Showing 16 results for Molecular Marker
, Reza Darvishzadeh, , , ,
Volume 7, Issue 3 (11-2016)
Abstract
One of the newest methods in plant breeding programs is mapping quantitative trait loci (QTL) with molecular markers. In order to identify QTL associated with some chemical traits such as chlorine, nicotine, sugar concentrations and ash in oriental tobacco, a population of 55 recombinant inbred lines coming from the cross Basma seres 31 × SPT406 were evaluated for above mentioned traits. QTL mapping was performed using linkage map developed on 103 recombinant inbred lines by 64 molecular markers including 14 SSR, 24 ISSR and 26 retrotransposone. The linkage map is composed of 7 linkage groups (LGs). Composite interval mapping revealed 5 QTLs associated with studied traits. Phenotypic variation explained by identified QTLs varied between 0.34 and 0.70. Any QTL was not detected for sugar concentration in tobacco leaves. Common markers between some of studied traits can be due to linkage or pleiotropic effects. The common markers lead to increase the efficiency of marker-assisted selection in plant breeding programs via simultaneously selection for several traits.
Z. Aghaali, R. Darvishzadeh, M. Aghaei,
Volume 9, Issue 1 (1-2018)
Abstract
Aims: The aim of the present study was to map the morphological traits in Iranian Basil accessions (Oscillum Oscillos) by Inter Simple Sequence Repeats (ISSRs) markers.
Materials & Methods: In this experimental study, 50 Iranian basil accessions from different geographical regions were used and the experiment was based on a completely randomized design. Extracting DNA and PCR was performed with 12 ISSR primers for Basil accessions. Components of variance, general heritability, and genetic and phenotypic variation coefficients were calculated by formula. Bayesian method, linear mixed model as well as Minitab 17, DARwin 5, Structure 2.3.3, Tassel 3, and SPSS 20 software were used. Findings: There was a positive correlation between the majority of traits for basil accessions. The highest coefficient of genetic variation was observed in stem diameter and internode length and the lowest was observed in flower number. Heritability varied between 3.63% and 94.24%. Foutrteen loci with 7 traits were recognized. The range of phenotypic changes varied from 3% to 29%. The highest number of locus was obtained for stem diameter traits and the lowest was obtained for lateral branch number. Six loci were specifically associated with only one trait and other loci were common in traits. The phenotypic variation varied between 17% and 29%.
Conclusion: Traits have a wide variety in Basil accessions and there is a positive correlation between the majority of them. The heritability of the traits varies from 3.63% to 94.24% and the range of the phenotypic changes varies from 3% to 29%. The highest number is for stem diameter traits and lowest is for lateral branch number. Six loci are specifically associated with only one trait and other loci are common in traits. The phenotypic variation varies between 29% ‐17%.
Volume 9, Issue 2 (4-2007)
Abstract
Pod length is one of the effective components on canola yield selection on the basis of which can increase not only the seed yield but also the oil yield. Molecular markers asso-ciated with long pod loci were identified in a doubled haploid population derived from a cross between the canola lines ‘Quantum’ (long pod) ‘China A’ (short pod) using RAPD and bulked segregant analysis. A molecular marker linkage map of 37 loci for this popu-lation was used to identify quantitative trait loci (QTL) controlling pod length of which two markers in two unlinked loci were selected by using an interval mapping model which explained 22% of phenotypic variation for pod length in this population. Selection for markers at two loci for increasing pod length resulted in a group of doubled haploid lines with an average 112 mm pod length that increased 15% of whole population mean. This shows that using these markers in the breeding program will enhance the breeding of long pod canola varieties.
R. Paknia, R. Darvishzadeh , F. Shahriari , S. Malekzadeh,
Volume 9, Issue 3 (9-2018)
Abstract
Aims: Sunflower (Helianthus annuus L.) is mainly cultivated for the extraction of edible oil, and Sclerotinia sclerotiorum is a pathogen in sunflower fields. The aim of this study was to indetify markers associated with resistance to Sclerotnia Scleritiorum diseases in sunflower, using association analysis.
Materials and Methods: In the present experimental research, a population including 100 lines of oily sunflower was cultivated. Traits such as contamination progress after 4, 8, and 12 days, 100 seeds weight of contaminated and non-contaminated plants, contaminated and non-contaminated plant yield, 100 seeds weight loss, and yield loss were studied. The molecular profiles of germplasm were prepred with 30 microsatellite primer pairs. Genetic structure analysis of population was performed based on Bayesian model.
Findings: The highest coefficient of variation was related to the yield loss (86.41%) and weight loss (78.48%), and the lowest was contamination progression after 8 and 12 days (26.47% and 20.44%), respectively. Based on the mixed linear model (MLM), 6 microsatellite markers related to traits were identified at the level of p≤0.01. The highest number of markers was associated with contamination progression after 8 days. The P733, P807, and P1256 markers were simultaneously associated with 3 traits.
