Analysis of genetic diversity in oilseed brassica germplasm through ISSR markers and isozyme profiling

Eleven Brassica germplasm were characterized through the application of 12 oligonucleotide Inter Simple Sequence Repeat (ISSR) primers. A total 1248 bands were amplified through polymorphic chain reaction and were visualized by agarose gel electrophoresis. Among the amplified marker bands 71.47% were polymorphic in nature and 352 bands were found to be monomorphic. The polymorphic bands of the amplified DNAs mostly ranged between 110 bp and 3 kb. Genetic distance among the germplasm ranged between 0.0468 and 0.7189. Moreover, three isozyme systems such as esterase, acid phosphatase and peroxidase were analyzed for allozyme variability that detected distinct 93 isozyme loci of which nearly 61.9% were polymorphic. Two dendrograms were constructed based on the ISSR profiling and isozyme data obtained through electrophoresis to find out the relatedness and phylogenetic relationship among the investigating Brassica germplasm. The clusters of the phylogenetic tree revealed 4 distinct groups of Brassica based upon their ISSR banding patterns and isozyme analysis. Nei’s genetic distance analysis provided strong information about the existence of variability among the germplasm of Brassica. All the germplasm was found to be clustered according to their respective species. Brassica carinata (Ethiopian mustard) showed individuality from all the germplasm studied and made a different branch in the phylogenetic tree suggesting its diverse origin. From the clustering pattern and genetic relationship obtained with ISSR markers and isozyme analysis, breeders can successfully identify the diverse germplasm from different cluster and use them in their future breeding program.

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Genetic diversity of Panax vietnamensis var. langbianensis populations in Lam Vien plateau - Vietnam detected by inter simple sequence repeat (ISSR) markers

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/17/4/14720 ◽

2020 ◽

Vol 17 (4) ◽

pp. 651-661

Author(s):

Le Ngoc Trieu ◽

Nong Van Duy ◽

Tran Van Tien

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Simple Sequence Repeat ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Sequence Repeat ◽

New Variety ◽

Gene Differentiation ◽

The Stability ◽

Simple Sequence

Panax vietnamensis var. langbianensis is a new variety from Lam Vien plateau of Vietnam. In this study, inter simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and variability of 115 individuals belonging to two naturally distributed populations of this variety, which classified by habitat. Genetic diversity at the taxon level was high (HeT = 0.284 and PPBT = 97.2 %). The result showed lightly higher genetic diversity in population in Lac Duong region (HeLD= 0.228 and PPBLD = 81.5 %) as compared to those located in Dam Rong region (HeDR= 0.213 and PPBDR = 79.4 %). The interpopulation gene differentiation was high (GST Total = 0.221) with the genetic distance among populations was DLD-DR = 0.191. Gene flow within populations was Nm = 0.8793. In Lac Duong population, the genetic diversity of older group (HeLD O = 0.233; PPBLD O = 77.1%) was higher than of younger group (HeLD Y = 0.214; PPBLD Y = 72.4 %) and the intergroup gene differentiation was GSTDL = 0.0205 with the genetic distance between these two group was DLD O-Y = 0.0061 showed the risk of reduction in genetic diversity. In Dam Rong population, the genetic diversity of older group (HeDR O = 0.204; PPBDR O = 75.2 %) was equal to younger group (HeDR Y = 0.209; PPBDR Y = 72.7 %) and the intergroup gene differentiation was GSTDR = 0.0304 with the genetic distance between them was DDR O-Y = 0.01393 showed the stability in genetic diversity. Data for genetic diversity and variation from this study can be used to further investigate and protect this variety for conservation and development purposes and for sustainable exploiting and use of these valuable natural resources.

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Identification of subterranean clover cultivars and their genetic relationships by isozyme analysis

Australian Journal of Agricultural Research ◽

10.1071/ar9840399 ◽

1984 ◽

Vol 35 (3) ◽

pp. 399 ◽

Cited By ~ 16

Author(s):

WJ Collins ◽

RC Rossiter ◽

Y Haynes ◽

AHD Brown ◽

DR Marshall

Keyword(s):

Natural Selection ◽

Genetic Distance ◽

Genetic Relationships ◽

Subterranean Clover ◽

Isozyme Analysis ◽

Isozyme Patterns ◽

Naturally Occurring ◽

Natural Isolates ◽

Isozyme Loci ◽

Esterase Patterns

Isozyme patterns for the 22 registered cultivars of Trifolium subterraneurn L. are described for 15 enzymes. The patterns discriminated among all cultivars except that Uniwager was isozymically identical with Geraldton, from which it was derived by deliberate mutation. The 17 cultivars which originally came from naturally occurring isolates, as well as Uniwager, appeared to be isozymically homogeneous, whereas three of the five bred cultivars (Nungarin, Esperance and Howard) were polymorphic for at least one locus. The cultivars indicated that T. subterraneum is highly polymorphic at isozyme loci. Excluding the complex esterase patterns, the species was polymorphic at 21 of 26 putative loci, with an average of 2.3 alleles detected per locus. Estimates of genetic distance between the cultivars stemming from natural isolates strongly supported the classification into three subspecies. In addition, the cultivar Woogenellup (syn Marrar) was well separated from all other cultivars of the subspecies subterraneum. Isozyme surveys should therefore provide critical evidence on the role such factors as introduction, natural selection, mutation and outcrossing have had in the origin of variation within subterranean clover in Australia.

