Molecular markers & plant breeding
Seyedeh Sepideh Seyed Mousavi; Arman Mahmoudi Otaghvari; Tahereh A. Aghajanzadeh; Hbib Zare
Abstract
The Hyrcanian forests have a remarkable variety of moss species which research on their taxonomy is of great importance. Since Forsstroemia remotifolia, Homalia besseri and Pseudoleskeella catenulata are exclusive and native mosses species of Hyrcanian forests, so in the current study, fourteen populations ...
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The Hyrcanian forests have a remarkable variety of moss species which research on their taxonomy is of great importance. Since Forsstroemia remotifolia, Homalia besseri and Pseudoleskeella catenulata are exclusive and native mosses species of Hyrcanian forests, so in the current study, fourteen populations from three provinces in the north of Iran including Golestan, Mazandaran and Guilan were collected at the same altitudes in autumn 2017. In order to reveal the relationships among these species and populations, a cluster analysis based on numerical taxonomy and zymogram patterns of peroxidases and superoxide dismutase with Euclidean distances was performed. Numerical taxonomy analysis showed plant length, marginal laminal cell length and middle laminal cell length are appropriate traits to distinguish the species of F. remotifolia, H. besseri and P. catenulata from each other as well as their populations. The zymogram analysis showed genetic variability among species and also within populations of F. remotifolia, H. besseri and P. catenulata. Accordingly, the isozyme banding pattern of peroxidases showed a total of 6, 7 and 5 bands for F. remotifolia, H. besseri and P. catenulata, respectively. However, 4 isozyme bands were detected for superoxide dismutase for all three species. Furthermore, the morphological analyses in some populations was not matched with the isoenzyme banding pattern of enzymes in the current study. In conclusion, the biosystematics studies (morphometry and zymogram patterns of peroxidase and superoxide dismutase) indicate the close relationship between F. remotifolia and P. catenulata.
Molecular markers & plant breeding
Faramarz Hoshyardel; Reza Darvishzadeh; Hamid Hatami Maleki; Marjan Jannatdoust
Abstract
Chloride is considered as the most important micronutrient in tobacco production. But excessive amounts of chloride accumulation in leaves of tobacco have many adverse effects on the tobacco quality, such as burning capacity. Identification of quantitative trait loci (QTL) involved in chloride accumulation ...
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Chloride is considered as the most important micronutrient in tobacco production. But excessive amounts of chloride accumulation in leaves of tobacco have many adverse effects on the tobacco quality, such as burning capacity. Identification of quantitative trait loci (QTL) involved in chloride accumulation would be beneficial for the improvement of tobacco quality. The objective of this study was to identify genomic regions associated with chloride accumulation by using a mapping population consists of 225 F2:3 families derived from hybridization between ‘Basma Seres 31’ and ‘SPT 406’ lines. Linkage map was constructed with 23 microsatellite (SSR) and 29 inter simple sequence repeat (ISSR) polymorphic markers which covered 570.8 cM of the tobacco genome. Thirty-four of these polymorphic markers were mapped to 7 linkage groups. Distance between two adjacent markers was 17.3 cM. Composite interval mapping (CIM) was used to identify QTLs controlling chloride accumulation. One QTL for chloride accumulation was identified on linkage group 3. The percentage of phenotypic variance (R2) explained by this QTL was 12.7%. A significant association was not found between ISSR markers and chloride accumulation. The outcome of present effort can be a basis for marker aided selection (MAS) in tobacco breeding programs.
Molecular markers & plant breeding
Asghar Estaji; Zahra Khazaei
Abstract
Tuber species are edible fungi and plant-symbiotic microorganisms that form a beneficial relationship with the roots of certain trees and plants (ectomycorrhizae). After interaction with a plant host, tuber species produced hypogeous fruit bodies of great economic value known as forest truffles. There ...
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Tuber species are edible fungi and plant-symbiotic microorganisms that form a beneficial relationship with the roots of certain trees and plants (ectomycorrhizae). After interaction with a plant host, tuber species produced hypogeous fruit bodies of great economic value known as forest truffles. There are different species of truffles, but based on species and place of origin varied their quality and market price. Truffle identification is based on morphological analysis maybe fail to distinguish them due to highly susceptible to environmental conditions. But using molecular markers to identify truffles can be more accurate, less expensive and reliable monitoring. In this context, twelve inter-simple sequence repeats (ISSR) primers were chosen for amplifying the genetic materials of black and brown truffles. In this study, a total of 57 polymorphic bands were amplified (an average of 5.18 bands). The Polymorphism Information Content (PIC) value and gene diversity (H) was with an average 0.37 and 0.50, respectively. During the ISSR screening good amplification products were obtained from primers based on GA, (AG) G, (AG)T, and GAC repeats. The population analysis result revealed that there are three main clusters A, B and C. Four strains Ardabil, Khalkhal, Zanjan and Urmia were identified to be in the group A cluster. The strains of at second and third groups were black and brown truffles respectively. The results indicated that truffles had two separate speciation events (DK = 2). According to DK = 2, the samples of Ardabil, Khalkhal, Zanjan and Urmia grouped in the same group and rest of truffles in other groups.
