scholarly journals Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-16 ◽  
Author(s):  
Shamshad Ul Haq ◽  
Pradeep Kumar ◽  
R. K. Singh ◽  
Kumar Sambhav Verma ◽  
Ritika Bhatt ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Segregation Analysis ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Average Density ◽  
Grass Species ◽  
Bulk Segregation Analysis ◽  
After Effect ◽  
Ssrs Markers ◽  
Molecular Marker Development

Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.

scholarly journals Application of wheat SSR markers for detection of genetic diversity in triticale (x Triticosecale witt. )

Genetika ◽  
2015 ◽  
Vol 47 (3) ◽  
pp. 983-992
Author(s):  
Zelmíra Balázová ◽  
Andrej Trebichalský ◽  
Zdenka Gálová ◽  
Radomíra Hornyák-Gregáňová
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Ssr Marker ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Average Frequency ◽  
Polymorphic Markers ◽  
Average Value ◽  
Ssrs Markers

Present study aims to testify usefulness of particular wheat SSR markers for the detection of genetic diversity degree in the set of 59 triticale cultivars and new lines coming from different European countries and USA. For this purpose, a set of fifteen SSR markers were used. One SSR marker (Xwmc429) gave a uniform spectrum. The set of fourteen polymorphic markers provided 94 alleles with an average frequency of 6.71 alleles per locus. The number of alleles ranged between 2 (Xbarc 195) and 10 (Xbarc 137). Resulting from the number and frequency of alleles, diversity index (DI), polymorphic information content (PIC) and probabilities of identity (PI) were calculated. An average value of PIC for 14 markers was 0.640, the highest value was calculated for wheat SSR marker Xgwm 46 (0.809). Based on UPGMA algorithm, a dendrogram was constructed. It was able to separate 57 of 59 cultivars (96,6 %) from each other. American new-line NE-422T significantly separated from all cultivars and new lines. Only two french cultivars Bienvenu and Wilfried had not been separated from each other. A tested set of SSR markers allowed to better understand genetic relationships among European cultivars and American new lines. In general, a dendrogram along with results of calculated genetic indicators such as PIC, PI and DI point out at SSRs markers as high informative and usefull tool in genetic diversity research between close-related species.

scholarly journals Detection of genetic divergence among Putative Ethyl Methane Sulfonate Mutants of Super Basmati using Microsatellite Markers

2020 ◽  
Author(s):  
Kiran Hameed ◽  
Bushra Sadia ◽  
Madiha Habib ◽  
Zia ul Qamar ◽  
Faisal Saeed Awan
Keyword(s):  
Genetic Diversity ◽  
Base Pair ◽  
Polymorphic Information Content ◽  
Rice Cultivar ◽  
Ethyl Methane ◽  
Allele Number ◽  
Methane Sulphonate ◽  
Ssrs Markers ◽  
Mutagenic Effects ◽  
Selection Of

Abstract Mutation is a resource of generating genetic diversity in crop plant for breeding as well as genetic analysis. Ethyl Methane Sulphonate (EMS) is frequently applied chemical agents in plants. The present study was completed to investigate the mutagenic effects of different concentration of EMS on yield contributing traits of super basmati. The seeds of rice cultivar (Super basmati) were mutagenized with different doses from 0-2% v/v of EMS with difference of 0.25% for determination LD50. The treated and non-treated plants were observed under different agronomic parameters. A total of 48 putative EMS mutants of super basmati were selected randomly to analyze genetic diversity using 25 SSR primers. These markers were located on twelve chromosomes of rice. SSRs analysis revealed that abroad level of genetic diversity was existed among mutants of super basmati. A sum of 91 alleles was identified of which 82 alleles were originated to be polymorphic and the rest of nine alleles were discovered as monomorphic. The range of allele number was 2-10 with mean of 3.64 alleles/locus. The value of polymorphic information content (PIC) was from 0.039 (RM5) to 0.878 (RM44) with mean of 0.439 for each locus. All mutants differentiated from each other in more than two set of primers due to presence or absence of unique bands on chromosomes at definite base pair. The size base pair range was 75-1000bp. Dendrogram located mutant indices into four major groups. Phylogenic analyses exposed 40-96% similarity. It is concluded that EMS induced genetic variability and SSRs markers (RM44, RM154, RM1, RM252, RM334, RM487, RM110 and RM257) could be employed for the selection of rice mutants throughout molecular breeding program.

scholarly journals Genetic Diversity and Molecular Characterization of Worldwide Prairie Grass (Bromus catharticus Vahl) Accessions Using SRAP Markers

Agronomy ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2054
Author(s):  
Limei Yi ◽  
Zhixiao Dong ◽  
Yu Lei ◽  
Junming Zhao ◽  
Yanli Xiong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Production Systems ◽  
Polymorphic Information Content ◽  
Distance Matrix ◽  
Molecular Data ◽  
Mantel Test ◽  
Grass Species ◽  
Srap Marker ