فصلنامه ژنتیک نوین
سال هشتم شماره 2 (پیاپی 33، تابستان 1392)

In conventional plant breeding, genetic variation is usually identified by visual selection. Currently, with the development of molecular markers in many crop species, it can be identified at the molecular level based on changes in the DNA and its effect on the phenotype. DNA-based molecular markers are the most powerful diagnostic tools to detect DNA polymorphism both at the level of specific loci and at the whole genome level. In the past, such markers were developed either from genomic DNA libraries (RFLPs and SSRs) or from random PCR amplification of genomic DNA (RAPDs) or both (AFLP). Recently, the availability of genomic DNA and cDNA sequences (ESTs) in the public databases has made marker development more direct and even cost effective. The common applications of those markers in agriculture sector are molecular characterization of germplasm, mapping of genes/QTLs and marker assisted selection (MAS). Advances in the area of marker discovery and SNP genotyping using EST-based marker assays are discussed in this review.

The present study demonstrated the effects of nonylphenol on Persian sturgeon (Acipenser persicus) vitellogenin (VTG) gene expression changes in juvenile Persian sturgeon liver with RT-cPCR and RT-qPCR techniques. For study of vitellogenin gene expression and 18S rRNA as a control gene expression, the liver of juvenile Persian sturgeon injected three times with 17bestradiol (5 mg/kg body wt/week) or NP (1, 10 and 100 mg/kg/week) in three weeks; have been used. Significant induction of VTG gene expression was detected in all treated groups in comparison with control group. According to this research, the ratio of VTG to 18s rRNA in group receiving 1 ßestradiol was 9.95±2.48 for VTG. All groups treated with nonylphenol have significant effect on expression of VTG gene by analyzing statistical software. These results are the first report for effect of the risk of xenoestrogen on Persian sturgeon and vitellogenin gene efficiency as biomarkers of xenoestrogens in Persian sturgeon have been accepted.

Thermophilic actinomycetes due to their ability to decompose the cellulolytic materials are of the main components of compost micro-flora of the button mushroom. Different methods including morphological, biochemical and molecular techniques have been used to separate the actinomycetes into different groups. PCR-based methods such as the pattern of amplified rDNA restriction analysis (ARDRA) have been shown to be useful in differentiating between bacterial species within a genus. Comparison of restricted fragments patterns from isolated bacteria with a database containing 16S rRNA gene sequences of all validly published filamentous from GenBank using In silico digestions is a rapid method for identification of actinomycetes. Thermophilic actinomycetes of compost were isolated on culture medium using dilution methods and incubation at 46°C. The 16S rRNA gene of each isolates were amplified by PCR and digested by restriction endonucleases. The restricted pattern for each enzyme was determined by electrophoresis. Unknown isolates were identified using amplified rDNA restriction analysis. Most isolated actinomycetes from the white button mushroom compost belonged to Streptomyces genus which has a significant role in degradation of plant residuals and compost production.

Septoria tritici bloth (STB), caused by Mycosphaerella graminicola (anamorph: septoria tritici) is one of the most devastating diseases of wheat (Triticum aestivum) and has a major impact on yields Worldwide. During the previous expression-profiling experiment, in addition to major resistant genes to STB (stb1-15), some defense-related genes have bean identified. To study expression pattern of the five defense-related genes including PR-1, Chitinase, Peroxidase, PR-5 and Protease inhibitor, over time, their level of expression were measured at 8 time points, from 0h to 6 days after inoculation in Wangshuibai as a resistant wheat cultivar and Falat as a susceptible one by semi quantitative (RT-PCR). The result showed that, infection of wheat by M. graminicola induced changes in expression of all five genes in both resistant and susceptible cultivar over time. Expression pattern of these genes indicated that all of five genes in resistant cultivar induced earlier than in susceptible cultivare. The RT-PCR analysis confirmed that expression of these genes in control resistance cultivare are much higher than susceptible cultivar in majority of the times during the 6-days time course. Thus, according this results can be concluded that these genes, along the main genes, increase and maintain resistance to Septoria tritici blotch in wheat.