Molecular markers & plant breeding
Atefeh Anjomshoaa; Hossein Jafary; Mohammad Reza Hassandokht; Mehdi Taheri; Vahid Abdossi
Abstract
Garlic rust is one of the most important diseases of garlic worldwide, which hardly can be controlled by applying fungicides while the weather condition goes on the favor of the disease progress. The NBS-profiling approach is one of the effective methods for separating the replicated parts of resistance ...
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Garlic rust is one of the most important diseases of garlic worldwide, which hardly can be controlled by applying fungicides while the weather condition goes on the favor of the disease progress. The NBS-profiling approach is one of the effective methods for separating the replicated parts of resistance gene analogues (RGA). In this study, 12 primers (NBS-LRR) were used on 16 Iranian garlic clones. Out of 499 scored marker sites in the range of 100 to 800 bp for NBS, from which 477 sites were multi-faceted (95.59 percent). The highest number of marker sites was for the primer combination NBS1-AluI and the lowest was for the primer combination NBS7-RsaI. The highest polymorphism occurred with combination NBS2-AluI and NBS1-AluI with 70 alleles and the lowest polymorphic composition occurred in NBS7- RsaI combination. The results of cluster analysis using UPGMA divided the clones into eight separate groups. This study showed that there is a significant diversity in the homologues of resistance genes in the Iranian garlic clones, which can be exploited in plant breeding programs. In addition, the results indicated that the NBS profiling technique is an efficient method for investigation on diversity of resistance genes in various plant species, including garlic. Using of NBS-profiling technique to study the diversity of resistance genes in garlic clones was addressed for the first time in the world in this study.
Molecular markers & plant breeding
Khalil Malekzadeh; Mohsen Mahmoodnia; Fatemeh Farzad Amirebrahimi
Abstract
Precise investigation of genetic diversity by means of novel molecular tools has made it possible to identify the superior genotypes among various male and female pistachio populations. Cytogenetic studies have shed light on the possible presence of distinct sex chromosomes in male and female genotypes. ...
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Precise investigation of genetic diversity by means of novel molecular tools has made it possible to identify the superior genotypes among various male and female pistachio populations. Cytogenetic studies have shed light on the possible presence of distinct sex chromosomes in male and female genotypes. In this study, 22 start codon targeted (SCoT) primers were used to investigate the genetic diversity of 22 male genotypes and 22 female cultivars of pistachio. A total of 434 loci were produced that 339 loci were polymorphism. The average value of polymorphic information content (PIC), marker index (MI), and resolving power (Rp), ranged from minimum 10, 0.5, and 1, to maximum 31, 11.40, and 17.86% subsequently. The genetic similarity between genotypes, were calculated using Jaccard's coefficient, ranged from 35 to 66%. The cluster analysis divided pistachio genotypes into six groups, and could efficiently differentiate the male and female genotypes. Analysis of molecular variance (AMOVA) classified the total diversity into intra- and inter- population diversities with a high genetic variation (92%) within populations. This study reveals that SCoT marker is a useful and valuable molecular tool to separate male and female pistachios and to determine the genetic diversity among the populations.
Molecular markers & plant breeding
Amin Azadi; Saeedeh Khani Bafrouei
Abstract
High-molecular weight (HMW (glutenin subunits are encoded by the Glu-1 loci (Glu-A1, Glu-B1 and Glu-D1 (on the long arms of chromosomes 1A, 1B and 1D. In the present study, we constructed genetic linkage map of Glu-D1and then investigated the allelic variation of HMW glutenin subunits at Glu-A1 and Glu-D1 ...
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High-molecular weight (HMW (glutenin subunits are encoded by the Glu-1 loci (Glu-A1, Glu-B1 and Glu-D1 (on the long arms of chromosomes 1A, 1B and 1D. In the present study, we constructed genetic linkage map of Glu-D1and then investigated the allelic variation of HMW glutenin subunits at Glu-A1 and Glu-D1 gene loci in 30 Iranian genotypes using Functional markers. Glu-D1 was located at 50.8 cM on chromosome 1D and it was tightly linked to wPt-3743 marker (>1 cM). QTL analysis using composite interval mapping detected one significant QTL for grain yield (GY) on chromosome 1D. This QTL (QYld.abrii-1D) was located between wPt-3743 and Glu-D1 gene locus. Allelic variation of HMW glutenin subunits showed the most frequent alleles were the null allele at Glu-A1and Dx2+Dy12 alleles at Glu-D1loci. The frequency of Null alleles or 1 and 2* were 40% and 60% respectively. Only 9 genotypes included allelic combination of Dx5+ Dy10 and the rest of genotypes had Dx2+Dy12 in the Glu-D1 locus. According to the Nei's genetic diversity index, alleles at Glu-A1 locus have more dispersion in genotypes compared to Glu-D1 locus. The cluster analysis of data based on the Simple Matching coefficient and UPGMC methods, classified the genotypes into four groups. Six genotypes including: Bezostaya, Tajan, Navid, Karaj1, Neyshabour, and Golestan had Ax2* and Dx5+ Dy10 subunits at Glu-A1 and Glu-D1 gene loci. Identification of genotypes with suitable allelic combinations can be used in breeding programs, especially in hybridization.
