scholarly journals TU-DAMD employment for molecular characterization of Salvia judaica and Salvia palaestina species

2021 ◽  
Vol 65 (1) ◽  
pp. 11-16
Author(s):  
Basel Saleh
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Annealing Temperature ◽  
Polymorphic Information Content ◽  
Pcr Amplification ◽  
Marker Index ◽  
C Cycle ◽  
Separated Sets ◽  
Polymorphism Level

Genetic diversity in perennial Salvia judaica Boiss (Judean sage) and Salvia palaestina Benth (Palestinian sage) species using touch-up directed amplification of minisatellite region DNA (TU-DAMD) has been performed in two separated sets; in the first set (set A) the initial annealing temperature was increased from 50 °C to 55 °C, whereas, in the second one (set B), it increased from 55 °C to 60 °C by 0.5 °C/cycle during the first 10 PCR amplification cycles. Fifteen DAMD primers have been tested for each set. Set (A) produced 89.39% polymorphism level (P%) with polymorphic information content (PIC) average of 0.33 and marker index (MI) average of 3.96. Whereas, in set (B) these values were recorded to be 94.02%, 0.34 and 3.98 for P%, PIC and MI, respectively. Data showed that the two mentioned sets successfully highlighted high polymorphism level between the two studied Salvia sp. This work studies genetic diversity of S. judaica and S. palaestina species using TU-DAMD test as a novel molecular marker.

scholarly journals Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Ujjal Kumar Nath ◽  
Dhiman Biswas ◽  
Sathishkumar Natarajan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Large Scale ◽  
Polymorphic Information Content ◽  
Pcr Amplification ◽  
Efficient Manner ◽  
Lilium Species ◽  
Population Structure Analysis ◽  
Wide Range ◽  
Functional Molecular Markers

Abstract Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

scholarly journals Genetic Diversity in Ficus Sycomorus L. Species (Moraceae) Using Rapd and Irap Markers

2013 ◽  
Vol 59 (3) ◽  
pp. 120-130 ◽  
Author(s):  
Basel Saleh
Keyword(s):  
Genetic Diversity ◽  
Pcr Amplification ◽  
Coastal Regions ◽  
Chain Reaction ◽  
Marker Index ◽  
Irap Markers ◽  
Irap Marker ◽  
Repeatability And Reproducibility ◽  
Ficus Sycomorus ◽  
Polymerase Chain

Abstract This study was conducted in order to assess accuracy, repeatability and reproducibility of the RAPD and IRAP techniques for determining the genetic variability in 10 Ficus sycomorus L. genotypes grown in the coastal regions of Syria. Thirty-six RAPD primers applied gave 352 discernible loci, of which 252 (71.59%) were polymorphic. Polymerase chain reaction (PCR) amplification with 36 RAPD primers gave an average of 9.778 selected markers/primers, with a maximum of 21 (OPA18) and a minimum of five (OPG11, OPK12 and OPT18). The amplification with 22 IRAP primers (single or combination) generated 178 bands, of which 151 (84.83%) were polymorphic, with an average of 11.125 selected markers/ primer, with a maximum of 17 (IRAP-TDK11F) and a minimum of seven (BREP1F+BREP1R, IRAP-TDK1F+IRAP- TDK1R and IRAP-TDK2F+IRAP-TDK2R). In the present investigation, the IRAP marker was more efficient than the RAPD assay, where the latter exhibited a lower marker index (MI) average (1.629) compared with the IRAP technique (2.941). Otherwise, F. sycomor4 genotype showed the highest dissimilarity compared with other genotypes studied in this investigation. Based upon the estimated percent disagreement values (PDV), we can suggest that there are three subspecies present among the 10 samples tested.

scholarly journals Evaluation of Genetic Diversity among Persian Fig Cultivars by Morphological Traits and RAPD Markers

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 613-619 ◽  
Author(s):  
Ghazal Baziar ◽  
Moslem Jafari ◽  
Mansoureh Sadat Sharifi Noori ◽  
Samira Samarfard
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Hierarchical Cluster ◽  
Fruit Trees ◽  
Group Method ◽  
Fars Province ◽  
Pair Group