Conclusion: Four lines including RHA274, H100A-83HR4, B45-03, and Iranian line with code 28 were identified with different genetic origins and high resistance levels. According to the general linear model (GLM) and MLM, 24 and 15 SSR markers are related to the traits, respectively. The P733, P807, and P1256 markers are simultaneously associated with 3 traits.
Volume 14, Issue 7 (12-2012)
Abstract
All species in the genus Lysiphlebus Förster (Hymenoptera: Braconidae, Aphidiinae) are solitary endoparasitoids of aphids, which are one of the most difficult and unknown taxonomic groups to identify. A pair of species-specific primers as a molecular marker was designed to identify the most abundant and important aphid parasitoid wasp, L. fabarum Marshall, collected from Guilan province (Iran). This primer pair, which produces a 148 bp fragment length, was developed for L. fabarum by using the ATPase 6 gene region of mitochondrial DNA. The lower detection limit to amplify DNA of L. fabarum in a singleplex PCR was determined to be 72 pg of parasitoid DNA/µl PCR which was enough to detect this parasitoid in early life stages within its host. The L. fabarum eggs cannot be detected within Aphis fabae Scopoli (Hemiptera: Aphididae) earlier than 12 hours after oviposition. A pair of species specific primers designed for L. fabarum can be used to monitor the wasp populations under field conditions.
Aydin Hassanzadeh, Mohammad Ali Tajick Ghanbary,
Volume 15, Issue 3 (6-2024)
Abstract
Aspergillus has many species that are important in medicine, agriculture, and various industries. The genus has 446 identified species, which are difficult to distinguish from each other with the use of morphological characteristics. Xylan 1,4-beta-xylosidase is an enzyme that catalyzes the hydrolysis process of xylose in xylooligosaccharides and is produced by different species of Aspergillus. This research was conducted with the aim of a bioinformatics study of the gene region related to this enzyme and to evaluate its similarities and differences in some Aspergillus species. The results showed that this gene region, due to the presence of conserved motifs, was able to distinguish some species studied in this research.
Volume 15, Issue 5 (9-2013)
Abstract
Molecular characterization of 19 Jatropha accessions that included 15 accessions of J.curcas and 4 different species was carried out using 3 different markers systems. Highest polymorphism (96.67%) was recorded by RAPD followed by DAMD (91.02%) and ISSR (90%). Polymorphism Information Content (PIC) was higher for DAMD (0.873) and almost equal for RAPD (0.863) and ISSR (0.862) markers, whereas Resolving Power (Rp) was found to be higher for RAPD as compared to the other two marker systems. Marker Index (MI) values varied greatly with highest (19.07) in RAPD. Shannon index (i), observed number of alleles (na), effective number of alleles (ne) and Nei’s genetic diversity (h) values were found to be significantly higher for ISSR as compared to RAPD and DAMD markers. Thus, all the markers proved to be equally efficient for diversity studies in Jatropha. Several alleles in all the markers indicated J. gossypiifolia as one of the parents of J. tanjorensis. Dendrograms and PCA plots generated based on RAPD showed three major clusters with J. integerrima and J. podagrica falling in group I, fifteen J. curcas accessions in group II, and J. gossypiifolia as an outlier in group III. DAMD markers also showed similar clustering pattern whereas ISSR showed last cluster of J. gossypiifolia and J. tanjorensis. These results may provide a future base for conservation and characterization of available Jatropha genetic resources.
Volume 15, Issue 6 (11-2013)
Abstract
The flowering and fructification period of the Chilean strawberry (Fragaria chiloensis (L.) Duch.) is restricted to approximately 2 mo, which seriously limits the commercial development of the species. The objective of the current investigation was to identify Inter Simple Sequence Repeat (ISSR) polymorphisms associated with flowering duration in accessions of F. chiloensis. The flowering duration data related to 41 accessions obtained over 3 years were analyzed, and a set of 40 ISSR primers tested. Two clusters were obtained through the Partitioning Around Medoids algorithm, with 23 vs. 18 accessions, and 64.1 vs. 95.6 days of flowering, respectively. Flowering duration, between the two groups, was significantly different. The years also revealed a significant effect, on flowering duration, between the two groups. Ten of the ISSR primers tested revealed reproducible and consistent banding patterns, displaying a total of 106 putative loci, of which 79 were polymorphic. Three ISSR loci (811779, 844670, 841980) were identified owing to their significant contribution to the differentiation among the accessions. Similarly, three ISSR loci (811600, 8121180, 841980) exhibited a significant correlation with the flowering duration variation. Locus 841980, which presented the highest level of correlation with flowering duration, was isolated, cloned and sequenced, but it showed only a low level of homology with the relevant sequences published in the GenBank database. The identified loci showing high correlation with the flowering time could help build Quantitative Trait Loci (QTL) maps for selection and improvement programs in the Fragaria sp. genus or other related species.
