scholarly journals Using SSR markers for evaluation of genetic variation among sesame (Sesamum indicum L.) accessions

2020 ◽  
Vol 19 (05) ◽  
pp. 9-19
Author(s):  
Toan D. Pham
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Oil Content ◽  
Sesamum Indicum ◽  
Average Genetic Distance ◽  
Annual Plant ◽  
High Genetic Diversity ◽  
High Genetic Similarity

Sesame (Sesamum indicum L.) is an annual plant belonging to the Pedaliaceae family which is the oldest of the oilseed plants. Sesame is known as the king of oilseeds because its seeds contain high oil content (50-60%). The objective of the study was to evaluate the genetic variation of sesame accessions based on ten SSR markers. The results showed that all sesame accessions showed high genetic similarity among individuals in each accession. Polymorphism information content ranged from 0.24 (TNB17) to 0.37 (MT20). HO varied from 0.04 (MT30) to 0.25 (GENE1). The highest HE was 0.37 (MT20) and the lowest HE was 0.28 (TNB17). The results also displayed the high genetic diversity among 7 sesame accessions. The genetic diversity distance varied from 0.0 to 1.0. Dendrogram analysis divided 7 sesame accessions into 5 clear groups at an average genetic distance of 0.25. The results achieved would be useful information for genetic evaluation and sesame breeding development in the future.

scholarly journals Genetic Similarity of Commerson’s Anchovy across Segara Anakan Cilacap Assessed Using Randomly Amplified Polymorphic DNA (RAPD) Markers

Jurnal Biota ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 42-50
Author(s):  
Muhammad Khoerol Anam ◽  
Adi Amurwanto ◽  
Kusbiyanto Kusbiyanto ◽  
Hendro Pramono ◽  
M Husein Sastranegara ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Differences ◽  
Population Genetic Study ◽  
Randomly Amplified Polymorphic Dna ◽  
High Genetic Diversity ◽  
Impressive Result

Segara Anakan areas can be divided into three different regions according to their salinity. Salinity differences suggested that Commerson’s anchovy population in that area can be divided into three subpopulations due to genetic differences. Genetic differences among subpopulation can be assessed through a population genetic study using random amplified polymorphic DNA. This study aims to evaluate the genetic variation and differences of Commerson's anchovy (Stolephorus commersonnii) collected at three different water salinities in Segara Anakan estuary Cilacap Indonesia. Total genomic DNA was isolated using the Chelex method. Genetic diversity and differences were assessed using RAPD markers and were analyzed statistically using an analysis of molecular variance, as implemented in Arlequin software.  The results showed that high genetic diversity was observed within the subpopulations. However, no significant genetic differences were observed among subpopulations which indicate genetic similarity. A high number of offspring are likely to cause high genetic variation within subpopulations.  Adult and larvae migration is the cause of genetics similarity across Segara Anakan. Another impressive result is that water salinity did not affect the genetic characteristic of Commerson,s anchovy. Genetic similarity of Commerson’s anchovy indicates that Segara Anakan forms a single genetic conservation unit.

Genetic Diversity and Population Structure of Germplasm Resources in Sesame (Sesamum indicum L.) by SSR Markers

2013 ◽  
Vol 38 (12) ◽  
pp. 2286-2296 ◽  
Author(s):  
Wen-Di YUE ◽  
Li-Bin WEI ◽  
Ti-De ZHANG ◽  
Chun LI ◽  
Hong-Mei MIAO ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Sesamum Indicum ◽  
Germplasm Resources

scholarly journals Genetic Similarity of Avena sativa L. Varieties as an Example of a Narrow Genetic Pool of Contemporary Cereal Species

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1424
Author(s):  
Magdalena Cieplak ◽  
Sylwia Okoń ◽  
Krystyna Werwińska
Keyword(s):  
Genetic Diversity ◽  
Avena Sativa ◽  
Genetic Similarity ◽  
Breeding Programs ◽  
Central European ◽  
Cereal Species ◽  
Genetic Pool ◽  
Selection Of ◽  
High Genetic Similarity

The assessment of the genetic diversity of cultivated varieties is a very important element of breeding programs. This allows the determination of the level of genetic differentiation of cultivated varieties, their genetic distinctiveness, and is also of great importance in the selection of parental components for crossbreeding. The aim of the present study was to determine the level of genetic diversity of oat varieties currently grown in Central Europe based on two marker systems: ISSR and SCoT. The research conducted showed that both these types of markers were suitable for conducting analyses relating to the assessment of genetic diversity. The calculated coefficients showed that the analyzed cultivars were characterized by a high genetic similarity. However, the UPGMA and PCoA analyses clearly indicated the distinctiveness of the breeding programs conducted in Central European countries. The high genetic similarity of the analyzed forms allow us to conclude that it is necessary to expand the genetic pool of oat varieties. Numerous studies show that landraces may be the donor of genetic variation.