Ficus carica L. is one of the most ancient fruit trees cultivated in Persia (Iran). The conservation and characterization of fig genetic resources is essential for sustainable fig production and food security. Given these considerations, this study characterizes the genetic variability of 21 edible F. carica cultivars in the Fars Province using random amplified polymorphic DNA (RAPD) markers. The collected cultivars were also characterized for their morphological features. A total of 16 RAPD primers produced 229 reproducible bands, of which, 170 loci (74.43%) were polymorphic with an average polymorphic information content (PIC) value of 0.899. Genetic analysis using an unweighted pair-group method with arithmetic averaging (UPGMA) revealed genetic structure and relationships among the local germplasms. The dendrogram resulting from UPGMA hierarchical cluster analysis separated the fig cultivars into five groups. These results demonstrate that analysis of molecular variance allows for the partitioning of genetic variation between fig groups and illustrates greater variation within fig groups and subgroups. RAPD-based classification often corresponded with the morphological similarities and differences of the collected fig cultivars. This study suggests that RAPD markers are suitable for analysis of diversity and cultivars’ fingerprinting. Accordingly, understanding of the genetic diversity and population structure of F. carica in Iran may provide insight into the conservation and management of this species.

scholarly journals Molecular characterization of groundnut (Arachis hypogaea L.) germplasm lines and varietal set for yield and yield attributing traits

2019 ◽  
Vol 79 (01) ◽  
Author(s):  
Anushree Pramanik ◽  
Sushma Tiwari ◽  
R. S. Tomar ◽  
M. K. Tomar ◽  
A. K. Singh
Keyword(s):  
Genetic Diversity ◽  
Arachis Hypogaea ◽  
Allelic Variation ◽  
Polymorphic Information Content ◽  
Kernel Weight ◽  
Arachis Hypogaea L ◽  
Genetic Assessment ◽  
Hundred Kernel Weight ◽  
Kernel Yield

The genetic assessment of 90 germplasm lines and six varieties of groundnut (Arachis hypogaea L.) were done with 13 morphological traits and 125 Simple Sequence Repeats markers. Out of 125 molecular markers, 26 were polymorphic and produced 105 alleles. The genetic diversity was found to be 52-83 per cent and Polymorphic Information Content (PIC) was 0.46-0.81 with a mean of 0.42 indicating higher magnitude of genetic diversity in the test genotypes. Analysis of molecular variance showed variation among and within individuals based on allelic variation. Principal Co-ordinate Analysis based on origin of the genotypes formed three major population groups and the genetic analysis determined by population structure divided all the germplasm lines in to 10 populations. Significant and positive correlation was observed between hundred kernel weight and hundred pod weight (r=0.769) and kernel yield (r=0.899); sound mature kernel and pod weight with kernel yield, weight of kernels and harvest index. Genotypes from distinct clusters may be selected in hybridization programme for groundnut improvement. The information on clustering of genotypes will be helpful in identification of novel and superior germplasm for hybridization and development of improved varieties.

scholarly journals Genetic Diversity Among Colletotrichum falcatum Isolates Causing Red Rot of Sugarcane in Subtropical Region of India

2014 ◽  
Vol 6 (3) ◽  
pp. 308-315
Author(s):  
Ratinderbir KAUR ◽  
Bipen KUMAR ◽  
Yogesh VIKAL ◽  
Gulzar Singh SANGHERA
Keyword(s):  
Genetic Diversity ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Red Rot ◽  
Colletotrichum Falcatum ◽  
Molecular Characteristics ◽  
Molecular Polymorphism ◽  
Pathogenic Variability

Silver Genetic diversity of Colletotrichum falcatum causing red rot of sugarcane was assessed based on morphological, pathological and molecular characteristics especially from sub-tropical Indian conditions. Sixteen isolates of this pathogen were collected based on the extensive survey on prominent varieties grown in the region along with some elite selections. Morphological observations (colony colour, mycelium pattern and sporulation) grouped the isolates into two distinct types (C1: light type and C2: dark type). However, quantitative data on colony diameter showed five clusters for these isolates. Pathogenic characterization of these isolates on fourteen standard differentials formed six groups, ingroup 1: (CF-Pb-1) isolates Cf-157, Cf-249 and Cf-248 were the most virulent while group 6 (CF-Pb-6) isolates Cf-60 and Cf-247 were the least one. The genetic relatedness among the isolates using Random Amplified Polymorphic DNA (RAPD) analysis revealed sufficient molecular polymorphism, which in turn confirmed the variation in virulence of different isolates. The data categorized different isolates into two major clusters and five independent lineages. Polymorphic information content (PIC) ranged from 0.701 to 0.929. Isolate Cf-223 was found to be genetically most diverse among all the isolates. Present study inferred that morphological grouping of most of the isolates showed positive correlation with the pathogenic variability while molecular diversity did not showed such associations.

scholarly journals MOLECULAR CHARACTERIZATION OF FIVE SELECTED BRINJAL (Solanum melongena L) GENOTYPES USING SSR MARKERS

2008 ◽  
Vol 21 (1) ◽  
pp. 01-06 ◽  
Author(s):  
A. K. M. Khorsheduzzaman ◽  
M. Z. Alam ◽  
M. M. Rahman ◽  
M. A. K. Mian ◽  
M. I. H. Mian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Banding Pattern ◽  
Genomic Dna ◽  
Molecular Level ◽  
Narrow Range ◽  
Solanum Melongena ◽  
Pcr Amplification ◽  
Simple Sequence