Molecular markers & plant breeding
Shiferaw Alayachew; Destaw Atnafu; Samuel Gedefa
Abstract
Hot pepper (Capsicum spp.) is an economically important spice widely cultivated and consumed in Ethiopia. In spite of its wide importance, there is no information available on the molecular genetic diversity of this crop. Cultivars characterization is an important link between the conservation and utilization ...
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Hot pepper (Capsicum spp.) is an economically important spice widely cultivated and consumed in Ethiopia. In spite of its wide importance, there is no information available on the molecular genetic diversity of this crop. Cultivars characterization is an important link between the conservation and utilization of plant genetic resources in various breeding programs. Using five ISSR primers, a total of 37 scorable bands were generated of which 35 (94.6%) were polymorphic bands. The diversity of polymorphic bands within population ranged from 51.35% to 91.89 % with a mean of 66.6 %, Nei’s genetic diversity of 0.19 - 0.30 with a mean of 0.28, and Shannon information index of 0.29 - 0.45 with a mean of 0.43. With all diversity parameters, the highest diversity was obtained from amhara2 populations, whilst the lowest was from Oromia2. From Jaccard’s pairwise similarity coefficient, Oromia1 and oromia2 were the most related populations exhibiting 0.956 similarity and Semn omo and Amhara 2 were the most distantly related populations with similarity of 0.827. Clustering was showed that there is strong correlation between geographic distance and genetic diversity of Ethiopian hot peppers cultivars because geographically closely related species have been clustered together. Amhara 2 populations exhibited the highest genetic diversity so that the populations should be considered as the primary sites in designing conservation areas for this crop in Ethiopia. Further, it is suggested that molecular markers are valid tags for the assessment of genetic diversity in Capsicum spp. cultivars.
Molecular markers & plant breeding
Ebrahim Ramadan; Galal Anis; Mohamed Gawish; Mostafa Elshenawy
Abstract
DNA fingerprinting has become an important tool for diversity assessment and varietal identification in plant breeding programs. Semi- random PCR primers targeting intron-exon splice junctions (ISJ) were used to evaluate the potential of these markers in identification and classification of rice genotypes. ...
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DNA fingerprinting has become an important tool for diversity assessment and varietal identification in plant breeding programs. Semi- random PCR primers targeting intron-exon splice junctions (ISJ) were used to evaluate the potential of these markers in identification and classification of rice genotypes. A total of 12 ISJ primers were used for screening fourteen Egyptian rice genotypes, including six Japonica, four Indica and four Indica/Japonica rice genotypes. A total of 117 amplified fragments were generated among which 76 fragments were polymorphic revealing average polymorphic ratio of 58.9%. Number of amplified fragments per genotype across the primers ranged from 65 in Japonica rice variety Sakha101 to 85 in Indica/Japonica rice variety Giza179. Number of polymorphic amplified fragments ranged from 3 for primer ISJ-1 to 24 for primer ISJ-2. The average numbers of amplified bands per primer per genotype were 16.71 and 10.24, respectively. Polymorphic information content (PIC) values ranged from 0.289 for ISJ-9 to 0.480 for ISJ-1 with an average of 0.375. The coefficient of similarities based on semi-random data among the studied genotypes ranged from 0.53 to 0.9 with an average of 0.66. All genotypes clearly grouped into two major clusters in the dendrogram at 58% similarity based on Jaccard’s similarity index. The first cluster represents the Indica and Indica/Japonica rice genotypes, while the second cluster represents the Japonica genotypes. These results indicate that fingerprinting using semi-specific DNA markers may be an efficient tool for varietal identification and assessing genetic diversity in rice. The results highlight the existing diversity among the studied genotypes and hence their potential use in breeding programs. The simplicity and reproducibility of ISJ markers indicates the potential utilization for molecular characterization, identification and purity assessment of rice genotypes.
Molecular markers & plant breeding
Karim Farmanpour Kalalagh; Mehdi Mohebodini; Alireza Ghanbari
Abstract
Cornelian cherry (Cornus mas L.), considered as the ancestor of cultivated trees in Arasbaran region, is a medicinally and economically plant species. However, little is known about genetic diversity, breeding programs, and population structure of this species in mentioned region. Keeping this in view, ...
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Cornelian cherry (Cornus mas L.), considered as the ancestor of cultivated trees in Arasbaran region, is a medicinally and economically plant species. However, little is known about genetic diversity, breeding programs, and population structure of this species in mentioned region. Keeping this in view, the main objectives of present study were to analysis the genetic diversity, phylogenetic relationships and population structure of cornelian cherry genotypes from Arasbaran region using Inter Simple Sequence Repeat molecular markers. Utilized primers amplified 153 bands, of which 98 bands were polymorphic (64% polymorphism). Highest Jaccard’s similarity coefficient was obtained 0.777. Based on Unweighted Pair Group Method with Arithmetic Averages, genotypes were divided into seven major groups. On the other hand, Principal Coordinate Analysis (PCoA) as a complementary method to cluster analysis demonstrated genotypes grouping in phylogenetic dendrogram. Relatively low amount of three main components in Principal Component Analysis (PCA) (41.464%) indicated the scattering distribution of utilized primers’ sequence in cornelian cherry genome. The mean values of polymorphism information content, marker index, resolving power, observed number of alleles, effective number of alleles, Nei’s gene diversity, and Shannon’s information index were 0.230, 1.769, 4.7, 1,642, 1.498, 0.271, and 0.392 respectively. Population structure analysis showed the seven groups or sub- populations (K= 7) when the amount of K value was set at K= 2 to K= 10, which demonstrated the results of phylogenetic dendrogram and Principal Coordinate Analysis (PCoA). Results of this study can be useful for planning future studies on cornelian cherry germplasm and breeding programs.
