scholarly journals Comparison among Methods and Statistical Software Packages to Analyze Germplasm Genetic Diversity by Means of Codominant Markers

J ◽  
2018 ◽  
Vol 1 (1) ◽  
pp. 197-215 ◽  
Author(s):  
Mario Pagnotta
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Open Access ◽  
Basic Principles ◽  
Statistical Software ◽  
Germplasm Collections ◽  
Software Packages ◽  
Dominant Markers ◽  
Selection Of

Co-dominant markers’ data are often analysed as if they were dominant markers, an over-simplification that may be misleading. Addressing this, the present paper aims to provide a practical guide to the analysis of co-dominant data and selection of suitable software. An overview is provided of the computational methods and basic principles necessary for statistical analyses of co-dominant molecular markers to determine genetic diversity and molecular characterization of germplasm collections. The Hardy–Weinberg principle is at the base of statistical methods to determine genetic distance, genetic diversity, and its distribution among and within populations. Six statistical software packages named GenAlEx, GDA, Power Marker, Cervus, Arlequin, and Structure are compared and contrasted. The different software packages were selected based on: (i) The ability to analyze co-dominant data, (ii) open access software, (iii) ease of downloading, and (iv) ease of running using a Microsoft Window interface. The software packages are compared analyzing the same dataset. Differences among parameters are discussed together with the comments on some of the software outputs.

scholarly journals Single Nucleotide Polymorphisms and Indel Markers from the Transcriptome of Garlic

2016 ◽  
Vol 141 (1) ◽  
pp. 62-65 ◽  
Author(s):  
Michael J. Havey ◽  
Yul-Kyun Ahn
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Characteristics ◽  
Single Nucleotide ◽  
Germplasm Collections ◽  
Indel Markers ◽  
Production Environments ◽  
Culinary Uses

Garlic (Allium sativum) is cultivated worldwide and appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great morphological variation and adaptability to diverse production environments. Molecular markers and phenotypic characteristics have been used to assess the genetic diversity among garlics. In this study, we undertook transcriptome sequencing from a single garlic plant to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid (DH) of onion (Allium cepa). Single nucleotide polymorphisms (SNPs) and insertion–deletion (indel) events were identified in 4355 independent garlic assemblies. A sample of the indels was verified using the original complementary DNA (cDNA) library and genomics DNAs from diverse garlics, and segregations confirmed by sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for estimates of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.

Assessment of Genetic Diversity of Rheum species (Endangered Medicinal Herb of Indian Himalayan Region) using Molecular Markers

2021 ◽  
Vol 16 (11) ◽  
pp. 147-154
Author(s):  
Anjali Uniyal ◽  
Akhilesh Kumar ◽  
Sweta Upadhyay ◽  
Vijay Kumar ◽  
Sanjay Gupta
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Fragment Length Polymorphism ◽  
Dna Polymorphisms ◽  
Inter Simple Sequence Repeats ◽  
Pharmaceutical Industries ◽  
Endangered Medicinal Herb ◽  
Identification And Characterization ◽  
Simple Sequence

The Rheum species are important medicinal plants that are facing extinction due to their unplanned development and overexploitation by pharmaceutical industries. DNA polymorphisms are not prone to environmental modifications, thus they are widely used for the identification and characterization of plants. The use of different molecular markers has enabled the researchers for the valuation of genetic variability and diversity in its natural zone of distribution. The conventional approach may take several years to yield this information. For the estimation of molecular and genetic variations in geographical zone of distribution, various molecular markers technique are available like RAPD (Randomly Amplified Polymorphic DNA), RFLP (Restriction fragment length polymorphism), ISSR (Inter-Simple Sequence Repeats), SSR and AFLP. The uses of different molecular markers for the study of genetic diversity have been discussed in the review.

Analisis Keragaman Genetik 28 Nomor Koleksi Kakao (Theobroma cacao L.) Berdasarkan Marka SSR

2017 ◽  
Vol 4 (1) ◽  
pp. 13 ◽  
Author(s):  
Ilham Nur ardhi Wicaksono ◽  
Rubiyo Rubiyo ◽  
Dewi Sukma ◽  
Sudarsono Sudarsono
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Plant Molecular Biology ◽  
Average Value ◽  
Germplasm Collections ◽  
Ctab Method ◽  
Parental Lines ◽  
Biology Laboratory ◽  
Superior Clones ◽  
Selection Of