Mojtaba Khayam Nekouei,
Volume 16, Issue 1 (12-2024)
Abstract
Iran stands out as a significant center of genetic diversity for alfalfa (Medicago sativa) worldwide, harboring diverse types of this plant. Ensuring the authenticity of alfalfa populations and varieties is crucial for farmers and seed producers, as the genetic makeup of this species directly influences forage and seed yield quality. In this study, we developed a method to identify and differentiate key Iranian cultivated alfalfa populations using microsatellite markers. We collected random samples, each containing 100 seeds, from various alfalfa accessions. Nine microsatellite loci were screened and employed to differentiate these populations based on specific allelic genotypes. Notably, the MTIC233, BI90, ACT009, TC7, MTIC183, MS30, MTIC238, and AFCA11 markers exhibited the highest differentiation ability. The genetic distance analysis revealed that 5-B and foreign accessions, as well as 29-N and foreign accessions, were the most distant from each other. Conversely, 27-G, 9-H, and 21-R exhibited the closest genetic similarity. The results revealed that, accessions 9-H, 21-R, 27-G, 25-B, 5-B, and 2-G shared a common genetic background, suggesting their close relatedness. Our proposed method allows straightforward identification of target alfalfa accessions within a short timeframe (one to two days) without the need for DNA extraction from leaves.
Volume 16, Issue 6 (11-2014)
Abstract
Exploitation of the full potential of any hybrid requires the possessing of genetically high-purity seeds. Commercial soybean hybrids have been developed using a cytoplasmic male sterility (CMS) system. In order to avoid reduction in yield caused by using low-purity seeds, development of a simple, rapid, and accurate method for hybrid purity assessment is of great essence and significance. Therefore, the parental lines of HybSoy 1 to 5 were screened using 160 Simple Sequence Repeat (SSR) makers, of which 8 markers exhibited polymorphism. A PCR-based assay with these markers detected both alleles of the parental lines in pure hybrids, proving their heterozygosity, whereas impurities were identified by the presence of only one parental allele. The confirmation of hybrid purity indicated that a single polymorphic marker was sufficient for detection of contaminations of these hybrids from their parents. It was also found that if a hybrid seed lot was contaminated by another hybrid or its parental lines, two or more appropriate markers could be used to easily detect such contamination. This method could accurately and effectively identify the hybrid purity in a predetermined sample of soybean hybrids constituted by deliberately mixing seeds of parental lines. This is the first report that demonstrates the utility of SSR markers for assessment of genetic purity of soybean hybrids.
Volume 17, Issue 7 (12-2015)
Abstract
To evaluate the genetic variations in eleven fennel populations in Iran, 55 accessions were analyzed by SRAP markers. Twelve primer combinations produced 171 polymorphic bands. The cumulative dendrogram delineated fennel accessions into five major groups in accordance to the geographical regions from which the populations were originated. About 43.57% of total genetic variation was detected among the populations, while 56.43% of total variation were observed within the populations. The studied populations showed high genetic differentiation (Gst= 0.52) and low gene flow (Nm= 0.46). Among the studied populations, Yazd and Kerman accounted for the highest values of PPB (%), Shanon index (I), and heterozygosity. The self-pollinated seeds were in the range of 2.01% in Paveh-2 to 9.24% in Isfahan-2 accessions. The essential oil content ranged from 0.62% in Isfahan-3 to 2.21% in Tabriz-3. Generaly, the dwarf populations viz., Tabriz and Paveh, had higher essential oil yield and their pollination was less affected by environmental factors than the average.
Volume 19, Issue 1 (1-2017)
Abstract
Inter Simple Sequence Repeat (ISSR) markers were used to assess the genetic diversity among 23 outcross and self pollinated populations of fennel collected from different geographical regions of Iran and some European countries. The experiment was carried out to determine the effect of self-pollination on morphological traits and genetic diversity in the next generation. Fifteen primers produced 248 polymorphic bands with an average of 16.53 fragments per primer in outcross populations, while 217 polymorphic fragments with an average of 14.46 fragments per primer were generated in self-pollinated populations. UPGMA dendrogram using Jaccard’s similarity coefficients placed outcross populations in five major groups. The maximum and minimum gene diversity over loci was observed in Albania (0.53) and Poland (0.42) populations, respectively. In general, European fennel populations revealed higher expected heterozygosity (0.47) in comparison with Iranian ones (0.35). Polymorphism Information Content (PIC) ranged from 0.37 to 0.49 in self-pollinated populations, while it varied from 0.39 to 0.46 in out-cross ones. The classification based on morphological data did not confirm the molecular ones in most cases. Self-pollination led to decline in plant height in most of the studied populations. In overall, plant height of the European populations (54-66.02 cm) was less than that of Iranian ones (55-109.54 cm). Self-pollination elevated the yield of essential oil in studied fennels through its influence on fruit set. In conclusion, Albania population had the highest oil content affected by self-pollination; hence, it can be introduced as one of the valued sources in fennel breeding programs aimed for oil yield improvement.
