Showing 13 results for Genetic Diversity
A. Alami, M. Taeb, A. Lotfi, Y. Sadeghian Motahar,
Volume 7, Issue 1 (4-2003)
Abstract
Thirty genotypes of pistachio cultivars and related species were evaluated for genetic diversity using three polymorphic isozymes, i.e. Esterase, Peroxidase and Malate dehydrogenase. Young leaves of pistachio were crushed with extraction buffer containing: 20% sucrose, 0.01 M dithiothretiol, 2% polyethylene glycol, and 8% polyvenyl polypyrollidone. Samples were analyzed using isoelectric focussing on polyacrylamide gels containing 2% (W/V) ampholyte. All the three isozymes revealed high degrees of polymorphism in pistachio cultivars and related species. Maximum polymorphism was observed for Est. enzyme. A total of 19 bands in Est. and 28 bands in MDH were observed in a wide range of pH gradient however, in Per. there were 11 bands all of which located in a narrow range of pH gradient. Cluster analysis based on the three system enzymes revealed that all the 30 pistachio genotypes were in 8 main classes and 20 subclasses and the extent of genetic similarity reduced from cultivated varieties to species, which were finally classified in 3 groups. Sarakhs variety, a wild type of P. vera, was classified in a group between cultivated varieties and species.
F. Shokoohifar, A. Bagheri, M. Falahati Rastegar,
Volume 7, Issue 2 (7-2003)
Abstract
The poor information available on variation of Ascochyta blight fungus is the most important factor limiting chickpea breeding programs for resistance to blight disease. In this study, efforts were made to detect genetic variation of the pathogen in Iran. The RAPD marker was employed to evaluate 26 isolates collected from 16 provinces. Twelve random primers were used to analyze genomic DNA of the isolates. Only ten primers showed polymorphism among isolates. Primer OPK-01 defined the highest number of polymorphism and primer OPK-09 confirmed relatively low degree of polymorphism. On the basis of this molecular marker, the estimated genetic diversity index was 98% and the pair-wise genetic distance of the isolates varied from 0.16 to 0.61. The least genetic distance belonged to isolates 20 and 22 from Qazvin and Golestan while the highest distance belonged to isolates 26 and 12 from Mazandaran and Markazi. The phylogenic tree was constructed by cluster analysis and all the isolates grouped to 22 genetic clusters at the 90% similarity level. The genetic groups were named from A to V and their distribution in Iran was determined. The results revealed that genetic variation among Iranian population of the pathogen is very high, and further that RAPD is a vigorous tool for genomic analysis of Ascochyta rabiei.
K. Zaynali Nejad, A. F. Mirlohi, G. Nemat Zadeh, A. Rezai,
Volume 7, Issue 4 (1-2004)
Abstract
To study the genetic diversity in 100 genotypes of rice, an experiment was conducted at the research farm of Rice Research Institute of Iran. The experimental design was a 10x10 simple lattice. The genotypes, mostly belonging to Isfahan Province and north of Iran, were evaluated on the basis of morphological traits and yield components. The results of analysis of variance demonstrated that the differences among genotypes were highly significant (p < 0/01) for all traits. High values of phenotypic and genotypic coefficients of variation were obtained for most traits, indicating high variability in the traits under study. Factor analysis revealed three factors which determined 90 percent of yeild variation and were named “grain number”, “plant type and structure” and “grain shape”, respectively. Cluster analysis by “Cubic Clustering Criterion” and “Pseudo Hotelling T2 Test” grouped genotypes in four clusters. Analysis of variance showed that the differences among clusters were highly significant for most traits.
M. Talebi Bedaf, B. E. Sayed-Tabatabaei, K. Razmjoo, B. Shiran,
Volume 10, Issue 2 (7-2006)
Abstract
Identification of grass species seems difficult due to the morphological similarities. However, selecting desirable parental genotypes of the crosses based on the genetic distances is considered as the most critical step in a breeding program. The aim of this study was to characterize grass species using AFLP techniques. Five species with five cultivars from each were selected and studied using AFLP reactions performed by PstI and MseI restriction enzymes. The obtained data was analyzed using NT SYS-pc Ver. 2.02 software and Jaccard’s method. Ten primer combinations amplified 1170 bands, all of which were polymorphic between cultivars and species. The maximum band (168) and the minimum number of band (81) were produced by P-AAG & M-CAG and P-ACT & M-CGC, respectively. The results also distinguished 5 species in 40% of genetic distances. Some of the markers were special to some special species that can be used in the identification of that species. Additionally, the results showed that AFLP techniques robust and efficient tools for the identification of genetic relationships of different genotypes within species. High levels of bands and polymorphism make AFLP one of the most powerful markers in the determination and classification of species and different cultivars of grass.
