Phylogenetic diverSity and relationShiP among annual CiCer SPecieS uSing random amPlified PolymorPhic dna markerS (original) (raw)
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Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers
Theoretical and Applied Genetics, 2002
Seventy five accessions belonging to 14 species of the genus Cicer were analysed with PCR-based molecular markers to determine their phylogenetic relationships. Eight of the species were annuals and included the Section Monocicer which contains cultivated chickpea (Cicer arietinum L.). The remaining six species were perennials (five from Section Polycicer and one from Section Acanthocicer). More than one accession per species was analysed in most of the wild species; within C. arietinum, 26 accessionsincluding Kabuli and Desi types, were studied. RAPD analyses using 12 primers gave 234 polymorphic fragments. Variability within species was detected. A dendrogram based on the Jaccard similarity index showed that the distribution pattern of variability between species was related to both growth habit and geographical origin. An accession of Cicer reticulatum was closer to accessions of Cicer echinospermum than to the four remaining of C. reticulatum, suggesting the possibility of gene flow between species. Cluster analysis for cultivated chickpea differentiated Kabuli and Desi types but we did not detect a clear relationship between groups and the geographical origin of the accessions.
Genetic Resources and Crop Evolution, 2007
In this study, the genetic diversity among 40 carnation cultivars and lines bred in Korea was assessed using random amplified polymorphic DNA (RAPD) fingerprinting and inter-simple sequence repeats (ISSR). For the polymorphism analysis, a total of 20 RAPD decamers and ten ISSR molecular markers were employed. A consensus phylogenetic tree was constructed using the binary data obtained from the banding pattern generated by the individual markers. Further, the cluster analysis using Jaccard's similarity coefficient based on the un-weighted pair group method with arithmetic mean (UPGMA) revealed the genetic similarity among the cultivars. Among the molecular markers, the highest percentage of polymorphism (77.7%) was obtained using ISSR markers. Further, the dendrogram constructed using the UPGMA-based hierarchical clustering algorithm displayed two main clusters with 'PB' in cluster I and other cultivars in cluster II with 80% genetic distance. Among the cultivars, 'PB' was distantly related to all other cultivars included in this study. Thus, a method for identifying polymorphism in carnation cultivars using a dual-marker system was established.
Plant Systematics and Evolution, 2012
Three molecular markers, including start codon targeted (SCoT) polymorphism, directed amplification of minisatellite-region DNA polymerase chain reaction (DAMD-PCR), and inter simple sequence repeat (ISSR) markers, were compared in terms of their informativeness and efficiency for analysis of genetic relationships among 38 accessions of eight annual Cicer species. The results were as follows: (1) the highest level of detected polymorphism was observed for all three marker types; (2) the rate of diversity for the three marker techniques was approximately equal, and the correlation coefficients of similarity were statistically significant for all three marker systems; (3) the three molecular markers showed relatively similar phylogenetic grouping for examined species. Diversity analysis showed that Cicer reticulatum is the closest wild species to the cultivated chickpea, and this finding supports the hypothesis that C. reticulatum is the most probable progenitor of the cultivated species. C. bijugum, C. judaicum, and C. pinnatifidum were clustered together, and in other clusters C. yamashitae and C. cuneatum were grouped close together. To our knowledge, this is the first detailed comparison of performance among two targeted DNA region molecular markers (SCoT and DAMD-PCR) and the ISSR technique on a set of samples of Cicer. The results provide guidance for future efficient use of these molecular methods in genetic analysis of Cicer.
PCR-Based Genetic Diversity in Chickpea (Cicer arietinum L.) Genotypes Using Random Primers
The study aims to develop DNA fingerprints for determining genetic diversity in a set of Indian grown chickpea genotypes using Random Amplified Polymorphic DNA (RAPD) technique. Analysis of 30 genotypes using 30 arbitrary decamer random primers revealed 149 PCR products, of which 130 were polymorphic, with a level of 87.24% polymorphism. Estimates of genetic similarity based on Nei and Li equation ranged from 0.16 to 0.88, indicating the genetic variability among the genotypes. A dendrogram showing the genetic distances was constructed based on RAPD data. Four genotypes, L-550, H-90-231, Katila and H-92-67, were highly diverse from the rest, indicating they are very far from rest of the genotypes on the hierarchical scale. Least genetic distance was found between H-86-143 and H-91-36. It was observed that RAPD analysis employing 30 polymorphic primers could provide a good estimate of genetic relationships in chickpea.
2005
Cicer reticulatum, C. echinospermum, C. bijugum, C. judaicum, C. pinnatifidum, C. cuneatum and C. yamashitae are wild annual Cicer species and potential donors of valuable traits to improve chickpea (C. arietinum). As part of a large project to characterize and evaluate wild annual Cicer collections held in the world gene banks, AFLP markers were used to study genetic variation in these species. The main aim of this study was to characterize geographical patterns of genetic variation in wild annual Cicer germplasm. Phylogenetic analysis of 146 wild annual Cicer accessions (including two accessions in the perennial C. anatolicum and six cultivars of chickpea) revealed four distinct groups corresponding well to primary, secondary and tertiary gene pools of chickpea. Some possible misidentified or mislabelled accessions were identified, and ILWC 242 is proposed as a hybrid between C. reticulatum and C. echinospermum. The extent of genetic diversity varied considerably and was unbalanced between species with greatest genetic diversity found in C. judaicum. For the first time geographic patterns of genetic variation in C. reticulatum, C. echinospermum, C. bijugum, C. judaicum and C. pinnatifidum were established using AFLP markers. Based on the current collections the maximum genetic diversity of C. reticulatum, C. echinospermum, C. bijugum and C. pinnatifidum was found in southeastern Turkey, while Palestine was the centre of maximum genetic variation for C. judaicum. This information provides a solid basis for the design of future collections and in situ conservation programs for wild annual Cicer.
The objective of this study was to evaluate the genetic relationships of 28 chickpea accessions from diverse origin using AFLP markers. On average, 13 polymorphic bands per primer were observed in AFLP analysis. The average polymorphic information content (PIC) was 0.71, ranging from 0.48 to 0.92. The lowest and the highest PIC value were recorded for primer P-GAG/M-GC and P-AT/M-GC, respectively. The average GD, based on F st values among the 21 accessions was 0.42, ranging from 0.61 to 0.16. From the UPGMA dendrogram, it is discernible that material taken for the analysis can be divided in four clusters. The results indicate that the greatest genetic diversity occurs in Afghanistan, Iran and Lebanon. In many cases, the diversity between individuals of an accession is as great as between individuals of different accessions. Based on DNA markers it is concluded that there are three centers of diversity for chickpea: Pakistan-Afghanistan, Iran-Turkey and Syria-Lebanon. India and Ethiopia, which were previously considered as a secondary center of diversity for chickpea, showed lower diversity than the above regions.
2019
To assess genetic diversity a set of 50 germplasm accessions of chickpea (Cicer arietinum) were screened for polymorphism using 102 simple sequence repeat (SSR) primers. All the 102 primers produced amplification with a total number of 219 alleles. One hundred and eighty four alleles were polymorphic whereas 35 monomorphic. The number and size of alleles amplified ranged from 1to 7 and 50 to 1500bp respectively. The PIC values of the primers ranged from 0.20 to 1.00. Primers H1O01, H1O09, H5E05 and P74 produced a unique band in genotypes H91-47, FG-711, H00-256 and CSG-8962 respectively which can be used for genotype identification. Two of the genotypes, HC-1 and HC-3, showed the maximum genetic similarity value of 0.91. HK99-27 and CSG-8962 are most diverse genotypes at a minimum value of similarity coefficient i.e. 0.68. This information may be further utilized in the identification of the genotypes.