scholarly journals New gSSR and EST-SSR markers reveal high genetic diversity in the invasive plant Ambrosia artemisiifolia L. and can be transferred to other invasive Ambrosia species

PLoS ONE ◽  
2017 ◽  
Vol 12 (5) ◽  
pp. e0176197 ◽  
Author(s):  
Lucie Meyer ◽  
Romain Causse ◽  
Fanny Pernin ◽  
Romain Scalone ◽  
Géraldine Bailly ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Invasive Plant ◽  
Ambrosia Artemisiifolia ◽  
High Genetic Diversity

scholarly journals EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS

2016 ◽  
Vol 16 (2) ◽  
pp. 71
Author(s):  
Rubiyo Rubiyo ◽  
Nur Kholilatul Izzah ◽  
Indah Sulistiyorini ◽  
Cici Tresniawati
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gel Electrophoresis ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Breeding Program ◽  
New Variety ◽  
Average Value ◽  
The Third ◽  
Ctab Method

Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.

scholarly journals Analysis of genetic diversity and population structure in Asparagus species using SSR markers

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Manish Kapoor ◽  
Pooja Mawal ◽  
Vikas Sharma ◽  
Raghbir Chand Gupta
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Mean Value ◽  
Discrete Groups ◽  
Base Pairs ◽  
High Genetic Diversity ◽  
Pharmaceutical Industries ◽  
Improvement Programs ◽  
Northwest India ◽  
Simple Sequence

Abstract Background Various Asparagus species constitute the significant vegetable and medicinal genetic resource throughout the world. Asparagus species serve as important commodity of food and pharmaceutical industries in India. A diverse collection of Asparagus species from different localities of Northwest India was investigated for its genetic diversity using simple sequence repeat (SSR) markers. Results Polymorphic SSR markers revealed high genetic diversity. Primer SSR-15 amplified maximum of 8 fragments while 3 primers, namely, SSR-43, SSR-63, and AGA1 amplified minimum of 3 fragments. Collectively, 122 alleles were amplified in a range between 3 and 8 with an average of 5 alleles per marker. The size of the amplified alleles ranged between 90 and 680 base pairs. Polymorphism information content (PIC) value varied from a highest value of 0.499 in primer AGA1 to a lowest value of 0.231 in primer SSR-63 with a mean value of 0.376 showing considerable SSR polymorphism. Dendrogram developed on the basis of Jaccard’s similarity coefficient and neighbor-joining tree segregated all the studied Asparagus species into two discrete groups. Structure analysis based on Bayesian clustering allocated different accessions to two independent clusters and exhibited low level of individual admixture. Conclusions The genetic diversity analysis showed a conservative genetic background for maximum species of asparagus. Only Accessions of Asparagus adscendens were split into two diverse clusters suggesting a wide genetic base of this species as compared to other species. Overall genetic diversity was high, and this germplasm of Asparagus can be used in future improvement programs. The findings of current research on Asparagus germplasm can make a momentous contribution to initiatives of interbreeding, conservation, and improvement of Asparagus in future.

scholarly journals Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2504 ◽  
Author(s):  
Katarzyna Bilska ◽  
Monika Szczecińska
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Conservation Genetics ◽  
Ssr Markers ◽  
Full Range ◽  
Mantel Test ◽  
Evolutionary Potential ◽  
Functional Variation ◽  
Genetics Research ◽  
Outlier Loci

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

scholarly journals Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

HortScience ◽  
2018 ◽  
Vol 53 (3) ◽  
pp. 283-287
Author(s):  
Xiu Cai Fan ◽  
Hai Sheng Sun ◽  
Ying Zhang ◽  
Jian Fu Jiang ◽  
Min Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Srap Markers ◽  
Average Percentage ◽  
Allele Number ◽  
Ssr Primers ◽  
Vitis Davidii ◽  
Simple Sequence

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

scholarly journals Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of EndangeredPolyporus umbellatus

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Yuejin Zhang ◽  
Yuanyuan Chen ◽  
Ruihong Wang ◽  
Ailin Zeng ◽  
Michael K. Deyholos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Large Scale ◽  
Gene Diversity ◽  
High Genetic Diversity ◽  
Information Index ◽  
Polyporus Umbellatus ◽  
Ssr Primers ◽  
Expressed Sequence

A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences inGanoderma lucidumobtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 naturalPolyporus umbellatusaccessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13P.umbellatusaccessions showed relatively high genetic diversity. The expected heterozygosity, Nei’s gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups.

Assessment of genetic diversity in sesame (Sesamum indicum L.) genotypes, using EST-derived SSR markers

2013 ◽  
Vol 16 (2) ◽  
pp. 93-103 ◽  
Author(s):  
Vijay Yepuri ◽  
Malathi Surapaneni ◽  
Vijaya Sudhakar Rao Kola ◽  
L. R. Vemireddy ◽  
B. Jyothi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Sesamum Indicum
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