<em>Analysis of genetic diversity of cacao germplasm collections using molecular markers has an important role in the assembly of new superior clones. The availability of commercial and superior local clones could increase the success of new superior clones’ assembly. Hence, the genetic diversity analysis of these materials needs to be done. The study was aimed to analyze genetic diversity of 28 cacao collections based on SSR markers that would be useful for selection of parental lines. The research was conducted in the Integrated Laboratory, Indonesian Industrial and Beverage Crops Research Institute, Sukabumi, and Plant Molecular Biology laboratory, Bogor Agricultural University, from November 2015 to May 2016.</em> <em>Analysis of genetic diversity was conducted using 28 cacao clones (13 superior local clones and 15 commercial clones). DNA was extraction using CTAB method, which then amplified by PCR technique using 20 SSR primers. The result showed that all SSR markers used in this study were polymorphic with an average value of PIC was high (57%). Phylogenetic tree constructed using DARwin program version 6.05 is divided into 3 major groups, which placed commercial and superior local clones together in each group. Superior local clones observed herein might have close relationships with commercial clones that have long been cultivated in Indonesia. Furthermore, some cacao clones could potentially be parental lines because they had high genetic distance. The results showed that SSR markers are powerful tools to determine potential parental lines, which is expected to increase the chances of heterosis in their progenies.</em>

Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers

Parasitology ◽  
2002 ◽  
Vol 125 (7) ◽  
pp. S51-S59 ◽  
Author(s):  
J. CURTIS ◽  
R. E. SORENSEN ◽  
D. J. MINCHELLA
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Microsatellite Markers ◽  
Natural Populations ◽  
Mitochondrial Marker ◽  
Tropical Regions ◽  
Blood Flukes

Blood flukes in the genus Schistosoma are important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found in Schistosoma mansoni and some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers for S. mansoni provided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.

scholarly journals Selection of ISSR Primers to Study the Genetic Diversity of Myrciaria floribunda O. Berg

2020 ◽  
pp. 23-28
Author(s):  
Luiz Sergio Costa Duarte Filho ◽  
Danielson Ramos Ribeiro ◽  
Allison Vieira da Silva
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
South America ◽  
Central America ◽  
Dna Extraction ◽  
Endemic Species ◽  
Germplasm Bank ◽  
Slow Growing ◽  
Selection Of ◽  
Issr Primers

The species Myrciaria floridunda O. Berg, popularly known as cambuí, belongs to the Myrtaceae family. Cambui is a native, non-endemic species that occur in diverse environments in Central America and South America. They are slow-growing plants with a shrub or sub-shrub habit. The fruits, the product of interest of the species, are small, spherical berries orange or red in colorturning to wine colorwhen they are ripe. The exploitation of the species is still mostly extractivist, carried out by traditional local families who, in times of fruiting of the species, leverage their income by selling fruits at fairs. The fruits can be eaten fresh, in the form of jellies, liquor or wine. To study the genetic diversity of the species using ISSR-type molecular markers, it is necessary to first isolate DNA in sufficient quality and quantity. Here, leaves for DNA extraction were collected from the active germplasm bank of the Federal University of Alagoas, Brazil. The DNA of the species was extracted using CTAB detergent methodology with modifications adapted to the species. Twelve ISSR primers were tested on DNA from two cambui genotypes. Of the twelve primers, eight were selected due to their polymorphism index above 50%, namely: UFAL-2, UFAL-3, UFAL-5, UFAL-6, UFAL-7, UFAL-8, UFAL-9 and UFAL-10.

scholarly journals Exploring Plant Genetic Variations with Morphometric and Molecular Markers

2021 ◽  
Author(s):  
Bushra Sadia ◽  
Faisal Saeed Awan ◽  
Fozia Saleem ◽  
Javaria Altaf ◽  
Abdullah Bin Umar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Variability ◽  
Human Population ◽  
Crop Improvement ◽  
Genetic Variations ◽  
Germplasm Collections ◽  
Crop Germplasm ◽  
Insight Into ◽  
Sorghum Germplasm

For centuries, crop improvement has served as the basis of food security of ever increasing human population. Though vast germplasm collections are available; their exploitation for crop improvement still depends upon efficient assessment of genetic diversity. Genetic variability is the key element in adaptation of plants to varying climates. While crops with narrow genetic diversity are vulnerable to stresses. The estimation of extent and pattern of genetic variability is a prerequisite for generating superior varieties. Genetic diversity analysis generates key information to dissect genetic variations in crop germplasm with the help of morphometrical, biochemical and molecular tools. Among these, DNA markers provide a reliable and detailed insight into the similarities and differences among crops. In this chapter, we discuss the applications of phenotypic and molecular markers to probe genetic divergence in crops and present case studies that describe the significance of these tools to characterize sorghum germplasm. Furthermore, we spotlight sorghum biodiversity exploration efforts worldwide and propose future directions.

scholarly journals Characterization of grass pea (Lathyrus sativus L.) germplasm collections for the beneficial agronomic traits

2018 ◽  
Vol 78 (3) ◽  
Author(s):  
Ashutosh Sarker ◽  
Karthika Rajendran ◽  
Murari Singh ◽  
Ali M.Abd El-Moneim ◽  
Hani Nakkoul
Keyword(s):  
Seed Yield ◽  
Seed Weight ◽  
Agronomic Traits ◽  
Phenotypic Selection ◽  
Germplasm Collections ◽  
Biological Yield ◽  
The Stability ◽  
Lathyrus Sativus L ◽  
Selection Of