Germplasm genetic diversity & plant breeding
Shahrbanoo Abbasi; amin Baghizadeh; Ghasem Mohammadi-nejad
Abstract
In order to study the genetic conditions of some agronomic traits in wheat, a cross was made between Gaspard and Kharchia varieties. F2, F3 and F4 progenies with parents were evaluated under drought conditions. Three-parameter model [m d h] considered as the best fit for number of fertile tiller and ...
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In order to study the genetic conditions of some agronomic traits in wheat, a cross was made between Gaspard and Kharchia varieties. F2, F3 and F4 progenies with parents were evaluated under drought conditions. Three-parameter model [m d h] considered as the best fit for number of fertile tiller and flag leaf length using generations mean analysis method. For number of grain per spike and main spike grain weight three-parameter model [m d i] was used. For number of spikelet per spike, grain yield and plant height four-parameter model [m d h i] was used. The heritability values ranged from 56% for flag leaf length to 81% for grain yield. The F3 generation with 100 individuals was used to construct a genetic linkage map. Using the method of composite interval mapping 3, 1, 5, 2, 2 and 1 QTLs were detected for plant height, grain yield, number of spikelet per spike, flag leaf length, main spike grain weight and number of fertile tiller respectively.
Molecular markers & plant breeding
Mohsen Mahmoodnia Meimand; Fatemeh Farzad Amirebrahimi; Hamid Reza Karimi; Khalil Malekzadeh; Ali Tajabadipour
Abstract
Genetic study of pistachio, especially male genotypes due to the effects of pollen on nut quality and quantity and next generation characterizations, help to improve its management and breeding programs. We studied the genetic diversity among 20 male and 36 female pistachio genotypes using ISSR marker. ...
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Genetic study of pistachio, especially male genotypes due to the effects of pollen on nut quality and quantity and next generation characterizations, help to improve its management and breeding programs. We studied the genetic diversity among 20 male and 36 female pistachio genotypes using ISSR marker. In total 178 DNA frgments were proliferated using 12 primers that 169 fragments were polymorphism. The average polymorphism information content (PIC) for the used primers were variable from 16 to up to 35%. Pistachio genotypes classified as five main categories by using cluster analysis. The most genetic similarity was between the ‘Poostkhormayee’and ‘Momtaz’ cultivars with 78% similarity and the lowest genetic similarity was between ‘Ravar3’ cultivar with ‘Ghazvini’cultivar and K40 genotype with 25% similarity. K38 male genotype had the lowest genetic similarity with female cultivars. Thus, it can be introduced as appropriate pollinizer for other studied cultivars. The results of analysis of molecular variance analysis showed that variability between male and female populations (8%) was lower than the variation within the populations (92%). Based on present results, ISSR marker was as a powerful tool to study the genetic variation among male and female pistachio genotypes.
Molecular markers & plant breeding
Farideh Nik khoy; Mohammadreza Shiri
Abstract
Comparing different methods of estimating the genetic diversity could define their usefulness in plant breeding programs. In this study, a total of 18 morphological traits and 20 simple sequence repeat (SSR) loci were used to study the morphological and genetic diversity among 20 maize hybrids selected ...
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Comparing different methods of estimating the genetic diversity could define their usefulness in plant breeding programs. In this study, a total of 18 morphological traits and 20 simple sequence repeat (SSR) loci were used to study the morphological and genetic diversity among 20 maize hybrids selected from different countries, and to classify the hybrids into groups based on molecular profiles and morphological traits. To collect morphological data, a field experiment was carried out using an RBCD design with three replications in Moghan, Ardabil, Iran. The highest estimates for genetic coefficients of variation were observed in anthesis-silking interval, followed by grain yields, leaf chlorophyll rates, kernel row numbers, and ear heights. The total number of PCR-amplified products was 84 bands, all of which were polymorphic. Among the studied primers,NC009,BNLG1108,BNLG1194,PHI026 and PHI057 showed the maximum polymorphism information content(PIC) and the greatest diversity. To determine the genetic relationship among maize hybrids, the cluster analysis was performed based on both morphological traits(using the Ward method) and SSR markers (using the CLINK method). The cluster analysis of morphological traits divided the maize hybrids into five groups. Furthermore, Maize hybrids were divided into seven main groups based on SSR markers. Principal coordinate analysis (PCoA) of a similarity matrix of hybrids for SSR data showed that the first 15 coordinates explained 97.21% of the total variance, whereas the first two coordinates explained only 33.14% of the total variance. Generally, results indicated that SSR markers were able to classify closely related maize hybrids more efficiently than morphological traits.
