فصلنامه ژنتیک نوین
سال شانزدهم شماره 4 (پیاپی 67، زمستان 1400)

Akhal-Teke horse is one of the oldest breeds in the south of Turkmenistan and north of Iran, which has been adapted to live in the harsh environmental conditions of Central Asia. This breed has been selected for speed for nearly 100 years; therefore, investigation of its genetic structure could improve breeding programs. The sequenced data of 86 horses from 16 breeds were downloaded from NCBI and used in this study. The phylogeny tree for the individual genome sequences was constructed. The PCA was performed using the software GCTA. In order to visualize population structure between different horse breeds, ADMIXTURE was used. The parsimony analysis revealed all breeds were divided base on geographical origins. Principal component analysis illustrated highest genetic distance among Akhal-Teke with Thoroughbred and Standard bred. Results of admixture demonstrated all individuals of Akhal-Teke assign strongly to one cluster in hypothetical population of k=4 and k=5. However, when the hypothetical population of k=2 and k=3 were done, the individual were appeared in 2 or 3 color. The mean number of ROH in Akhal-Teke was lower than Thoroughbred, Sorraia, Standard bred and Quarter and ROH>1000kb was more. Therefore, comparing to these breeds the inbreeding was lower in Akhal-Teke. The highest value of linkage disequilibrium in all bean distance was detected in Thoroughbred. After that, two breeds of Akhal-Teke and Standard bred had similar pattern. In conclusion, comparing to Thoroughbred and Standard bred, Akhal-Teke was less influenced by breeding program and the level of heterozygosity was moderate. Therefore, considering the use of this breed in the disciplines of sprinting, endurance, jumping and dramatic movements, it seems that the genetic diversity at the genome level of this breed can be used in the breeding program in this field.

In this study,the genetic diversity and population structure of 90 Ferula assa foetida L. genotypes were evaluated using 13 ISSR primers. The results indicated that ISSR primers reproduced a total of 186 polymorphic bands with an average of 14.38 bands per primer. The mean values of marker index (MI) and  the polymorphic information content (PIC) for ISSR primers were 4.98  and 0.37, respectively, and showed that ISSR primers were highly efficient in the identification of genetic diversity in Ferula populations. In comparison between the studied populations, the population of Kerman includes 33 genotypes based on the values of the number of effective alleles (Ne), heterozygous values (H), Shannon index (I), and the total number of alleles (Na) observed was more diverse. The analysis of molecular variance  (AMOVA) results showed that 8% of the total changes are related to  between population diversity, while 92% of the changes are justified by within population diversity. In other words, ISSR primers showed significant genetic diversity between and within wild relatives. Cluster analysis and population structure divided all evaluated genotypes into 5 main categories, respectively. According to the results obtained from this analysis, the value of K=5 was in the optimal range. These results illustrate that there is a relatively high genetic diversity in the Ferulas  population  and ISSR markers are beneficial tools for studying genetic diversity in this germplasm.

Nucleases catalyze the cleavage of phosphodiester bonds in nucleic acids. TatD DNase is a conserved evolutionary protein expressed in various organisms, but its function has not been completely recognized. The aim of this research was to identify tatD genes in Bacillus sp. B2 isolated previously from soil in Damghan. The molecular identification of the isolate was performed by 16S rRNA amplification and sequencing. Two sets of degenerate primers were designed for tatD genes, and the amplified sequences were analyzed with BLAST. Deduced amino acid sequences of the tatD genes were aligned with the known TatD DNase from E. coli. The secondary structure of the TatD proteins and the presence of conserved domain were analyzed through PSIpred and CD-Search tools, respectively. The 16S rRNA sequence of Bacillus sp. B2 revealed 100% identity to the sequences of B. cereus, B. thuringiensis, and B. anthracis. Moreover, the amplified tatD1 and tatD2 genes showed more than 90% identity to tatD DNase of Bacillus species. The alignment of the obtained TatD sequences with TatD DNase from E. coli showed that metal ion-binding and catalytic residues were conserved among them. Secondary structures of the TatD1 and TatD2 were similar to the TatD DNase of E. coli, and CD-Search indicated that both TatD proteins belonged to metallo-dependent hydrolases superfamily. According to these results, the Bacillus sp. B2 isolate had two different tatD genes. It seems that tatD has been duplicated and evolved in the genome of some Bacillus species. Identification and characterization of TatD from various organisms is valuable for understanding its role as a conserved evolutionary protein.

