scholarly journals Informative Inter Simple Sequence Repeat (ISSR) primers for genetic analysis of coconut (Cocos nucifera L.) germplasm

CORD ◽  
2005 ◽  
Vol 21 (02) ◽  
pp. 34 ◽  
Author(s):  
R. Manimekalai
Keyword(s):  
Information Content ◽  
Polymorphism Information Content ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Rapid Screening ◽  
Sequence Repeat ◽  
Marker Index ◽  
Simple Sequence ◽  
Issr Primers

Inter Simple Sequence Repeat (ISSR) markers are versatile and used in a number of applications viz. genetic diversity estimation, phylogenetic relationship and gene tagging in different crops. In coconut, the ISSR markers are being reported here for the first time. In the present paper, thirty-five  primers targeting to amplify the inter microsatellite  regions were screened  using  thirty  different  coconut  germplasm  accessions.  The  ISSR  primers  were evaluated based on polymorphism information content and marker index.  Out of 35 primers screened,  19 primers  produced  clear amplification  pattern.  The polymorphism  information content varied between 0.019 and 0.386, whereas, the marker index ranged from 0.019 to 5.673  among  the  primers.    Based  on  the  high  marker  index,  five  and  ten  primers  were selected.  The similarity  matrices  were constructed  separately  for five, ten and 19 primers using NYSYS software and the correlation was tested using Mantel’s test. There was high correlation  between five and ten primers with 19 primers. Hence, the primers with higher marker index (5 and 10 primers) were regarded as informative  primers. These informative primers can be used to develop more polymorphic markers in coconut for rapid screening of germplasm materials.

scholarly journals Screening of homokaryotic protoclones of Agaricus bisporus (J. Lge) Imbach by colony characters and ISSR markers

2010 ◽  
Vol 39 (1) ◽  
pp. 119-122 ◽  
Author(s):  
Mahmudul Islam Nazrul ◽  
Fan Xiao Lin ◽  
Bian Yin-Bing
Keyword(s):  
Simple Sequence Repeat ◽  
Agaricus Bisporus ◽  
Morphological Characters ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Fruiting Bodies ◽  
Sequence Repeat ◽  
Slow Growing ◽  
Simple Sequence ◽  
Issr Primers

Among ten slow-growing protoclones of Agaricus bisporus (J. Lge) Imbach, all appressed colonies showed slower growth rate and spawn run, and inability to produce fruiting bodies in substrate. Seven of 40 inter-simple sequence repeat (ISSR) primers amplified 78 reproducible fragments, 48.93% were polymorphic, each producing 7 to 16 bands ranging from 0.10 to 2.10 kbp, sufficient to differentiate the protoclones from each other. Appressed protoclones were homoallelic at a number of loci that were heteroallelic in the parent, suggesting that they represented rare homokaryons. Thus, using morphological characters along with ISSR, polymorphisms could be useful for quick, easy, and accurate in distinguishing homo- and heterokaryotic isolates. Key words: Agaricus bisporus (J. Lge) Imbach; Homokaryon; ISSR; Protoclone DOI: 10.3329/bjb.v39i1.5537Bangladesh J. Bot. 39(1): 119-122, 2010 (June)

Inter Simple Sequence Repeat markers for analysis of molecular diversity and genetic structure of eighteen Dendrobium cultivars in Sri Lanka

2018 ◽  
Vol 6 (3) ◽  
pp. 91-102
Author(s):  
Thanuja Dilrukshi Dharmarathna ◽  
H.M.D.A.K. Herath ◽  
P.A. Weerasinghe ◽  
H.M.V.G. Herath
Keyword(s):  
Information Content ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Morphological Characters ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Information Index ◽  
Expected Heterozygosity ◽  
Simple Sequence

The genus Dendrobium is one of the largest genera in the family Orchidaceae having more than thousand species over the world with diverse morphological characters. Dendrobium is a popular ornamental plant with complex genetic background which emphasize on the species identification at molecular level. The present study was aimed to identify Inter-Simple Sequence Repeat (ISSR) markers capable of detecting genetic polymorphism to characterize 18 hybrid, commercially available Dendrobium cultivars. Genomic DNA of each cultivar was extracted using CTAB method. A total of 17 different ISSR primers were evaluated. Only the reproducible bands were scored and number of different alleles (Na), number of effective alleles (Ne), Shannon’s Information Index (I), Expected heterozygosity (He), Unbiased expected heterozygosity (UHe), polymorphic percentage and polymorphic information content (PIC) of each primer were calculated. The highest Shannon’s Information Index (0.537±0.08) was recorded by the primer UBC 826 while the highest polymorphic information content (PIC) was generated by primer UBC 807. The PIC values of the primers were ranged from 0.0068 to 0.451, indicating that primers are moderately informative. In total, 631 bands representing 120 loci were amplified showing 85.71% - 100% polymorphism. The genetic similarities between individuals were compiled in the Nei’s genetic identity matrix in order to construct the UPGMA dendrogram. Principle component analysis (PCA) and clustering analysis were done to divide different cultivars into groups. The analysis revealed the presence of four major clusters and two minor clusters among the cultivars. The study suggested that the ISSR markers originated from eight primers 12, 155, UBC 807, UBC 812, UBC 826, UBC 835, UBC 841 and UBC 842 can be used in the detection of molecular variation among cultivars in the genus Dendrobium.