Volume 20, Issue 2 (3-2018)
Abstract
Progress in plant breeding requires a broad genetic basis. Knowledge of genetic diversity in cultivated species and their wild relatives is of critical importance for breeding purposes. The red clover, T. pratense,grows wildly in Iran in a vast range of habitats, mainly along the Zagros and Alborz Mountains. Despite being economically important in many other countries, information regarding the genetic diversity of this species in Iran is significantly lacking. In this study, the genetic diversity of 56 genotypes of red clover collected from Iran and one genotype of T. diffusum, used as outgroup, was evaluated using nine SRAP markers. The nine SRAP primer combinations created a total of 294 bands from DNA of 57 genotypes, from which 291 (98.9%) were polymorphic. All the measured parameters showed significantly high genetic diversity in the Iranian genepool of T. pratense with no clear geographic partitioning of genotypes. However, genotypes collected from around Tehran, Isfahan, and Kermanshah-Hamedan were loosely clustered with their co-regional genotypes. Based on the results of the STRUCTURE analysis, genotypes were genetically divided into two clusters, but these were not correlated with the eco-geographical groups. There was no correlation between genetic distance and geographic distance of genotypes. The result of this study showed value in sampling the Iranian genepool of the red clover, with the Western and the Northwestern genepools in more depth, for conservation and breeding purposes.
Volume 20, Issue 6 (11-2018)
Abstract
The aim of the present study was to evaluate the geographical distribution, infestation degree, and diversity of Potato Cysts Nematode (PCN) in Algeria, including the southern regions. Accurate identification of PCN is essential to determine the appropriate control methods to be used in an Integrated Pest Management program. PCNs were found in forty percent (12 out of thirty) of localities sampled. The average population density of PCN was much higher in the southern regions, compared to the northern regions (9.8 cysts per 100 cm3 vs.4.6 cysts per 100 cm3). The southern potato production areas were more infested with PCN than those of the north (7 from 25 fields in North vs. 5 from 5 fields in the South). Globodera pallida occurred predominantly in the northern region of Algeria, whereas G. rostochiensis occurred predominantly in the southern regions. No mixtures of these species were found in any of the positive studied localities. These species were confirmed by the molecular analysis based on PCR with species-specific primers, ITS-rDNA, and cytochrome b of mtDNA. The low molecular diversity and their phylogenetic association with the European populations of PCN suggest that Algerian populations were probably introduced from Europe, probably by infested seed-potato.
Volume 20, Issue 6 (11-2018)
Abstract
Seventy-five isolates of the fungus Zymoseptoria tritici, collected from seven wheat producing provinces in Iran, were studied using the molecular markers ISSR and SSR to determine its structure and genetic variations within its populations. Results indicated that the populations of the causal agent of this disease had a relatively high level of genetic diversity, with the total average genetic diversity (Ht) of 0.34 in the studied samples. When the genetic diversity was divided by the genetic diversity within and between the tested fungal populations, intra-population and inter-population genetic diversities were, respectively, 69 and 31%. Moreover, results showed that there was a strong gene flow between the studied provinces. The maximum genetic diversity among the studied provinces was observed in Ardebil and Khuzestan Provinces, and cluster analysis also revealed that the fungal populations of these two provinces had the greatest similarity with each other.
Volume 25, Issue 5 (9-2023)
Abstract
Tomato is one of the worldwide major foods consumed fresh, cooked, or processed. Mineral elements, vitamins, and antioxidant content of tomatoes are of interest because of their nutritional value and beneficial health effects. The present study was performed to evaluate the macro- and micro-elements contents of leaves and fruits of seven wild tomato species, in addition to morphological traits. Wild tomato species had variations for all elements in fruits. Coefficient of variation was calculated for elements as 18.50 to 94.32% for potassium and phosphor, respectively. Most of the wild tomato species had higher content of all mineral elements than cultivated tomato. Resistance genes (Frl, I-2, I-3, Mi-3, Pto Ty-1, Ty-3 and Sw-5) of wild tomato species were screened using molecular markers. LA1971, with six resistant genes, and LA1393 and LA1777, with five resistant genes, were considered the most promising parental candidates for breeding. The results of the analysis of mineral elements of seven wild tomatoes species are useful for future tomato breeding.