In this study records of 6221, 4261, 3112, 2240 and 2370 related to the birth weight (BW), weaning weight (WW), 6-month weight (6MW), 9-month weight (9MW) and yearling weight (YW) were collected by Qazvin Jahad-e-Keshavarzi organization during 1998 to 2009, were used to estimate genetic parameters, genetic progress, phenotypic, genetic and environmental trends. (Co) variance components and genetic parameters were estimated with different models which including direct genetic effects, with and without maternal additive genetic as well as maternal permanent environmental effects, using restricted maximum likelihood (REML) method. The most appropriate model for each trait was determined based on likelihood ratio tests. Best Liner Unbiased Prediction (BLUP) of breeding values and genetic and phenotypic trends of the traits were estimated as the regression of average predicted breeding values and phenotypic values over birth years, respectively. Environmental trends were assessed as the difference between phenotypic and genetic trends. Mixed model methodology based on a multivariate animal model was used for prediction of breeding value. Estimated direct heritability obtained from the most appropriate model were 0.13±0.03, 0.29±0.04, 0.16±0.03, 0.31±0.03 and 0.19±0.02 for BW, WW, 6MW, 9MW and YW, respectively. Total genetic progress after 10 years for BW, WW, 6MW, 9MW and YW were 69, 593, 329, 364 and 417 g, respectively. Genetic trend for BW, WW, 6MW, 9MW and 12W were 6.3±1, 56.2±8, 31.5±8, 39.1±2 and 42.9±4 g per year, respectively, and phenotypic trends for traits were -68.7±4, - 42.1±6, 59.6±2, 65.4±5 and 131.7±10 g per year, correspondingly.

Accurate and positive identification of plant genotypes, especially those of fruit trees, is very important in implementing breeding programs and in preserving germ plasms. Evaluation of genetic diversity is essential in identifying different genes, estimation of genetic distances between and within individuals and populations and determination of heterosysis. In spite of reach pistachio genetic resources in Iran, a few studies have been conducted on this genus. In the present study, genetic diversity of 38 male and female pistachio genotypes in Faizabad region of Khorasan province were investigated using RAPD markers. The fifteen primers used produced 115 polymorphic loci. The highest number of loci (12) were for primer. The average of polymorphic loci percentage was 92.83. The resolving power for primers ranged from 1.36 to 7.89, averaging.The lowest genetic similarity 0.18) was between genotypes ‘Garme Siah’ and ‘Sefid Sabuni1’ and the highest of that (0.70) detected between ‘Badami Sefid3’ and ‘Genotype7’. Cluster analysis based on Dice similarity coefficients and UPGMA method divided the genotypes into 8 at similarity level of 0.41.The results showed the exictence of the high genetic diversity in the studied genotypes and a good performance of the RAPD markers for study of the genetic diversity of pistachio.

The bacteria Erwinia amylovora is the causal agent of fire blight disease in Maloideae fruit trees. In order to the evaluation of pathogenic intensity relation with strains genetic characterizations, in this research genetic diversity of three gene clusters including hrp, ams and dsp, interfering the pathogenicity were compared using PCR-RFLP marker. Moreover, the diversity of bacterial plasmid pEA29 were evaluated with PEANT pair primers. The used strains were 17 strains from Iran's domestic hosts and Ea273 strain from America. After designing the specific primers on mentioned gene clusters and PCR reaction, products were digested with AluI, BglII, HhaI, MboI, PstI, SalI and TaqI enzymes. In addition 5 ams gene cluster PCR products in 5 strains with geographical spread were sequenced. The results didnt show any variation in binding site and band length of different gene cluster primers. Moreover digestion with restriction enzymes created identical restriction pattern in all strains. Also PCR products sequencing of ams gene cluster showed complete similarity that represents very high genomic conservity in this gene cluster. The diversity assessment of amplified region with PEANT primers in pEA29 plasmid confirmed the length and sequence differences of this region in different strains. It seems that conservity level of this plasmid is much lower than genome of this bacteria.

The program GENALAND has been developed in recent years as a statistical program for genetic structure analysis. Integrating genetic data obtained from dominant and co-dominant markers with spacial data and without pre-defining the population boundaries can obtain number of homogeneous groups and a map of spacial distribution. Such information about population genetic structure can be used for conservation and management of species. In the current study genotypic data produced by nine microsatellite loci of 13 populations of Petaurus breviceps were used to investigate the spatial distribution of these populations and correlate the obtained spatial structure with environmental and landscape features. The result showed that four homogenous groups can be defined within these populations which are separated and isolated from each other due to habitat clearance and land use change. Maintaining the size of patches and establishing corridors between populations need to be consider in management and conservation of species.