Molecular markers & plant breeding
Zeinab Nazemi; Mehrshad Zeinolabedini; Mohammad Taher Hallajian; Naser Bouzari; Parastoo Majidian; Mohammad Ali Ebrahimi
Abstract
Apricot is grown in a wide range of climatic conditions in Iran, however, it is frequently damaged by late spring frost. In this case, identification of new genotypes tolerant to cold stress is indispensably needed. The objective of this study was to evaluate the genetic population and relationships ...
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Apricot is grown in a wide range of climatic conditions in Iran, however, it is frequently damaged by late spring frost. In this case, identification of new genotypes tolerant to cold stress is indispensably needed. The objective of this study was to evaluate the genetic population and relationships among 27 apricot accessions (Prunus armeniaca) by 30 microsatellite markers and 11 morphological traits. Based on the PIC values, the SSR loci (UDP96001, UDP96003, UDP98412 and UDP98411) were the most informative markers. The morphological traits were categorized into three components which explained 91.23% of total variation. The two-dimensional PCA plot exhibited that the highest degree of fruit quality and quantity belonged to the susceptible cultivar of Shahrood 48 which showed to be the favorable parent for the production of resistant mutants with high value of fruit traits to late spring frost. Moreover, the close relatedness of Shahrood 48 and its mutants according to the molecular analyses (including a Bayesian clustering approach and a Partial repeated bisection) confirmed the results of fruit traits analysis. The findings suggest that the wide diversity present in Iranian apricot genotypes could be used as a genetic resource for conservation and development of new cultivars resistant to late spring frost and for designing further apricot breeding programs. The promising new mutant genotypes tolerant to cold stress will be evaluated based on morphological markers in further breeding studies.
Molecular markers & plant breeding
Hadi Kharestani; Ali Asqar Nasrolah Nejad Qomi; Ali Ashraf Mehrabi
Abstract
Genomic relationships and diversity of 37 wild and cultivated wheat (Triticum sp.) possessing A genome include four T. urartu (Au), thirteen wild einkorn (Am), four cultivated einkorn (Am), seven durum wheat (BBAuAu), three T. zhukovskyi (AtAtAmAmGG) and six common wheat (BBAuAuDD) were evaluated by ...
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Genomic relationships and diversity of 37 wild and cultivated wheat (Triticum sp.) possessing A genome include four T. urartu (Au), thirteen wild einkorn (Am), four cultivated einkorn (Am), seven durum wheat (BBAuAu), three T. zhukovskyi (AtAtAmAmGG) and six common wheat (BBAuAuDD) were evaluated by simple sequence repeats (SSR) analysis. Genetic distance was calculated by Nei and Li using UPGMA for construct phylogenetic tree. 24 out of 35 primer pairs amplified and 22 pairs produced polymorphic amplicons (109 alleles). The highest amplified fragments (11 alleles) and polymorphism information content (0.90) was for Xgwm165-4A locus. The highest and the lowest genetic distance within groups for T. urartu and T. zhukovskyi were 0.86 and 0.55, respectively. The most similarity was between T. urartu and wild einkorn species (0.009). The highest dissimilarity observed between cultivated einkorn and common wheat,although T. urartu was more close to durum and common wheat than other diploid species.
Molecular markers & plant breeding
Pavan Kumar Velpula; Dwarkesh Singh Parihar; Rajasekhar Pinnamaneni
Abstract
Tomato (Solanum lycopersicum L.) is an important vegetable crop and acts as model plant for fruit development studies. Besides that, post-harvest damage is a devastating phenomenon often associated with ripening process in tomato which in turn leads to greater yield loss. Understanding the genetics, ...
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Tomato (Solanum lycopersicum L.) is an important vegetable crop and acts as model plant for fruit development studies. Besides that, post-harvest damage is a devastating phenomenon often associated with ripening process in tomato which in turn leads to greater yield loss. Understanding the genetics, molecular and biochemical pathways is the key to overcome the existing situation. In the present study, we have identified a delayed ripening mutant and used in identification of linked marker for delayed fruit ripening. Initially, BML-03 (delayed ripening mutant line) was crossed with BIL-29 (normal ripening inbred line) to produce F2 population. Bulked segregate analysis was carried out using 245 SSR markers. Out of which, five SSRs were found to be polymorphic between parental lines and respective bulks along with a segregating genotype of mapping population. A population of 227 F2 plants was screened with five polymorphic SSR markers and the data were used in linkage analysis. Three SSR markers were found to be co-segregating with the delayed ripening phenotype and resulted in a linkage map which covered the map distance of 3.4 cM. Out of 3 markers TGS0070 was found to be closely linked to the fruit ripening locus and was successfully validated using other ripening specific F2 population BML-28 x BIL-3.