Five brinjal (Solanum melongena L.) genotypes were selected for characterization using Simple Sequence Repeats (SSR) markers. All the genotypes showed considerable variation in respect of morphological, anatomical and biochemical aspects. For study of relatedness, plant genomic DNA was extracted by CTAB based method using 11 randomly selected primers produced from Calgene Inc. USA. The primers developed 22 bands through PCR amplification out of which 15 from 3 primers and were polymorphic. Genetic similarities of SSR profiles were estimated based on Jaccard’s coefficient value. The dendrogram generated two clusters and they were clearly distinct and separated from each other. Cluster-I consisted of genotypes TURBO and BL009; and cluster-II comprised of genotypes EG058, EG075 and ISD006. Genotype TURBO and BL009 were identified as the diverse genotype and showed a maximum of 17% dissimilarity from EG058, EG075 and ISD006. The similarity value ranged from 0.83 to 1.00 which indicated the presence of narrow range of genetic diversity at molecular level but have still a possibility of crossing among the genotypes of two clusters. The banding pattern of different genotypes could be utilized as reference for further comparisons.DOI: http://dx.doi.org/10.3329/bjpbg.v21i1.17041

scholarly journals Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)

Forests ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 61 ◽  
Author(s):  
Chengcai Zhang ◽  
Xiaohua Yao ◽  
Huadong Ren ◽  
Jun Chang ◽  
Jun Wu ◽  
...  
Keyword(s):  
Genetic Study ◽  
Polymorphic Information Content ◽  
Genetic Research ◽  
Geographic Origin ◽  
Pcr Amplification ◽  
Genetic Studies ◽  
New Development ◽  
Ssr Loci ◽  
Simple Sequence

Research Highlights: The distribution of simple sequence repeat (SSR) motifs in two draft genomes of pecan was evaluated. Sixty-six SSR loci were validated by PCR amplification in pecan. Twenty-two new development markers can be used for genetic study in genus Carya. Background and Objectives: Pecan has good nutritional and health benefits and is an important crop worldwide. However, the genetic research in this species is insufficient. One of the main reasons for this is the lack of enough accurate, convenient, and economical molecular markers. Among different marker types, SSR loci are enormously useful in genetic studies. However, the number of SSRs in C. illinoinensis (Wangenh.) K. Koch is limited. Materials and Methods: The distribution of SSR motifs in the pecan genome was analyzed. Then, the primers for each SSR were designed. To evaluate their availability, 74 SSR loci were randomly selected and amplified in pecan. Finally, 22 new SSRs and eight former ones were picked to evaluate the genetic diversity in 60 pecan genotypes and to determine their transferability in other Carya species. Results: 145,714 and 143,041 SSR motifs were obtained from two draft genomes of ‘87MX3-2’ and ‘Pawnee’, respectively. In total, 9145 candidate primers were obtained. Sixty-six (89.19%) primers amplified the target products. Among the 30 SSRs, 29 loci showed polymorphism in 60 pecan genotypes. The polymorphic information content (PIC) values ranged from 0.012 to 0.906. In total, 26, 25, and 22 SSRs can be used in C. cathayensis Sarg., C. dabieshanensis W. C. Cheng & R. H. Chang, and C. hunanensis W.C. Liu, respectively. Finally, the dendrogram of all individuals was constructed. The results agree with the geographic origin of the four species and the pedigree relationships between different pecan cultivars. Conclusions: The characterization of SSRs in the pecan genome and the new SSRs will promote the progress of genetic study and breeding in pecan, as well as other species of genus Carya.

scholarly journals Development and Characterization of Microsatellite Markers, Genetic Diversity and Population Structure Analysis in Sapota (Manilkara Zapota (L.) P. Royen)

2021 ◽  
Author(s):  
Kundapura Venkataramana Ravishankar ◽  
Pavithra Sathanandam ◽  
Prakash Patil ◽  
Ajitha Rekha ◽  
Iyyamperumal Muthuvel ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Illumina Hiseq ◽  
Next Generation Sequencing Technology ◽  
Manilkara Zapota ◽  
Population Structure Analysis ◽  
Genomic Markers ◽  
Structure Assignment

