonorhynchus adiscus, Cyprinus carpio, Schizocypris altidorsalis were collected. To perform phylogenetic analyzes 5’ end sequence of gene COI were produced. For phylogenetic analysis Neighbor-Joining and Maximum likelihood methods were used. The results resolved six phylogenetic groups among the analyzed specimens. Accordingly, the maximum genetic divergence was 27.1% between P. rhadinaeus and C. idella and the minimum genetic divergence was 10.8% between C. carpio and S. zarudnyi.  }, Keywords = {DNA barcoding, Chah-nimeh, Zabol, Fish, Phylogenetics, COI}, volume = {14}, Number = {4}, pages = {291-296}, publisher = {Genetics Society}, url = {http://mg.genetics.ir/article-1-97-en.html}, eprint = {http://mg.genetics.ir/article-1-97-en.pdf}, journal = {فصلنامه علمی ژنتیک نوین}, issn = {2008-4439}, eissn = {2008-4439}, year = {2020} } @article{ author = {}, title = {Transgenic cotton expressing synthesized antifungal NaD1 gene confers enhanced resistance to fusarium wilt and verticillium wilt}, abstract ={ Cotton (Gossypium hirsutumL.) is one of the most significant cash crops as it is the backbone of the global textile industry. Although conventional breeding is already being used to solve the problems related to cotton, there is a rampant reduction in the yield and quality of cotton due to insect pests and fungal pathogens. The diseases that pose the major threat to cotton production are Fusarium and Verticillium wilts. NaD1, a plant defense protein from Nicotian aalata, was found to have effective antifungal activity against many filamentous fungi including two of the major cotton pathogens, Fusarium oxysporum f. sp. Vasinfectum (Fov) and Verticillium dahlia. In the present study synthetic Nicotiana alata Defense 1 (NaD1) gene, under the control of a CaMV 35S constitutive promoter, was transferred  into cotton, the transformation of shoot tip explants was achieved via Agrobacterium tumefaciens LBA4404. PCR and RT-PCR analyses showed that NaD1 was successfully incorporated into the cotton genome and expressed in transgenic lines. Comparing to the wildtype, NaD1-transgene cotton plants showed enhanced protection against V. dahlia. The success of this work may act as a stepping stone in the development of new cotton cultivars with improved fungal disease resistance and thus can play a major role in reducing loss due to the widely prevalent fungal diseases in cotton.  }, Keywords = {NaD1gene, Cotton, Verticillium dahlia, Fusarium oxysporum, Agrobacterium tumefaciens}, volume = {14}, Number = {4}, pages = {297-308}, publisher = {Genetics Society}, url = {http://mg.genetics.ir/article-1-116-en.html}, eprint = {http://mg.genetics.ir/article-1-116-en.pdf}, journal = {فصلنامه علمی ژنتیک نوین}, issn = {2008-4439}, eissn = {2008-4439}, year = {2020} } @article{ author = {}, title = {Effect of water stress on expression level of MTNAF, MTNAC and GMAC genes in lentil (Lens culinaris M.)}, abstract ={Iran with rainfall of 240 mm per year belongs to arid and semi-arid regions of the world. Lentil (Lens culinaris M.) is one of the most important legumes around the world. In this study, levels of water stress (including irrigation up to 50% of field capacity and 25% of field capacity) for 7 days were applied on lentil seedlings in a completely randomized design with three replications in greenhouse. After treatment, shoots and roots were harvested and the expression of NAC genes was analyzed using qRT-PCR method. The expression analysis of NAC genes was performed in three biological and two technical replications. The means comparison by Duncan test showed a significant difference among all three gene expressions in the aboveground tissues. The GmNAC expression was significant in both treatments, but for MtNAC and MfNAC genes, significant differences were observed in 25% stress condition compared to control. Although MfNAC expression increased in both shoots and roots, the expression in shoot was much higher than root. In roots, significant differences were observed in 25% stress condition comparing to control. In shoots, expression of MtNAC gene was significantly increased in both stress treatments and in roots, only treatment 25% showed a significant difference with control. The increase in expression in the roots was less than shoot. In shoots, expression of GmNAC gene in the treatment of 50% was higher than treatment of 25% but the increase in expression in the root was same in both stress treatments. In general, MtNAC and MfNAC genes appear to be more important in the shoot. The current study is the first report of expression analysis of MfNAC, MtNAC and GmNAC genes in lentil under water stress conditions.  }, Keywords = {Drought stress, lentil, NAC gene, qRT-PCR}, volume = {14}, Number = {4}, pages = {309-318}, publisher = {Genetics Society}, url = {http://mg.genetics.ir/article-1-96-en.html}, eprint = {http://mg.genetics.ir/article-1-96-en.pdf}, journal = {فصلنامه علمی ژنتیک نوین}, issn = {2008-4439}, eissn = {2008-4439}, year = {2020} } @article{ author = {}, title = {Detection of polymorphism in IGF-I gene and its association with condition factor in the Persian sturgeon fish (Acipencer persicus)}, abstract ={The goal of this study was to detect polymorphisms in Insulin like growth factor-I gene of Persian sturgeon fish (Acipencer persicus) using PCR-SSCP technique and also to investigate their association with fish growth traits (condition factor, body length & weight). In this research, 95 Persian sturgeons were randomly selected and fin clip for DNA extraction were taken from caudal fin. DNA was extracted using modified salting out method and two fragments of 171 and 362 bp in 5/-UTR and 3/-UTR regions of IGF-I gene were amplified, respectively. Genotyping of individuals showed three different banding patterns of M, K and G for the fragment of 171 and 362 bp with the frequency of 13, 39, 48 and 31, 49, 20 percent in Persian sturgeon samples, respectively. The genotype K at 3/-UTR and genotype M at 5/-UTR marker site were the most frequent genotypes. Marker-trait analysis using SAS statistical software indicated no significant association between observed banding patterns of marker loci and growth traits in Persian sturgeon. Considering the important role of IGF-I as a probable candidate gene effective on growth related traits, survey of this marker sites are recommended for larger-size populations  }, Keywords = {Persian sturgeon, Polymorphism, PCR-SSCP, 3/-UTR, 5/-UTR, Acipencer persicus}, volume = {14}, Number = {4}, pages = {319-326}, publisher = {Genetics Society}, url = {http://mg.genetics.ir/article-1-118-en.html}, eprint = {http://mg.genetics.ir/article-1-118-en.pdf}, journal = {فصلنامه علمی ژنتیک نوین}, issn = {2008-4439}, eissn = {2008-4439}, year = {2020} } @article{ author = {Vosoughi, Najmeh and Gomarian, Masoud and GhasemiPirbalouti, Abdollah and Khaghani, Shahab and Malekpoor, Fatemeh}, title = {The effects of water deficit stress and chitosan on cineole synthase gene expression and 1,8-cineole content in sage (Salvia officinalis)}, abstract ={Common sage (Salvia officinalis) is one of the most important medicinal and aromatic plants and possesses anticancer, antioxidant and antimicrobial properties. One of the essential oil components of the sage plant is monoterpene, 1,8-cineole, that is responsible for some of these effects. The effect of foliar application of chitosan (control, 0.0, 0.25 and 0.50 g/L) under different levels of water deficit (FC = 60, 75 and 100%) were investigated on the expression level of cineole synthase gene in the roots and accumulation of 1,8-cineole content in the leaves of the sage plants. The experiment was conducted as factorial based on completely randomized design with three replications. The level of gene expression was determined by real time PCR in plant roots and the 1,8-cineole content was identified by gas chromatography/mass spectrometry in leaves. Results indicated that the expression of studied gene and 1,8-cineole content were strongly up-regulated with water deficit. Furthermore, foliar application of chitosan (specially in 0.5 g/L) effectively up-regulated the cineole synthase gene expression in roots and 1,8-cineole content in the shoots. Overall, water deficit stress was more effective than chitosan in the up regulation of cineole synthase gene and 1,8-cineole synthase content. The maximum level of cineole synthase gene expression and 1,8-cineole content were observed in mild drought stress and 0.5 g/L chitosan condition. Slight water deficit stress had no effect on gene expression but the final product was increased in shoots. For the first time, our results indicated that water deficit stress and chitosan could increase cineole synthase gene expression in the roots of common sage. Therefore, chitosan along with water deficit probably increase 1,8-cineole content in shoots, in part, through increasing the expression level of 1,8-cineole synthase gene in roots.   }, Keywords = {Essential oil, GC-MS, Monoterpene, real time PCR}, volume = {14}, Number = {4}, pages = {327-336}, publisher = {Genetics Society}, url = {http://mg.genetics.ir/article-1-125-en.html}, eprint = {http://mg.genetics.ir/article-1-125-en.pdf}, journal = {فصلنامه علمی ژنتیک نوین}, issn = {2008-4439}, eissn = {2008-4439}, year = {2020} } @article{ author = {}, title = {Genetic structure and assignment tests of Kurdish horse based on microsatellite markers}, abstract ={As the progress of molecular genetics techniques, it is now possible to determine the relationship between individuals and their evolutionary process. In this study, the genetic structure and assignment test of Kurdish horses breed to its origin or Arab and Turkmen horses breed were investigated using 12 microsatellite markers recommended by the International Society for Animal Genetics (ISAG). For this purpose, blood samples from 238 Kurd, 36 Arab and 30 Turkmen horses were taken in their distribution areas. DNA was extracted from Blood samples by the salting-out method. DNA fragments were amplified by multiplex PCR reaction using fluorescently labeled primers and determined by capillary electrophoresis. The mean of observed and effective alleles for all markers was 9.9 and 4.71, respectively. The highest and lowest expected heterozygosity was obtained for ASB17 (0.83) and HTG4 (0.71) markers, respectively. Cluster analysis using the UPGMA method and the Dice coefficient differentiated each breed. The result of the Bayesian Assignment test showed that all individuals correctly assigned to its population, so it seems that these markers are useful for the assignment test. Overall, the results of this study showed that the microsatellite markers used in this study showed high genetic diversity, so the use of these markers for genetic diversity study and assignment test of the Kurdish horse is recommended. So, these markers can be used to determine the exact origin of the Kurdish horse breed and eliminated the non-purebred horses from the reproductive process.  }, Keywords = {Assignment test, Genetic diversity, Kurdish horses, Microsatellite markers.}, volume = {14}, Number = {4}, pages = {337-344}, publisher = {Genetics Society}, url = {http://mg.genetics.ir/article-1-115-en.html}, eprint = {http://mg.genetics.ir/article-1-115-en.pdf}, journal = {فصلنامه علمی ژنتیک نوین}, issn = {2008-4439}, eissn = {2008-4439}, year = {2020} } @article{ author = {KIANI, SOGHRA and shiran, behroz and ahmadi, jafar and fallahi, hossien and fabrikiourang, sedegheh}, title = {Study of proline accumulation and gene expression of P5CS at vegetative and flowering stages of Dracocephalum kotschyi under drought stress}, abstract ={Dracochephalum kotschyi is an endemic medicinal plant in iran belonging to Lamiaceae family known as Zarin-Giah. Under osmotic stresses, proline accumulation is an important response of plants to these conditions. Proline is a compatible osmolyte which affects many cellular and molecular aspects of a plant in both normal and stressful situations. Proline is shown to be involved in plant development in normal conditions and in conferring resistance to a plant under biotic and abiotic stresses. Δ1-pyrroline-5-carboxylate synthetase )P5CS), one of the two main enzymes in the proline biosynthesis pathway of the glutamate precursor, has been demonstrated to play a significant role in proline accumulation in plants under drought stresses. In this research, the effect of different levels of drought stress was investigated on the relative water content, chlorophyll content, proline accumulation and P5CS gene expression in Dracocephalum kotschyi at two growth stages. This experiment was conducted as a factorial experiment with two factors including drought stress and growth stages in a completely randomized design with three replications. Drought stress treatments includes severe (25% FC), moderate (50% FC), low (75%FC) drought stress and control (100%FC). Growth stage includes vegetative and flowering stages. Analysis of variance showed that drought stress significantly increased P5CS gene expression and proline content while decreased chlorophyll a, b, total and relative water content. The highest expression level of P5CS gene and maximum amount of proline were observed at flowering stage under moderate drought stress (50% FC) conditions.