Molecular markers & plant breeding
Mostafa Haghpanah; Seyed Kamal Kazemitabar; Seyed Hamidreza Hashemi; Seyed Mohammad Alavi
Abstract
Urtica dioica is an important medicinal plant which is widely distributed in Mazandaran province (North of Iran). In this study for the first time Amplified Fragment Length Polymorphism (AFLP) and Inter-simple Sequence Repeat (ISSR) markers were used for detection of genetic polymorphism in Mazandaran ...
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Urtica dioica is an important medicinal plant which is widely distributed in Mazandaran province (North of Iran). In this study for the first time Amplified Fragment Length Polymorphism (AFLP) and Inter-simple Sequence Repeat (ISSR) markers were used for detection of genetic polymorphism in Mazandaran nettle. Ten AFLP primer combinations and seventeen ISSR markers were utilized. AFLP produced 830 scorable bands out of which 90.21% were polymorphic. ISSR primers amplified 234 bands, 181 being polymorphic (77.3%). Average heterozygosity for AFLP and ISSR markers were 0.25, 0.23 respectively. Marker Index obtains 22.25 for AFLP and 15.57 for ISSR. The number of cluster computed was same for both molecular makers but location of samples in branch were different. The total compare of these two marker systems shown AFLP marker was a useful tool for detection of U. dioica’sgenetic diversity. This plant is very variable and is genetically distinct in east, west and north of Mazandaran.
Molecular markers & plant breeding
Mehrshad Zeinalabedini; Parastoo Majidian; Jalil Dezhampour; Motahareh Khakzad; Maryam Farsi
Abstract
Prunus rootstocks play an important role in modern horticulture and commercial orchards owing to their responsibility for a wide range of characters from compatibility with cultivars to adaptation to biotic and abiotic stresses. In this study, Thirty Prunus rootstock samples were tested by 25 microsatellite ...
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Prunus rootstocks play an important role in modern horticulture and commercial orchards owing to their responsibility for a wide range of characters from compatibility with cultivars to adaptation to biotic and abiotic stresses. In this study, Thirty Prunus rootstock samples were tested by 25 microsatellite markers in order to identify the genetic identity and relationships among them.17 SSR markers were useful in the discrimination of the samples on the basis of their unique molecular identities. Samples with similar codes such as (HS-401/HS-402/HS-403), (HS811/HS507/HS737/GF677), (HS126/HS-202), (HS-802/HS602) and (HS522/HS003/HS302) were shown mislabeled trees. Based on partial repeated bisection (RB ) data, the samples were grouped into six clusters which the largest cluster contained nine genotypes (all APPL, APU2 and APPU3). The second largest cluster consisted of eight genotypes (all AM, all APL, APU1, APU3 and APH10). APH rootstocks were placed into clusters two, three and six as well as cluster one which included only APPU rootstocks. The highest amount of the average internal similarities (Isim ) (0.973) belonged to cluster six, whereas the minimum amount of Isim (0.924) belonged to cluster three. The minimum level of the average external similarities (Esim ) was related to groups one (0.664) and six (0.638) indicating the highest genetic distance from other groups. The genetic identities and relatedness generated in this study provide a standard for further breeding attempts and will be used as a reference the cultivation of these promising newly released genotypes.
Molecular markers & plant breeding
Ali Aalami; Mohammad Alizadeh; Reza Shirzadian-Khorramabad; Ali Akbar Ebadi; Heydar Azizi
Abstract
The identification of genomic loci involved in control of quantitative traits receives growing attention in plant molecular breeding. The present study was carried out to evaluate the genetic variability among 48 rice genotypes and determine the genomic regions associated with ten grain related important ...
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The identification of genomic loci involved in control of quantitative traits receives growing attention in plant molecular breeding. The present study was carried out to evaluate the genetic variability among 48 rice genotypes and determine the genomic regions associated with ten grain related important traits. A total number of 63 alleles were detected by 18 selected SSR markers from different chromosomes with an average of 3.5 alleles per marker. A model-based Bayesian approach subdivided 48 evaluated rice genotypes into three major subgroups with the consideration of the highest value of ΔK. The mean r2 value for all loci pairs on the same chromosome was 0.053. A total of 38 significant marker-trait associations were identified (P< 0.05) that explaining more than 32% of the total variation. RM315, RM3428, RM289, RM16, RM574 and RM156 markers had highest R2 and most association with assayed traits, respectively. The findings of this study revealed association of grain properties in rice with some SSR markers that could serve as target genomic regions for further research such as MAS, fine mapping and candidate gene discovery in rice breeding programs.
Molecular markers & plant breeding
Jithin Thomas; V.J. Dominic
Abstract
Rice (Oryza sativa L.) is one of the most significant cereal crops, about 3 billion people, nearly half the world's population; depend on rice for survival and it offers up to 80% of daily energy intake in most of the Asian countries. Knowledge of the distribution, extent and pattern of genetic variation ...