Genetic diversity in wild Lens spp. using inter simple sequence repeat (ISSR) marker

2015 ◽  
Vol 38 (5) ◽  
Author(s):  
Padmavati G. Gore ◽  
M. K. Rana ◽  
Kuldeep Tripathi ◽  
Mohar Singh ◽  
I. S. Bisht ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Molecular Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Principal Coordinates ◽  
Cultivated Species ◽  
Simple Sequence ◽  
Issr Primers

Genetic diversity was assessed in 50 accessions of seven <italic>Lens</italic> species using ISSR markers. The collection included accessions of the cultivated species <italic>L. culinaris</italic> and six wild species, <italic>viz</italic>., <italic>L. culinaris</italic> ssp. <italic>odemensis, L. culinaris</italic> ssp. <italic>orientalis</italic>, <italic>L.</italic> <italic>orientalis, L. nigricans, L. lamottei</italic> and <italic>L. ervoides.</italic> The 23 ISSR primers amplified a total of 368 bands with an average of 16 bands per primer. Maximum number of 20 bands was amplified using each of the primers ISSR-34 and ISSR-835. All the primers were found to be polymorphic. PIC values ranged from 0.02 to 0.80. The primers ISSR-807, ISSR- 809, ISSR- 827, ISSR- 847, ISSR-28 and ISSR- 37 were found to be very useful for analyzing the molecular diversity of the genus <italic>Lens</italic>. Cluster Analysis and Principal Coordinates Analyses placed the 50 accessions into two groups and complemented each other.

Preliminary Assessment of Genetic Diversity in Cultivated Glycyrrhiza uralensis, G. inflate and G. glabra by Chemical Fingerprint and Inter-Simple Sequence Repeat Markers

2011 ◽  
Vol 347-353 ◽  
pp. 1318-1325 ◽  
Author(s):  
Ting Liu ◽  
Hai Ming Lin
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Glycyrrhiza Uralensis ◽  
Sequence Repeat ◽  
Chemical Fingerprint ◽  
Chemical Fingerprints ◽  
Simple Sequence ◽  
Issr Primers

The two main secondary metabolites in Glycyrrhiza Species are Glycyrrhizic acid and liquiritin. They are considered as active ingredients . The content of these compounds showed variation in different species. Standard chemical fingerprints were generated from cultivated Glycyrrhiza uralensis, G. inflate and G. glabra, which could be identification markers. Five efficient inter-simple sequence repeat (ISSR) primers were screened and optimized for detecting the genetic diversity in three cultivated Glycyrrhiza uralensis, G. inflate and G. glabra. By using two characteristic peaks compare with three cultivars, Glycyrrhiza uralensis and G. glabra were bigger similarity than G. inflate. The results is in accordance with the results by ISSR markers. The higher genetic diversity in G. inflate was useful to more broad breeding. Our result suggest that provides an optimized method for assessment genetic diversity of cultivated Glycyrrhiza uralensis, G. inflate and G. glabra using Chemical fingerprint and ISSR markers which is useful for further investigation in breeding.

scholarly journals Genetic diversity and interspecific relationships of some Allium species using inter simple sequence repeat markers

2015 ◽  
Vol 22 (2) ◽  
pp. 67-75 ◽  
Author(s):  
Leila Samiei ◽  
Mahnaz Kiani ◽  
Homa Zarghami ◽  
Farshid Memariani ◽  
Mohammad Reza Joharchi
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Allium Species ◽  
Interspecific Relationships ◽  
Simple Sequence

In this study genetic diversity and interspecific relationships of 11 Allium L. species from Khorassan province of Iran including 32 accessions were investigated by inter simple sequence repeat (ISSR) markers. Nine ISSR primers produced a total of 80 polymorphic markers and revealed high polymorphism among the studied species. The average gene diversity, effective number of alleles and Shannon’s information index were 0.2, 1.28 and 0.3, respectively. Allium kuhsorkhense exhibited the greatest level of variation (He: 0.18), whereas A. stipitatum demonstrated the lowest level of variability (He: 0.05). UPGMA (Unweighted Pair Group Method with Arithmetic mean) analysis showed that Allium accessions have a similarity range of 0.60 to 0.95. Allium scapriscapum composed the most distant group in the dendrogram. The clustered groups of Allium species clearly reflect the recent taxonomic concept of the genus at the subgenus and section levels. The present study showed that the ISSR technique is an effective molecular approach for analyzing genetic diversity and relationship in Allium species.Bangladesh J. Plant Taxon. 22(2): 67-75, 2015 (December)

Extent of clonality, genetic diversity and decline in the endangered mallee Eucalyptus imlayensis

2007 ◽  
Vol 55 (5) ◽  
pp. 548 ◽  
Author(s):  
Elizabeth A. James ◽  
Keith L. McDougall
Keyword(s):  
Simple Sequence Repeat ◽  
Ex Situ Conservation ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Lower Number ◽  
Ex Situ ◽  
Sequence Repeat ◽  
Eastern Australia ◽  
Number Of Stems ◽  
Simple Sequence

Eucalyptus imlayensis Crisp & Brooker is a rare mallee known from one location in south-eastern Australia. Discovered in 1977, the population has declined in number and health of stems since 1998. Inter-simple sequence repeat (ISSR) markers were used to assess genetic variation and clonality. Only five multilocus genotypes were distinguished from 27 samples and the proximity of like genotypes within the population is consistent with the population being largely clonal. This means that the species has a much lower number of genetic individuals than is suggested from a census of the number of stems present. The implications of this finding for ex situ conservation of the species are discussed.

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