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ISSR based analysis of genetic diversity in some endangered species of Allium subg. Melanocrommyum

Genetika ◽

10.2298/gensr1801059r ◽

2018 ◽

Vol 50 (1) ◽

pp. 59-68

Author(s):

Jalal Rezaei ◽

Zare Mehrjerdi ◽

Hassan Mastali

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

Genetic Distance ◽

Gene Diversity ◽

Program Planning ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Polymorphic Band ◽

Upgma Cluster Analysis ◽

Two Populations

Melanocrommyum, a subgenus of the Allium genus, is found in different regions of Iran and is in danger of extinction due to excessive exploitation. This study aimed to determine the genetic diversity in 170 individuals representing 17 wild populations belonging to six endangered species of Allium subg. Melanocrommyum using inter simple sequence repeat (ISSR) markers. The 10 selected ISSR primers produced 178 polymorphic fragments (100%). Polymorphic band number varied from 12 (primer 8) to 22 (primer 2). The average observed number of alleles, effective number of alleles, Shannon?s indices and Nei?s gene diversity were 1.48, 1.2, 0.2 and 0.1, respectively. According to Nei?s genetic distance, the lowest genetic distance (0.048) was observed among both two populations of A. elburzense (Emamzadeh Ebrahim and Kamelat), and two populations of A. subakaka (Jame Shoran and Ghalelan) while the highest distance (0.097) was observed among a population of A. kurdistanicum (Taze Abad Oryeh) with both A. pseudobodeanum (Shen Jari), and A. derderianum (Dareh Oson) populations. In UPGMA cluster analysis, the populations were grouped into four main clusters at a cutoff value of 0.07. The analysis of molecular variance showed that the maximum value of genetic variation was found within the populations (68%), where as a low genetic differentiation was observed among the populations (32%). Our results revealed that ISSR molecular markers are useful to display the diversity in Allium genus and can be used to improve the classification accuracy. This study provided valuable information for the conservation of these species and breeding program planning.

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APPLICATIONS OF ISSR MARKERS IN STUDIES OF GENETIC DIVERSITY OF Pityrocarpa moniliformis

Revista Caatinga ◽

10.1590/1983-21252020v33n417rc ◽

2020 ◽

Vol 33 (4) ◽

pp. 1017-1024

Author(s):

FRANCIVAL CARDOSO FELIX ◽

KYVIA PONTES TEIXEIRA DAS CHAGAS ◽

CIBELE DOS SANTOS FERRARI ◽

FÁBIO DE ALMEIDA VIEIRA ◽

MAURO VASCONCELOS PACHECO

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Distance ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Shannon Index ◽

Resolving Power ◽

Development Programs ◽

Diversity Studies ◽

Issr Molecular Markers

ABSTRACT Pityrocarpa moniliformis (Benth.) Luckow & R. W. Jobson (Fabaceae) is a native brazilian species with high potential for economic development programs in semiarid regions, mainly related to the production of honey, animal food and firewood. Thus, the objective of this work was to select Inter-Simple Sequence Repeat (ISSR) molecular markers for genetic diversity studies, as well as to test the efficiency of this approach in quantifying the genetic diversity of a natural P. moniliformis population. For this, 28 ISSR molecular markers were tested, evaluating the total number of loci, polymorphism rate and the Polymorphism Information Content (PIC) for the selected primers, the “Marker Index”, and the “Resolving Power”. Genetic diversity parameters (Nei genetic distance and Shannon index) were evaluated for 30 individuals located in Macaíba, Rio Grande do Norte State, Brazil. Seven primers were selected, which provided 74 loci, with 82% being polymorphic, while the PIC value was 0.344. The Nei genetic distance was 0.244, and the Shannon index was 0.374. Therefore, ISSR molecular markers (UBC 827, 840, 844, 857, 859, 860 and 873) are considered efficient in studying the genetic diversity of populations for the selection of matrices and germplasm banks, and may contribute to the conservation and genetic improvement of P. moniliformis populations.