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Rice (Oryza sativa L.) is one of the most significant cereal crops, about 3 billion people, nearly half the world's population; depend on rice for survival and it offers up to 80% of daily energy intake in most of the Asian countries. Knowledge of the distribution, extent and pattern of genetic variation is useful for estimation of any possible loss of genetic diversity and its role in breeding programs. This work assessed the genetic diversity among 25 coastal rice populations of five regions of Kerala (South India) using 18 microsatellite markers. A mean PIC value of 0.37 and an average of 3.5 alleles per loci were observed. Mean Heterozygosity value of 0.29 and gene diversity value of 0.41 was attained. AMOVA demonstrated that genetic differentiation was significant at P< 0.001 and FST index value of 0.035 was obtained. Of the total diversity, 57.76% was attributed within individuals, 38.71% was attributed among individuals within populations and 3.53% among populations. Information regarding the amount of genetic variations in these salt tolerant coastal accessions and genetic relationship between genotypes are essential for designing effective breeding programs. Especially, to meet the differentiated goals of plant breeding such as breeding for increasing yield, wider adaptation, desirable quality, pest and disease resistance.
Molecular markers & plant breeding
Mohammad-Ali Ebrahimi; Masoud Tohidfar; Mahsa Karimi; Fatehmeh Zawarei
Abstract
One concern about using transgenic plants is the genetic variation that occurred from theirs tissue culture and regeneration. Molecular markers are an important element for efficient and effective determination of genetic variation. The present work was carried out to assess the genetic uniformity of ...
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One concern about using transgenic plants is the genetic variation that occurred from theirs tissue culture and regeneration. Molecular markers are an important element for efficient and effective determination of genetic variation. The present work was carried out to assess the genetic uniformity of transgenic cottons (Bt and chitinase lines), using RAPD, ISSR molecular markers and SDS-PAGE analysis. Similarity matrix for RAPD marker based on Nei and Li’s coefficient revealed that pairwise value between Bt and chitinase cottons and their conventional counterpart plant was 93% and 95% respectively. Also, similarity matrix for ISSR marker revealed that pair wise value between Bt and chitinase lines and their conventional counterpart was 94% and 96% respectively. Pairwise similarity coefficient among two transgenic plants and their conventional counterpart ranged from 0.94 to 0.99 SDS-protein patterns exhibited four major bands, molecular weight ranged from 10 KD to 35 KD. Similarity matrix for protein patterns revealed that pairwise value between Bt and chitinase lines and their conventional counterpart was 100%.All protein bands of three cultivars are the same and no polymorphic bands was detected. Pairwise similarity coefficient among two transgenic plants and their conventional counterpart ranged from 0.94 to 0.99. These lines could be used for more in-dept.evaluation and biosafety studies on their way to commercialization
Molecular markers & plant breeding
Zeinab Mohammadi; Atefeh Sabouri; Sedigheh Mousanejad
Abstract
Association analysis is a useful method for evaluation of significant association between molecular marker and phenotype of trait. This study was performed to evaluate association between traits related with powdery mildew resistance and molecular markers. This investigation was performed using 77 barley ...
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Association analysis is a useful method for evaluation of significant association between molecular marker and phenotype of trait. This study was performed to evaluate association between traits related with powdery mildew resistance and molecular markers. This investigation was performed using 77 barley genotypes and AFLP markers. In phenotypic evaluation, reaction of seedlings to powdery mildew was evaluated and the infection type and intensity were assessed based on 0-9 scale as the most important traits associated with resistance. Also in this study, the genetic diversity of genotypes was evaluated using seven combination primers EcoRI/MseI. The average percentages of polymorphism and polymorphic information content were 92.37% and 0.43, respectively. General evaluation of the statistics of genetic diversity showed that among seven primer combinations, three combinations of E90-M160, E100-M160, and E100-M150 were higher value than others and had a more obvious effect in the detection and separation of barley genotypes. Association analysis was performed using four statistical models of GLM and MLM applying TASSEL software. In the complete MLM model, 33 markers showed significant association in the 5 percent probability level with traits and the highest coefficient of determination was related to marker E80-M150-3 that explained 14% of variations of infection intensity. E80-M510-3 and E80-M160-22 markers were showed significant association (pr<0.05) with both characteristic the severity and type of infection that can represent the effective role of this genomic region in resistance to powdery mildew. If the results are confirmed, it can be a suitable candidate for conversion to SCAR specific marker.
Molecular markers & plant breeding
Hajar Abedinpour; Nad Ali Babaeian Jelodar; Gholam Ali Ranjbar; Behrouz Golein
Abstract
Having knowledge about genetic relationships among accessions is necessary for developing breeding strategies to produce improved cultivars. In present study, genetic diversity and inter-relationship among 29 genotypes of citrus were comparatively analyzed using morphological and RAPD markers. Significant ...
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Having knowledge about genetic relationships among accessions is necessary for developing breeding strategies to produce improved cultivars. In present study, genetic diversity and inter-relationship among 29 genotypes of citrus were comparatively analyzed using morphological and RAPD markers. Significant variability was observed among citrus genotypes for 61 quantitative and qualitative morphological characters of leaves, fruits and seeds. Furthermore, the RAPD markers revealed a high polymorphism rate (91.82 %). A pair-wise similarity value between genotypes ranged from 0.14 to 0.97 with average of 0.62. Both morphological and molecular analysis indicated a high degree of variation among studied genotypes. In current research, genotypes “pummelo” and “mandarin” were confirmed as true species of citrus in distinct cluster. Results of present study proved that both of morphological and molecular markers are potential tools for determining genetic diversities and genetic relationships of citrus genotypes and can be used in citrus breeding programs.