To study the genetic and allelic diversity in the genes encoding glutenin and gliadin proteins in wheat landraces, 98 Triticum accessions belonging to four species: T. aestivum, T. boeoticum, T. durum and T. uartu collected from different provinces of Iran were used. 13 pairs of low molecular weight glutenin primers (LMW-GS), four pairs of high molecular weight glutenin primers (HMW-GS) and four pairs of gliadin primers were amplified 1327, 548 and 152 segments, respectively. The highest genetic diversity was observed in the Glu-3A gene block, which belongs to the low molecular weight glutenin, and 13 primer pairs amplified a total of 34 alleles from 180 to 1500 bp in length, of which 11 alleles were previously reported and 23 alleles were identified as possibly new alleles. In the Glu-A1 gene block, which belongs to the high molecular weight glutenin, most allelic polymorphisms were amplified by the primers Glu-A1 and Xrj5. In the Gli-A2 gene block, only one allele was amplified by two specific primers: Gli-AS6 and Gli-AS5. The highest and lowest number of effective alleles belonged to T. aestivum and T. uartu. The average of Nei diversity index was 0.19 and its highest and lowest values ​​were related to T. aestivum and T. uartu. Based on the clustering method, 98 accessions were divided into two main groups. In the first main group, the accessions related to two species T. aestivum and T. durum were placed, which shows the greatest genetic similarity between the two species. In the second main group were placed two wild species T. boeticum and T. uartu. In overall, a large allelic diversity was observed for low molecular weight glutenin subunits in the studied Triticum species, which highlights the potential of these species as a valuable germplasm for breeding programs aimed to the bakery quality improving in wheat.

Considering the increasing advances in the field of genetic engineering, proving its importance in achieving food security in the world and also increasing the global exchanges of its products, like other modern technologies, considerations have been expressed about its products. Therefore, regulations such as Cartagena Protocol on Biosafety at the international level and the National Biosafety Law of the Islamic Republic of Iran at the national level have been approved to gain the trust of consumers. According to these criteria, products containing genetically modified (transgenic) organisms are labeled to inform consumers and give them the chance of decision-making. For labeling these products, the ability to detection and identification of genetically modified organisms is needed. Therefore, in this study, a rapid method for detection and identification of 14 events of transgenic maize in 4 shipments of maize imported from Brazil has been presented. Of these 14 events, 12 are approved by the Ministry of Jihad Agriculture. The other two events have not yet received the necessary permissions and are considered as hypothetical unauthorized events. Detection and identification of these 14 events was optimized using multiple polymerase chain reactions using 7 reactions with the same program, so that in each reaction two events were detected. This method has advantages such as saving time and costs. Tracking results on four imported shipments showed that all four shipments had no hypothetical unauthorized events and the contents of all shipments tested were different combinations of approved events. These results are in full compliance with the information provided in the profile of Iran in Biosafety Cleaning House.

The structures from which mature microRNA molecules can be derived (i.e., pri-microRNA and pre-microRNA) have special properties distinguishing them from similar molecules and make them identifiable for enzymes and processors. These properties are mostly influenced by the characteristics of the secondary structure of the RNA molecule. Therefore, several algorithms have been designed to predict the secondary structure of polynucleotide sequences. CTAnalyzer is an algorithm aimed to digitalize the characteristics of RNA secondary structures and categorize these structures using key properties in identifying microRNA molecules. In the current research, CTAnalyzer, by defining adequate filters and rulesets, was used to examine and categorize the derived secondary structures from the genome sequence of Azadirachta indica. The aim of this study was to investigate the efficiency of CTAnalyzer in identifying the structural details of double-stranded RNA and categorizing them based on their structural properties. For this purpose, a similarity alignment was conducted between known viridiplantae mature microRNAs and the whole genome sequence of A. indica using BLASTn algorithm. Following the bidirectional elongation for 80217 identified regions across A. indica genome with adequate homology and also the exclusion of coding sequences, the secondary structure prediction procedure was carried out for the remaining 38067 sequences. The agreed values of criteria for microRNA secondary structures was defined in the software and could to identify candidate microRNA sequences. According to the results obtained from CTAnalyzer, out of all the 566754 evaluated secondary structures, 482 (~%0.08) structures with all properties accepted for microRNAs were identified.