M. Bahar, S. Ghobadi, V. Erfani Moghaddam, A. Yamchi, M. Talebi Bedaf, M. M. Kaboli, A. A. Mokhtarzadeh,
Volume 10, Issue 2 (7-2006)
Abstract
To determine genetic diversity among some Iranian local varieties of alfalfa, six geographically diverse populations including: Bami, Rahnani, Nikshahri, Yazdi, Hamadani (from Isfahan), Hamadani (from Shiraz) along with Ranger, an American commercial variety, were evaluated using a set of 24 EST-SSR primers developed from cDNA library of Medicago truncatula and three microsatellite loci, identified from genomic library of M. sativa. Of the pairs of primers tested, four loci from EST-SSRs (AW9, BEE, TC6 and TC7) and genomic microsatellite (Afctt32), were found appropriate for assessing genetic diversity between these alfalfa genotypes. In total, 46 alleles were detected from the five loci in the samples of alfalfa examined. The number of alleles per locus in populations ranged from six to eleven and genetic diversity indices of loci were variable from 0.62 to 0.87 for the populations. Genetic relationship analysis of EST-SSR data revealed separation of Iranian populations from Ranger. It is likely that the parental origin of primary population from which Ranger has been derived is different from that of Iranian populations. Iranian local populations of alfalfa in this study were grouped in two main clusters. Alfalfa populations Hamadani and Rahnani, which are adapted to cold claimates, were grouped in one cluster and populations Bami, Yazdi and Nikshahri, belonging to the trpoical areas, were placed in the next cluster. The positioning of EST-SSR loci in coding regions of genome, possibly increases the usefulness of these markers to clarify inter specific genetic relationships among alfalfa populations.
M. Falahati-Anbaran, A. A. Habashi, M. Esfahany, S. A. Mohammadi, B. Ghareyazie,
Volume 10, Issue 3 (10-2006)
Abstract
Annual medics are used for hey production, soil protection, biological fixation of N2 and green manure. In the present study, the inter and intra specific genetic diversity and relatedness of 4 diploid and two tetraploid (M. rugosa and M. scutellata) annual medics were evaluated using microsatellite markers. PCR analysis was performed on genomic DNA from individual plant and PCR products were detected using standard polyacrylamide sequencing gel. Totally twenty five polymorphic alleles were observed in the studied species. Average intra-specific genetic diversity ranged from zero (0.0) in both M. rugosa and M. scutellata to 0.114 in M. minima species, and the level of genetic diversity was similar in both M. orbicularis and M. truncatula species. Analysis of molecular variance (AMOVA) was used to partition the overall genetic diversity into within and among species, and between diploids and tetraploids. The results revealed significant (P<0.05) inter and intra-specific genetic variation. Pairwise comparisons based on Fst indicated significant differences among all of the species. Clustering analysis using UPGMA algorithm based on coancestary coefficient revealed a clear genetic relationship among species. The hypothesis on a common origin of two tetraploid species was supported by UPGMA clustering and phylogenetic analysis. The high level of Genetic diversity in spiny pod species respect to spineless pod species suggested the high importance of species with spiny pods in annual medics evolution. The findings support the usefulness of microsatellite markers for assessing inter and intra specific genetic diversity, differentiation and genetic relationships.