Molecular markers & plant breeding
Elham Mehrazar; Ali Izadi-Darbandi; Mohsen Mohammadi; Goodarz Najafian
Abstract
Marker assisted selection (MAS) is a tool for breeding, screening, and genetic characterization of germplasm. Allelic variation of both high and low molecular weight glutenin subunits (HMW/LMW-GS) is associated with the rheological properties of wheat flour. In this study, we investigated glutenin pattern ...
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Marker assisted selection (MAS) is a tool for breeding, screening, and genetic characterization of germplasm. Allelic variation of both high and low molecular weight glutenin subunits (HMW/LMW-GS) is associated with the rheological properties of wheat flour. In this study, we investigated glutenin pattern using SDS-PAGE and their PCR based on DNA markers in 60 advanced wheat lines and cultivars with different origins. Specific DNA markers regarding to Glu-1 loci, such as 1319 bp, 669 bp and 450 bp fragments were respectively validated for 2*, 17+18, 5+10 alleles. These alleles showed the highest allelic percentage in Glu-1 loci in studied cultivars. However the Null, 7+8 and 5+10 alleles showed the highest allelic percentage in advanced lines. In this study, 23%, 40% and 37% of cultivars respectively, got good (10), moderate (8-9) and weak (4-7) quality scores. In advanced lines, 18%, 44% and 38% got good, moderate and weak quality scores respectively. Ten specific DNA PCR markers were also detected for genotyping Glu-B3 alleles. The most frequent Glu-B3 alleles in wheat cultivars were i, a, b and d with 24%, 21%, 20% and 12%, respectively.Specific PCR markers regarding to the reported Glu-B3 alleles were produced as 621bp, 1095bp, 1570 bp and 662bp consequently. The most frequent Glu-B3 alleles in advanced lines belonged to a, i and d alleles with 35%, 26% and 21% respectively. The results provided useful information for breeding program to improve breadmaking quality and develop new cultivars.
Molecular markers & plant breeding
Saumya Awasthi; Jai Prakash Lal
Abstract
Literatures have reported that a lot of drought related genes were cloned and individual gene showed positive effects under controlled stress experiments, but were not much effective in the field. Although, the progresses by conventional breeding approaches were achievable as some drought varieties have ...
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Literatures have reported that a lot of drought related genes were cloned and individual gene showed positive effects under controlled stress experiments, but were not much effective in the field. Although, the progresses by conventional breeding approaches were achievable as some drought varieties have been released to the farmers in the recent years but this is not adequate to cope up with the future demand of high yield for rice, as drought seems to spread to more regions and seasons. Therefore, marker assisted selection came into lime light for accelerating and giving pace to plant breeding.From the cross (Sarjoo- 52× Nagina- 22) × Sarjoo- 52, plants were selected on the basis of presence of gene MQTL1.1responsible for the drought tolerance. These lines have been subjected to further breeding and trial tests. Agronomic performances and physiological behavior of these lines are also under track. The results showed that the variety Sarjoo 52 could be efficiently converted to a drought tolerant variety in a backcross generation followed by selfing and selection, involving a time of two to three years. Polymorphic markers for foreground and background selection were identified for the high yielding variety to develop a wider range of drought tolerant variety to meet the needs of farmers in the drought-prone regions. This approach demonstrates the effective use of marker assisted selection for a major QTL in a molecular breeding program.
Molecular markers & plant breeding
Nader Eyvaznejad; Reza Darvishzadeh
Abstract
Many agriculturally important traits are complex, affected by many genes and the environment. Quantitative trait loci (QTL) mapping is a key tool for studying the genetic structure of complex traits in plants. In the present study QTLs associated with yield and agronomical traits such as leaf number, ...
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Many agriculturally important traits are complex, affected by many genes and the environment. Quantitative trait loci (QTL) mapping is a key tool for studying the genetic structure of complex traits in plants. In the present study QTLs associated with yield and agronomical traits such as leaf number, leaf length, leaf width, plant height, stem and head diameter were identified by using 70 recombinant inbred lines (RILs) from the cross (♀) PAC2 × RHA266(♂). RILs and their parents were evaluated in a rectangular 8´9 lattice design with two replications. High genetic variability and transgressive segregation were observed in all studied traits. Genetic gain representing the difference between 10% of selected RILs and their parents was significant for most of the studied traits. Positive and significant genotypic and phenotypic correlations were observed among the studied traits. QTL analysis was performed using a recently developed SSR and SNP sunflower linkage map. The map consists of 210 SSRs and 11 SNP markers placed in 17 linkage groups (LGs). The total map length is 1,653.1 cM with a mean density of 1 marker per 7.44 cM. Composite interval mapping (CIM) procedure detected 21 QTLs involved in genetic control of studied traits. The phenotypic variance explained by the identified QTLs varied from 1.13 to 73.70%. QTLs such as HMBPP associated with the expression of more than one trait could increase the efficiency of marker-assisted selection (MAS) and genetic progress in sunflower.