scholarly journals Genetic Divergence of Flax Genotypes (Linum Usitatissimum L.) Utilizing Microsatellite Markers

2017 ◽  
Vol 5 (1) ◽  
pp. 123-129 ◽  
Author(s):  
Sumita Nag ◽  
Jiban Mitra
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Linum Usitatissimum ◽  
Rank Correlation ◽  
Natural Fibre ◽  
Similarity Coefficients ◽  
Oilseed Crops ◽  
Linum Usitatissimum L ◽  
Ssr Primers ◽  
Ssr Loci

Flax (Linum usitatissimum L.), stoods in position third, being the largest natural fibre crop and simultaneously one of the five preeminent oilseed crops in the world. SSR/microsatellite markers are extensively utilized for genetic diversity analysis and cultivar identification considering their myriad abundance, co-dominant inheritance, steep polymorphism, reproducibility, and comfort of assay by PCR. Ten microsatellites were amplified in 27 genotypes of Flax. The study was undertaken to assess the genetic diversity in flax and to select most diverse genotypes for future breeding program. Primer efficiency parameters were studied. The 10 SSR loci amplified a total of 41 alleles that were used for genetic analysis. Most primers have PIC value greater than 0.5 and the LU6 marker was highly polymorphic PIC = 0.95. Estimates of RP̅ were highest for the primer LU1 (0.68). The maximum MI was observed for the primer LU10 (3.56). The H and D ranged from 0.26 to 1.78 and 0.36 to 5.40, respectively. According to Spearman rank correlation, PIC and MI were most important parameters in assessing the efficiency of whole set of 10 SSR primers. Dendrogram was constructed using the genetic similarity coefficients using UPGMA. PCo-A was also performed in support. Genetic diversity in Flax was revealed at molecular level.

scholarly journals Microsatellite markers-based characterisation of elephant grass (Pennisetum purpureum) harvested from selected locations in South-West Nigeria

2020 ◽  
Vol 37 (1) ◽  
pp. 38-45
Author(s):  
O.A. Okukenu ◽  
A.A. Olajide ◽  
P.A. Dele ◽  
M. Wheto ◽  
B.T. Akinyemi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Dna Extraction ◽  
Morphological Characterization ◽  
Ethanol Solution ◽  
Pennisetum Purpureum ◽  
Elephant Grass ◽  
South West ◽  
Ssr Primers ◽  
Genetic Index

This study was carried out to characterise Pennisetum purpureum harvested from some selected locations in S outh-W estern Nigeria using microsatellite markers. Leaf parts of growing young elephant grass (Pennisetum purpureum) were harvested and immediately preserved in ethanol solution before DNA extraction. Two (2) SSR primers (CTM59 and Xtxp278) were used to assess genetic diversity in Pennisetum purpureum. The result shows that 72% of the molecular variations in the elephant grass exists within the population with 28% among the population; there were no unique characteristics among the Nine (9) populations. Nei genetic index ranged from 0.067 (lowest) observed between Isokan and Odeda populations to 0.158 (highest), between Ifedore and Ikoyi Populations. Morphological characterization showed moderate diversity with two major clusters and one minor cluster. Keyword: Elephant grass; cultivars; locations; markers

scholarly journals Molecular Characterization and Similarity Relationships among Flue-Cured Tobacco (Nicotiana tabacum L.) Genotypes Using Simple Sequence Repeat Markers

2012 ◽  
Vol 40 (2) ◽  
pp. 247
Author(s):  
Soheila GHOLIZADEH ◽  
Reza DARVISHZADEH ◽  
Babak ABDOLLAHI MANDOULAKANI ◽  
Iraj BERNOUSI ◽  
Seyed Reza ALAVI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Allele Number ◽  
Nicotiana Tabacum L ◽  
Ssr Loci ◽  
Actual Degree ◽  
Similarity Relationships

Characterization of genetic diversity has long been a major goal in tobacco breeding programs. Information on genetic diversity is essential for a rational use of genetic resources. In the present study, the genetic variation among 72 flue-cured tobacco genotypes was evaluated using microsatellite markers (SSRs). A set of 104 alleles was generated at 30 SSR loci. The mean number of alleles per locus (na) and the effective allele number (ne) were 3.467 and 2.358, respectively. The expected heterozygosity ranged from 0.29 to 0.75 with average of 0.54. Several methods were used to construct the similarity matrices and dendrograms. The co-phenetic correlation coefficient, which is a measure of the correlation between the similarities represented on the dendrograms and the actual degree of similarity, was calculated for each dendrogram. Among the different methods, the highest value (r=0.76368) was observed for the UPGMA created based on Jaccard’s similarity coefficients. The genetic similarity among the tobacco genotypes calculated by using Jaccard’s similarity coefficient ranged from 0.08 to 0.84, suggesting the presence of high molecular genetic variability among the studied tobacco genotypes. Based on UPGMA clustering method all studied flue-cured tobacco genotypes, except for ‘Glustinusa Rasht’, were placed in three distinct groups. We observed an obvious heterotic pattern in the studied flue-cured germplasm corresponding to genetic distances and classification dendrogram, which persuades exploitation of heterosis in flue-cured tobaccos.