M. Bahar, M. R. Mohammadi, C. Ghobadi,
Volume 10, Issue 4 (1-2007)
Abstract
The identification of potato cultivars is a recurrent objective of potato research. The research is prompted by the increasing number of potato cultivars and the importance of seed purity. In developing a reliable method for identification of the imported potato cultivars and determining their genetic relationship, the capacity of 10 polymorphic simple sequence repeat markers (SSRs) was evaluated for the analysis of 28 commercial cultivars of potato. The number of alleles detected at different loci ranged from 3 to 10 alleles with a total of 57 for all loci and a mean of 5.7 alleles per locus. In the 28 potato cultivars analyzed, the number of heterozygous genotypes per locus varied between 6 to 28 with an average number of heterozygous genotypes per locus of 18, considering the 10 loci studied. Based on the resulting dendrogram of jacquard's similarity coefficient and UPGMA analysis, the potato cultivars were placed in two major groups. However, the results from similarity coefficient confirmed the close phylogenetic relationships among members in each cluster. The dendrogram derived from SSRs data clustered together Kenebek, Florida and Atlantic which are known as American potato cultivars, but Stanbuli, an old cultivar in Iran, was placed in concert with European cultivars. This finding might be an indication that this cultivar along with other unidentified cultivars, growing in local fields, has been introduced from European countries to Iran. The results obtained illustrate the appropriate utility of SSRs to assess genetic relationships of potato cultivars and develop a PCR- based tool for evaluation of potato seed purity.
E. Feyzian, M. Jalali Javaran, H. Dehghani, H. Zamyad,
Volume 11, Issue 41 (10-2007)
Abstract
Germplasm collection is the base of plant breeding. Iran is one of the most important centers of genetic diversity due to different climates and the old civilization.In this study we decided to collect melon accessions. The north and center of Iran were selected for this purpose. Fifteen qualitative and six quantitative traits were measured on thirty eight accessions. The cluster analysis by the use of UPGMA method and Jaccard coefficient helped separate the horticultural groups of Cucumis melo L. (Cantaloupensis, Inodorus, Flexousous, Reticulatus). The relationship between 30 of these accessions was assessed using 10 RAPD primers. The polymorphism was determined to be19%. The cluster analysis could not separate the horticultural groups of Cucumis melo L., showing that these groups are closely related. However, VB84 primer separated the tow Snakemelon.
K. Samei, A. Arzani, S. A. M. Mirmohammadi Maibody,
Volume 12, Issue 45 (10-2008)
Abstract
Field crop landraces are valuable genetic sources. Twenty populations of Persian clover (Trifolium resupinatum L.) collected from different areas of Iran were used in this study. DNA extractions were carried out using minipreparation method with equal amount of leaves from 30 plants of each population. DNA samples from 20 clover populations were evaluated using semi-random (ISJ) markers. Ten primers out of 30 which used IT (intron-targeting) and ET (exon-targeting) primers produced repeatable bands. Cluster analysis was conducted using NTSYS software and UPGMA method based on Jaccard's similarity matrix. Primers totally produced 111 bands, of which 93 bands (%93) were polymorphic among clover genotypes. The greatest and least amplification fragments belonged to IT15-31 and ET18-4 primers, respectively. Average band number per primer was estimated 11.1 bands. Furthermore, IT primers produced more polymorphic DNA fragments with higher resolution. Based on cluster analysis and cutting dendrogram in 0.8 similarity coefficients, clover populations were divided into five groups in which Kazerun and Kermanshahi (1) individually formed a separate cluster. According to similarity matrix, the least similarity (%42) belonged to Alvijan and Kazerun and the highest similarity belonged to Chegeni and Haftchin Hamedan. Clustering based on semi-specific PCR method almost substantiated the grouping based on geographical origin. Considering the results, it is concluded that PCR-based semi-random marker technique can be used for genetic diversity study of Persian clover as well as discrimination of its cultivars.
H. Arabnezhad, M. Bahar, A. Taj Abadi Pour,
Volume 12, Issue 45 (10-2008)
Abstract
Microsatellite DNA markers isolated from wild species khinjuk (Pistacia khinjuk Stocks.) were used to evaluate the genetic diversity available in Iranian pistachio cultivars. Out of the 27 SSR primers tested initially, 25 could amplify the DNA in different pistachio cultivars, of which 19 primer pairs produced clear bands. Based on the amplification profiles of the genotypes by the remaining primer pairs, eight primers produced a monomorphic product and other 11 microsatellites markers were found polymorphic among the genotypes. The number of putative alleles amplified by each polymorphic SSR locus ranged from two to eleven alleles with a total of 48 alleles. An average of alleles and observed heterozygosity per locus was 3.69 and 0.69 respectively, showing that these microsatellites are highly informative for pistachio fingerprinting. The UPGMA cluster plots based on nei index placed the 20 commercial pistachio cultivars into a major group containing three distinguished subgroups however, genotypes, namely, Ghazvini zudras and Sarakhs (wild P. vera), were clearly situated into two distinct clusters, distant from the domesticated genotypes studied here. Both Ghazvini zudras and Sarakhs are known as small-fruited genotypes which are grown in restricted regions. Therefore, the distinctness of these genotypes can be attributed to their geographical isolation and morphological characteristics. It seems that Ghazvini zudras probably originated from Sarakhs variety which posses an important role in development of pistachio cultivars. The present study revealed that the khinjuk pistachio microsatellites are well distributed in the genome of P.vera , and are informative for estimating the extent of genetic diversity and characterization of pistachio cultivars.