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Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

Plant Genetic Resources ◽

10.1017/s1479262121000162 ◽

2021 ◽

pp. 1-11

Author(s):

Karishma Kashyap ◽

Rasika M. Bhagwat ◽

Sofia Banu

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Inter Simple Sequence Repeat ◽

Northeast India ◽

Issr Markers ◽

Citrus Reticulata ◽

Brahmaputra Valley ◽

Indian Food ◽

Cultivated Populations ◽

High Level

Abstract Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

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Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽

10.1139/g10-065 ◽

2010 ◽

Vol 53 (10) ◽

pp. 769-777 ◽

Cited By ~ 1

Author(s):

Melanie Mehes-Smith ◽

Paul Michael ◽

Kabwe Nkongolo

Keyword(s):

Dna Sequences ◽

Random Amplified Polymorphic Dna ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Pinus Monticola ◽

The Family ◽

Species Specific ◽

Rapd And Issr ◽

Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

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Multiple Origins of a Mitochondrial Mutation Conferring Deafness

Genetics ◽

10.1093/genetics/145.3.771 ◽

1997 ◽

Vol 145 (3) ◽

pp. 771-776 ◽

Cited By ~ 1

Author(s):

Timothy P Hutchin ◽

Gino A Cortopassi

Keyword(s):

Phylogenetic Analysis ◽

Genetic Distance ◽

Ribosomal Subunit ◽

Sensorineural Deafness ◽

Nucleotide Substitutions ◽

Mitochondrial Mutation ◽

Distance Analysis ◽

Multiple Origins ◽

Mtdna Haplotypes ◽

Mtdna Sequence

A point mutation (1555G) in the smaller ribosomal subunit of the mitochondrial DNA (mtDNA) has been associated with maternally inherited traits of hypersensitivity to streptomycin and sensorineural deafness in a number of families from China, Japan, Israel, and Africa. To determine whether this distribution was the result of a single or multiple mutational events, we carried out genetic distance analysis and phylogenetic analysis of 10 independent mtDNA D-loop sequences from Africa and Asia. The mtDNA sequence diversity was high (2.21%). Phylogenetic analysis assigned 1555G-bearing haplotypes at very divergent points in the human mtDNA evolutionary tree, and the 1555G mutations occur in many cases on race-specific mtDNA haplotypes, both facts are inconsistent with a recent introgression of the mutation into these races. The simplest interpretation of the available data is that there have been multiple origins of the 1555G mutation. The genetic distance among mtDNAs bearing the pathogenic 1555G mutation is much larger than among mtDNAs bearing either evolutionarily neutral or weakly deleterious nucleotide substitutions (such as the 4336G mutation). These results are consistent with the view that pathogenic mtDNA haplotypes such as 1555G arise on disparate mtDNA lineages which because of negative natural selection leave relatively few related descendants. The co-existence of the same mutation with deafness in individuals with very different nuclear and mitochondrial genetic backgrounds confirms the pathogenicity of the 1555G mutation.

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Mammalian species identification using ISSR-HRM technique

Science Progress ◽

10.1177/00368504211026163 ◽

2021 ◽

Vol 104 (2) ◽

pp. 003685042110261

Author(s):

Wannapimol Kriangwanich ◽

Korakot Nganvongpanit ◽

Kittisak Buddhachat ◽

Puntita Siengdee ◽

Siriwadee Chomdej ◽

...

Keyword(s):

Species Identification ◽

Mammalian Species ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Forensic Sciences ◽

Illegal Trade ◽

Body Parts ◽

Contributing Factors ◽

Biodiversity Crisis ◽

Issr Primers

Wildlife trading and the illegal hunting of wildlife are contributing factors to the biodiversity crisis that is presently unfolding across the world. The inability to control the trade of animal body parts or available biological materials is a major challenge for those who investigate wildlife crime. The effective management of this illegal trade is an important facet of wildlife forensic sciences and can be a key factor in the enforcement of effective legislation surrounding the illegal trade of protected and endangered species. However, the science of wildlife forensics is limited by the absence of a comprehensive database for wildlife investigations. Inter-simple sequence repeat markers (ISSR) coupled with high resolution melting analysis (HRM) have been effectively used for species identification of 38 mammalian species. Six primers of the ISSR markers were chosen for species identification analysis. From six ISSR primers resulting in a range of accuracy of 33.3%–100% and 100% in terms of precision in every primer. Furthermore, 161 mammalian samples were 100% distinguished to the correct species using these six ISSR primers. ISSR-HRM analysis was successfully employed in determining mammal identification among varying mammalian species, and thus could serve as an effective alternative tool or technique in the species identification process. This option would offer researchers a heightened level of convenience in terms of its performance and the ease with which researchers or field practice veterinarians would be able to interpret results in effectively identifying animal parts at wildlife investigation crime scenes.

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