Evidence of the domestication history of flax (Linum usitatissimum L.) from genetic diversity of the sad2 locus

2005 ◽  
Vol 112 (1) ◽  
pp. 58-65 ◽  
Author(s):  
Robin G. Allaby ◽  
Gregory W. Peterson ◽  
David Andrew Merriwether ◽  
Yong-Bi Fu
Keyword(s):  
Genetic Diversity ◽  
Linum Usitatissimum ◽  
Linum Usitatissimum L ◽  
History Of

scholarly journals Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Suping Feng ◽  
Helin Tong ◽  
You Chen ◽  
Jingyi Wang ◽  
Yeyuan Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genomic Library ◽  
Trinucleotide Repeats ◽  
The Other ◽  
Diversity Analysis ◽  
Dominant Type ◽  
Genetic Diversity Analysis ◽  
Ssr Loci ◽  
Ssr Development

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

scholarly journals Genetic Diversity Analysis of Linseed (Linum usitatissimum L.) at Bilaspur Plain Region of Chhattisgarh

2021 ◽  
Vol 5 (6) ◽  
pp. 59-63
Author(s):  
Pallavi Manhar ◽  
Roshan Parihar ◽  
NK Choure ◽  
AP Agrawal ◽  
Dhanendra Kumar
Keyword(s):  
Genetic Diversity ◽  
Linum Usitatissimum ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis ◽  
Linum Usitatissimum L ◽  
Plain Region

scholarly journals Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259146
Author(s):  
Venugopal Vidya ◽  
Duraisamy Prasath ◽  
Mohandas Snigdha ◽  
Ramasamy Gobu ◽  
Charles Sona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Zingiber Officinale ◽  
Eastern India ◽  
Coding Sequences ◽  
North Eastern ◽  
Ssr Primers ◽  
Ssr Loci ◽  
North Eastern India

Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine. A considerable extent of genetic diversity in ginger occurs in the Western Ghats and North-Eastern India. However, genetic diversity studies at the molecular level in ginger is limited due to limited availability of genetic and genomic information. In the present study, for the first time, we have identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from ginger. We obtained 16,790 EST-SSR loci from 78987 unigenes, and 4597 SSR loci in the predicted 76929 coding sequences from RNA-Seq assembled contigs of ginger through Illumina paired-end sequencing. Gene ontology results indicate that the unigenes with SSR loci participate in various biological processes such as metabolism, growth, and development in ginger. One hundred and twenty-five primer pairs were designed from unigenes and coding sequences. These primers were tested for PCR optimization, characterization, and amplification and identified 12 novel EST-SSR markers. Twelve flanking polymorphic EST-SSR primers were validated using 48 ginger genotypes representing North-Eastern India and different eco-geographical adaptations by PCR amplification and allele sizing through capillary electrophoresis. Twelve EST-SSR primers generated a total of 111 alleles with an average of 9.25 alleles per locus and allele sizes ranging between 115-189bp. This study implies that the SSR markers designed from transcriptome sequences provides ample EST-SSR resources, which are helpful for genetic diversity analysis of Zingiberaceae species and molecular verification of ginger genotypes.

scholarly journals Molecular Analysis of Genetic Diversity and Geographic Origin within an Ex Situ Germplasm Collection of Cherimoya by Using SSRs

2007 ◽  
Vol 132 (3) ◽  
pp. 357-367 ◽  
Author(s):  
P. Escribano ◽  
M.A. Viruel ◽  
J.I. Hormaza
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Germplasm Collection ◽  
Ex Situ ◽  
Group Method ◽  
Pair Group ◽  
Ssr Primers ◽  
Upgma Cluster Analysis ◽  
Ssr Loci ◽  
Simple Sequence

Cherimoya (Annona cherimola Mill.) is an underused fruit crop with a clear niche for expansion in subtropical climates. In this study, 16 simple sequence repeat (SSR) loci were used to find molecular polymorphisms among 279 cherimoya accessions from a worldwide ex situ field germplasm collection. A total of 79 amplification fragments were amplified with 16 pairs of SSR primers, with an average of 4.9 bands/SSR. Mean expected and observed heterozygosities averaged 0.53 and 0.44, respectively. The total value for the probability of identity was 4.34 × 10−8. The SSRs studied resulted in 267 different fingerprinting profiles, of which 258 were unique genotypes; the rest were putative cases of synonymies or mislabeling errors. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis indicated the relationships among the analyzed accessions, showing some specific groups related to their geographical origins. Analysis of molecular variance (AMOVA) was performed to examine the distribution of genetic variation of the 148 accessions collected from putative cherimoya origin areas in Ecuador and Peru, showing that the major variations occurred within valleys in each country. The results confirmed the usefulness of microsatellites for identification of genetic diversity and geographic origin of cherimoya and are discussed in terms of their implications for ex situ conservation of cherimoya genetic resources.

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