The pharmaceutical properties of artemisia are partially attributed to their essential oils, containing a wide variety of active phytochemicals, such as monoterpenes, sesquiterpenes and triterpenes. Among important terpens are β-amyrin, β-caryophyllene, Linalool and β-Pinene that are used as anticancer, analgesic, antimicrobial, antioxidant and anti-inflammatory. In this study, we have examined the relative expression levels of four genes of β-amyrin synthase, β-caryophyllene synthase, Linalool Synthase, and β-Pinene Synthase in eight species of Artemisia by real-time PCR. We used 18S rRNA as a control gene.Maximum and minimum expression levels of β-amyrin synthase, β- caryophyllene synthase, Linalool Synthase and β-Pinene Synthase were observed related to A. annua at the flowering stage of A. scoparia (1.62) and the seedling stage of A. sieberi (-50.85), the flowering stage of A.campestris (56.28) and the flowering stage of A. vulgaris (-10.74), the budding stage of A. scoparia (15.86) and the budding stage of A. sieberi (-20), the budding stage of A.campestris (53.57) and the budding stage of A. diffusa (-23.49), respectively.

Mastitis is one of the most prevalent diseases of dairy cattle. In order to create genetic resistance to the disease, it is essential to identify resistant genes to mastitis. Toll-like receptors are the suitable candidate genes for enhancing genetic resistance to mastitis in Holstein cows. In this research, polymorphism of TLR4 gene’s promoter and its association with somatic cell count in a herd of Holstein cows in Isfahan was studied. For this purpose, DNA was extracted from 100 blood sample of Holstein cows. Two primers were used for amplifying the promoter of TLR4’s gene. These primers amplified 274bp fragments using polymerase chain reaction (PCR) method. The amplified fragments showed A and B genotypes with 0.74 and 0.26 frequency respectively. The results of this study showed that these two different genotypes have significant effect on somatic cell count in the studied herd (P<0/01). With respect to low heritability of somatic cell count (0.093) and deficiency of direct selection for improving of this characteristic, selection on the basis of TLR4 genotypes can efficiently used for increasing genetic resistance to mastitis.

Two wetland and estuarine types of wild Common carp, Cyprinus carpio, are found in the Caspian Sea and its basin as one of the natural habitats of this species. Considering the importance of the genetic variation and population structure studies for management and conservation of species, variation of control region (D-loop) in wild stocks of common carp in the south-western Caspian Sea was investigated using PCR-RFLP. Eighty adult wild common carp were collected from two stations including Sorkhankol wild refuge and Caspian Sea estuary (40 individuals from each station) and forty enzymes were screened to find any genetic differences between the noted stations. Only four enzymes (TasI, SmaI, SspI and ApoI) were polymorphic the results showed three composite haplotypes between the two stations. Haplotypes BBBA and AAAB were recognized only in Sorkhankol station while all individuals that captured from Caspian Sea estuary were presented only by one haplotype (AAAA). It can be concluded that the PCR-RFLP method in mtDNA D-loop region is a suitable maker for maternal inheritance studies of the wild common carp populations. Based on the results, it could be concluded that there were low level of genetic differences between two wetland and estuary types of the wild common carp in the southwestern Caspian Sea. The results of this study may be used for conservation and restocking program of wild common carp in the region.

Alzheimer’s disease (AD) is a progressive neurodegenerative disease that is characterized by memory loss and personality changes. Mutations in amyloid precursor protein (APP) are known to cause early-onset Alzheimer’s disease (EOAD). The aim of this study examined the variation of exons 16 and 17 APP gene mutation in cognitive function EOAD, these exons were hot spot in different investigation, and so were chosen. In this study, 24 patients with 48 individuals as control group were used. After PCR amplification, genotypes were analysis with sequencing method. Single nucleotide substitutions at exon 16 of the APP gene at position T12931884A in intron 1 which had 26 nucleotides to coding region was found in one Iranian patient with AD, but no other variations were found in exons 16 and 17 of APP gene in EOAD. Exons 16 and 17 are not hot spot in Iranian AD patients.