Abstract Manilkara zapota (L.) P. Royen, a widely adaptable and popular tree meant for its appetizing fruits in tropics with no genomic resources like microsatellite markers. In order to develop genomic markers primarily for sapota, we sequenced partial genomic DNA using next generation sequencing technology on the Illumina HiSeq 2500 platform. We analyzed a total of 3.3 Gb data that were assembled into 6396224 contigs. From these contigs, 3591 simple sequence repeats were identified. Among the different type of repeats mononucleotide repeats (59.1%) were predominant followed by dinucleotide (28.6%) and trinucleotide repeats (8.2%). Primers were designed for 1285 microsatellite regions from which 30 randomly selected primers were standardized and employed for amplification in 53 genotypes of sapota. We observed 692 alleles from 30 loci with a polymorphic information content ranged from 0.85 to 0.96 with a mean of 0.9118. The probability of identity ranged from 0.002 to 0.043 with a mean of 0.012. Genetic diversity assessed by neighbour-joining and STRUCTURE assignment tests showed admixed population with 3 groups. Analysis of molecular variance revealed a significant F st value of 0.69659 indicating high genetic differentiation among the 53 genotypes. The developed microsatellites will be advantageous in assessing genetic diversity, developing linkage map and also molecular characterization of genotypes

scholarly journals Characterization of Nigerian Sesame (Sesamum Indicum L.) Using Random Polymorphic DNA (RAPD) Marker

2019 ◽  
pp. 77-84
Author(s):  
Alege Gbenga Olorunshola
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Similarity Index ◽  
Pcr Amplification ◽  
Sesamum Indicum ◽  
Uv Illumination ◽  
Sesame Genotypes ◽  
High Level

The assessment of genetic diversity among 23 sesame genotypes (Sesamum indicum L.) obtained from different locations across 10 states in Nigeria was carried out using Random Amplified Polymorphic DNA (RAPD) technique. The field trial tests were carried out on the 23 sesame accessions for two seasons to have uniform genotypes from each accessions. A standard protocol of CTAB with slight modifications was employed for DNA extracted from the harvested seeds. The extracted DNA samples were observed under UV illumination using agarose gel electrophoresis after staining with ethidium bromide. A total of 7 primers were used for PCR amplification, 5 of which have been previously used to discriminate sesame genotypes from other countries. Only 3 of the 7 primers considered produced strong amplification with the selected 23 sesame samples. A total of 47 amplified products were produced by the 3 primers among the 23 accessions all of which are 100% polymorphic. The estimates of similarity index for the 23 accessions ranged from 0.29 to 0.92. Cluster analysis revealed 2 main clusters with some of the accessions from different geographical origin cluster together in the same group which might indicate the involvement of human factor in the spread of sesame varieties in Nigeria. The relevance of RAPD to this study was evident from the high level of polymorphism reported in this study. There is therefore existence of adequate genetic diversity among the 23 Nigerian sesame accessions for sesame breeders to develop improved varieties.

scholarly journals Molecular characterization of a farmer-preferred maize landrace population from a multiple-stress-prone subtropical lowland environment

2021 ◽  
Vol 22 (2) ◽  
Author(s):  
Fortunate Makore ◽  
Edmore Gasura ◽  
Caleb Souta ◽  
Upenyu Mazarura ◽  
John Derera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Allelic Variation ◽  
Polymorphic Information Content ◽  
Heterotic Group ◽  
Heterotic Groups ◽  
Multiple Stress ◽  
Maize Landrace ◽  
Landrace Population

Abstract. Makore F, Gasura E, Souta C, Mazamura U, Derera J, Zikhali M, Kamutando CN, Magorokosho C, Dari S. 2021. Molecular characterization of a farmer-preferred maize landrace population from a multiple-stress-prone subtropical lowland environment. Biodiversitas 22: 769-777.  The study was conducted to assess genetic diversity of 372 maize lines using 116 single nucleotide polymorphism (SNP) markers. Three hundred and forty-seven lines were S1 lines (coded J lines) from a local maize landrace population and twenty-five were the widely used standard lines. The number of alleles per marker ranged from two to four and the average was three alleles.  The average polymorphic information content (PIC) value of 0.405 indicates high genetic diversity for maize lines evaluated in this study. Population structure revealed three distinct sub-populations. Sub-population 1 contained two J lines; sub-population 2 contained five J lines and sub-population 3 contained the rest of the J lines and all the standard lines. Analysis of molecular variance (AMOVA) identified 22% variance among and 78% variance within the three subpopulations, indicating high gene exchange and low genetic differentiation. Hierarchical cluster analysis further divided the lines into nine subgroups placing some of the J lines into known heterotic groups', i.e.,  J30_3, J393_4, J393_3, and J393_1 in CIMMYT heterotic group B. Allelic variation observed can be a source of allele combination for breeding programs interested in widening their genetic base. The private alleles that were present in the J lines suggest availability of stress-tolerant genes that breeders can incorporate in new hybrids.

Sign in / Sign up

Export Citation Format

Share Document