}, Keywords = {Dracocephalum kotschyi, Drought stress, P5CS, Proline, Zarrin-giah}, volume = {14}, Number = {4}, pages = {345-356}, publisher = {Genetics Society}, url = {http://mg.genetics.ir/article-1-123-en.html}, eprint = {http://mg.genetics.ir/article-1-123-en.pdf}, journal = {فصلنامه علمی ژنتیک نوین}, issn = {2008-4439}, eissn = {2008-4439}, year = {2020} } @article{ author = {}, title = {Comparative Evaluation of Boosting, SS-GBLUP, SS-BayesA Methods: Consideration of Genomic Data Imputation}, abstract ={Recently, single-step approaches were proposed to overcome the genotyping limitation for some animals. Having considered high genomic performance and utilizing both genotyped and nongenotyped animals, single-step genomic prediction models became the prevailing tool in genetic evaluations of livestock. The objective of current study was to investigate the role of genetic relationships between the training and validation populations and different genomic architecture with simulated genomic data imputation on performance of Boosting, single-step genomic best linear unbiased prediction (SS-GBLUP) and single-step BayesA (SS-BayesA) methods. For this purpose, genomic populations were simulated to reflect variations in number of QTL (10, 100 and 1000) for 29 chromosomes. To simulate a real condition, we randomly masked markers with 70% missing rate for each scenario; afterwards, hidden markers were imputed using FImpute software, and imputation accuracy was estimated. To estimate genomic breeding values, Boosting, SS-GBLUP and SS-BayesA methods were applied for original and imputed genotypes during G1 and G3 generations. According to results, GEBV accuracy was influenced by the relationships between the training and validation populations for ungenotyped animals higher than genotyped ones in both original and imputed genotypes. In both original and imputed genotypes, Boosting model showed the lowest accuracy for genotyped animals. SS-GBLUP method showed an obvious advantage over SS-BayesA and Boosting methods with the scenarios of high QTL. Generally, the relationships between training and validation populations contributed to GEBV accuracy in the single-step and Boosting analysis, and the advantages of SS-BayesA model was more apparent when the trait was controlled by fewer QTL.  }, Keywords = {Genomic Relationship, Genomic Selection, Genomic Accuracy, Machine Learning, Single- Step Method}, volume = {14}, Number = {4}, pages = {357-366}, publisher = {Genetics Society}, url = {http://mg.genetics.ir/article-1-128-en.html}, eprint = {http://mg.genetics.ir/article-1-128-en.pdf}, journal = {فصلنامه علمی ژنتیک نوین}, issn = {2008-4439}, eissn = {2008-4439}, year = {2020} } @article{ author = {Ghaffari, Mokhtar and Nejati-Javaremi, Ardeshi and Sadeghi, Mostafa and Moradi-shahrebabak, Mohamm}, title = {Study of polymorphism in the ATP1A1 gene and its association with conception rate in Holstein and Sarabi breeds}, abstract ={The objective of this study was the detection of polymorphism in ATP1A1 gene and its association with conception rates in Holstein and Sarabi cows by PCR-SSCP method. For this purpose, blood samples were taken from 124 cows. DNA was extracted from whole blood using modified salting-out method and polymerase chain reactions were performed for amplification of 330bp fragment of the bovine ATP1A1gene. The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method was used to scan for the mutations within the amplified regions. Subsequently, a numbers of samples per each band pattern were sequenced for identification of Single Nucleotide Polymorphism (SNP). The results of the sequencing and alignment using available sequences in NCBI two SNPs in the ATP1A1 gene that one of those was located in exon14 and another one in intron14 area and the mutation located in exon area was along with no changes in amino acid and obtained protein of this gene. For evaluating of association between this locations and conception rate trait, the band pattern (haplotype) were considered in the model. The results showed that the observed haplotypes in the ATP1A1 gene is not significantly correlated with conception rate.  }, Keywords = {Heat stress, Haplotypes, SNP, PCR-SSCP}, volume = {14}, Number = {4}, pages = {367-371}, publisher = {Genetics Society}, url = {http://mg.genetics.ir/article-1-105-en.html}, eprint = {http://mg.genetics.ir/article-1-105-en.pdf}, journal = {فصلنامه علمی ژنتیک نوین}, issn = {2008-4439}, eissn = {2008-4439}, year = {2020} }