Genetic uniformity is one of the most important prerequisites in micropropagation of plant species. In the present study, the genetic fidelity of 28 plantlets of damask rose(Rosa damascena ) derived from three different media treatments supplemented with various concentrations of Plant Growth regulators(PGRs) was assessed by SCoT and ISSR markers. solid MS medium was used for the establishment stage of explants and regenerated shoots  were subcultured in VS medium supplemented with three different combinations of PGRs. For rooting, the plantlets were subcultured on MS medium supplemented with IAA and IBA and the rooted plants were transferred and acclimated in the greenhouse. Genomic DNA of in vitro raised clones was extracted from young leaf tissues. 20 SCoT and 20 ISSR primers were used to evaluate of the genetic fidelity of in vitro propagated plantlets. Out of 40 primers screened, only 14 SCoT and 11 ISSR primers produced clear and scorable bands. 25 SCoT and ISSR primers amplified 139 loci, of which only 35 bands were polymorphic. The average number of polymorphic bands per primer were 1.5 and 1.3 for SCoT and ISSR markers respectively. Based on the estimated genetic parameters and results of data analysis, in general, a low variability was detected among the tissue culture-raised plantlets. Particularly, the plantlets derived from the media II and III shower a lower variability than those derived from the media I; hence, the media II and III can be successfully employed for the commercial multiplication of damask rose without much risk of genetic instability.

Drought stress is a serious threat to agriculture and one of the best options to deal with this problem is the symbiosis of mycorrhiza, which in addition to maintaining the water content in plant tissues can improve the absorption of elements that are deficient in drought conditions and physiological and molecular changes under stress conditions. In this study, the symbiosis effect of mycorrhiza on morphology, proline and expression of UGT73C6  gene in GF677 hybrid rootstock under drought stress was investigated. Due to increasing drought stress, most morphological traits including leaf number, leaf length, root volume, fresh and dry weight decreased, but with the presence of mycorrhiza, leaf length and width decreased and with decreasing root length, root volume increased, as did fresh and dry weight also increased compared to the control. Proline decreased in symbiosis and under stress conditions relative to non-symbiosis ones. All factors of drought stress, mycorrhiza, time and their combination in root tissue had a significant and highly variable effect on UGT73C6  gene expression, but changes in leaf expression were much less severe because the root has both symbiosis conditions and initial exposure to drought stress. In general, symbiosis with mycorrhiza improves plant tolerance to drought stress.

Wheat is one of the most important crops in the world and Iran, and wheat powdery mildew is one of the major wheat diseases that cause yield reduction. Transcription factors are good candidate genes for genetic manipulation to enhance plants stress tolerance. Recently, scientific reports have revealed that the G2-like members in plants are involved in response to pathogens. In order to identify the wheat G2-like members and predict their functions, information of the G2-like protein family was collected from databases such as TFDB and Ensembl. Then, members of this gene family in rice and Arabidopsis were used against proteins and genome of wheat. After removing the duplicate sequences, 83 gene loci encoding 136 protein transcripts were identified. The phylogenetic tree was constructed based on the G2-like protein sequences in wheat with 6 known G2-like in other plants, which divided the family into 6 groups. Based on classification of this family, it could be suggested that groups I, II and V are involved in the processes of powdery mildew response, chloroplast development, and flowering time, respectively. Motif predictions of G2-like protein family illustrated that most members belonging to the same group contain similar motif combinations, which indicates the accurate grouping in the phylogenetic tree and the similar function of members of a group. Chromosomal mapping of the G2-likes in wheat showed that G2-likes are present on all chromosomes. The highest and lowest number of G2-like genes is present on chromosome 6B, and chromosomes D and 3A, respectively.

Plant viruses cause many important diseases and are responsible for reducing crop yield and quality throughout the world. Fast and accurate identification of viruses in a sample is desirable for inspection, quarantine services and disease management. Recently, Next-generation sequencing (NGS) techniques have been developed that represent a flexible approach to plant pathogen detection. Since 2009, NGS techniques have begun to apply in some areas of plant virology consisting of virus/viroid genome sequencing, detection, and discovery, ecology, and epidemiology. The NGS techniques are rapid, highly efficient, and low cost, and allow the sequencing of many data gigabases in a few hours. It’s a generic approach to virus/viroid identification that requires no prior knowledge of the host or virus. Only by sequencing of total small RNAs in an NGS run, identification of DNA/RNA containing viruses and viroids are possible. This article reviews the rapid and recent achievement in the applying of NGS techniques for the diagnosis of viruses and viroids in their hosts.