C. Ghobadi, M. Khosh-Khui, B.e. Sayed-Tabatabaei,
Volume 12, Issue 45 (10-2008)
Abstract
Grapevine (Vitis vinifera L.) is a clonally propagated major fruit crop. In grapevine, identification of genotypes with amplographical features is often based on mature plant characteristics that may be affected by environmental conditions. This approach lacks objectivity and reliability. Recently, molecular markers have proved to be supplementary techniques to analyze genetic diversity and examine genetic relationships existing between cultivars in a range of horticultural crops. In this study, twenty genotypes from grapevine (V.vinifera species) grown in Isfahan province were characterized by RAPD technique to understand the extent of diversity and relatedness. Fifty random primers were used for the RAPD study. Of those, twenty four informative primers which generated reproducible polymorphic bands were used for grouping the genotypes. PCR products of the genotypes’genome revealed a total of 315 bands, out of which 282 were found to be polymorphic. Average number of 13 bands was obtained per primer and the amplification produced ranged in size from 300 bp to 3000 bp. The dendrogram constructed using UPGMA cluster analysis differentiated the genotypes into two major clusters, nineteen in one group and Madar-o-Bache genotype has been placed in a separate one, indicating its high genetic diversity compared to the rest of the genotypes. Intra-clustering within cluster A grouped the genotypes in four sub-clusters as expected from their genetic background. The results of the study revealed that the RAPD technique is a relevant technique to determine genetic diversity, genomic analysis and to examine genetic relationship in grapevines.
Zh Osamny, A Siosemardeh,
Volume 13, Issue 47 (4-2009)
Abstract
Studying genetic diversity is important because a decrease in genetic variability might result in a reduction of the plasticity of the crops to respond to changes in climate, pathogen populations, or agricultural practices. In this study, 72 Sardari wheat (Triticum aestivum L.) ecotypes were analyzed by AFLP markers and 17 phenotypic characters. Three pairs of EcoRI/MseI primer combinations produced 1582 polymorphic bands (with mean percentage of polymorphic 73.92%). Cluster analysis using Jaccard coefficient and the entire AFLP data divided all ecotypes into eight major groups. Mean, coefficient of variation, phenotypic, genotypic and environment variance were calculated in each quantitative character. Cluster analysis using Euclidian distance through the quantitative characters divided all ecotypes into six major groups. Comparison of genetic distances obtained from AFLP and agronomic data showed low correlation between the two diversity measurements (0.02). The results showed a high degree of genetic diversity between the Sardari ecotypes, suggesting that Sardari is not a single cultivar, but it is the mass of ecotypes and could be introduced in the gene bank.
R Ravesh, B Shiran, A Alavi, J Zarvagis,
Volume 13, Issue 47 (4-2009)
Abstract
In this study, 45 Pleurotus isolates with a wide range of geographical origins (in five provinces of Iran: Isfahan, Chaharmahal Bakhtiary, Kohkiloye boyrahmad, Lorestan and Fars) were collected. A random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) was used to assess the genetic diversity in ten populations of the Pleurotus eryngii complex. The use of ten primers allowed the production of 150 polymorphic bands. In addition, the evalution of the principal ecological and morphological characters provided further evidence for discriminating between populations. The results show a higher level of diversity of RAPD polymorphism in the populations. 28.67% of the RAPD diversity was among populations and 71.33% was within populations. In the RAPD patterns, Pleurotus strains growing on Ferula assa-foetida, Ferula ovina and Prangus ferulacea formed distinct groups. In this study, the resolution of the RAPD-PCR analysis was better than the morphological analysis.