At ICARDA, germplasm collections obtained from five countries namely, Bangladesh, Ethiopia, Syria, Nepal and Pakistan were grouped in to seven sets of trials (BANG1, BANG2, ICARDA, ETH1, ETH2, NEP, PAK) and evaluated in two experimental locations, Tel Hadya and Breda over eight years. Characterization was done for the most desirable agronomic traits such as days to first flowering, days to 95 % maturity, biological yield, seed yield, hundred seed weight and Harvest index. Significant genotypic and interaction effect were found for the expression of the traits. Substantial amount of variability was revealed in the germplasm collections for most of the traits. High broad sense heritability was observed for days to first flowering and hundred seed weight indicating early phenotypic selection of these two traits. The stability over years for the seed yield (in terms of the CV), identified promising accessions such as ILG2178 in BANG1 and ILG1721, ILG1632, ILG1624, ILG1540 and ILG1501 for future breeding.

scholarly journals Molecular Markers for the Detection of Genetic Drift: The Case of Pea and Ryegrass

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 692c-692
Author(s):  
Charles J. Simon ◽  
Richard C. Johnson
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Plant Introduction ◽  
Gene Frequencies ◽  
Virus Eradication ◽  
Genetic Changes ◽  
Germplasm Collections ◽  
Loss Of Genetic Diversity ◽  
Western Regional ◽  
Vigorous Plant

Maintenance of genetic resources within the National Plant Germplasm System includes preserving the genetic constituency of accessions as close to the original sample as possible. Genetic changes that can arise during seed regeneration include both an overall loss of genetic diversity within heterogenous accessions and changes in the gene frequencies within accessions. Two germplasm collections are being examined with molecular methods at the Western Regional Plant Introduction Station (WRPIS) for evidence of such genetic change. In the case of pea, gross observation of seed and plant characters indicate that vigorous plant culling during a comprehensive Pea Seedbourne Mosaic Virus eradication program a decade ago resulted in the overall loss of genetic diversity in some heterogenous accessions. Isozyme data has corroborated these observations. Molecular markers are beginning to be used, both to quantify possible genetic changes in accessions as a result of the eradication process, and to document success in reintroducing diversity by repeating the eradication process with additional seed from archival seedlots. In the case of ryegrass, the practice of bulking the seed harvested from regeneration plots may bias the seedlot toward genotypes that are more fruitful. Isozyme analysis after two regeneration cycles showed that balanced sampling (equal seed no./plant) maintained allele frequencies close to the original seed sample. A bulk harvest sample and a sample with an equal number of spikes harvested from each plant showed some significant change in allele frequency, but no significant changes were seen in the allelic richness of accessions, or in the level of an accession's overall heterozygosity. A regeneration sample with an equal number of seed/plant will therefore best preserve gene frequencies within accessions, but loss of an accessions overall diversity will not diminish as a result of less than ideal sampling methods in ryegrass.

scholarly journals GENETIC CHARACTERIZATION OF GALOBA DURIAN (AMONUM SPP.) IN AMBON ISLAND BASED ON RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD)

2018 ◽  
Vol 3 (1) ◽  
pp. 27-33
Author(s):  
Fuadiska Salamena ◽  
Cecilia Anna Seumahu
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Characterization ◽  
Kidney Diseases ◽  
Random Amplified Polymorphic Dna ◽  
Quantitative Result ◽  
Dna Amplification ◽  
Polymorphic Band ◽  
Qualitative And Quantitative

Galoba durian is one of the endemic floras from Maluku. Galoba durian is a species belonging to the Amomum genera Zingiberaceae family. It is also used as a medicinal plant for waist and kidney diseases. Based on the color of the fruit, galoba durian is divided into two nmely red galoba durian and green galoba durian. Distribution of this plant in Ambon can found in a few places such as highland and coastal area. Different locations influence phenotypic of plants, but may not show different genetic characteristic. Genetic diversity can detected by molecular markers. Genetic characterization from galoba durian using RAPD markers has not been done before. This study aimed to analyze genetic diversity from galoba durian using molecular markers RAPD. Samples of plants are used red galoba durian from Hatu and green galoba durian from Hatalae. The result of the first study, characterization of the morphology of the galoba durian, showed that both galoba have almost similar characteristics. Further DNA was tested by qualitative and quantitative. Result shows good qualitative and quantitative of DNA genomic. The second study was amplification by PCR-RAPD. DNA amplifications were performed using 3 primers out of 9 screened random primers. The primers selection was based on hight polymorphism. DNA amplification has 36 bands which were 100% polymorphic. The size of each bands from visualization of agarose was determined by linear regression. Number of band amplified was range from 120 to 1612 bp. Polymorphic band of RAPD showed the highest  genetic diversity. It can be concluded that the two plants of galoba durian are different species

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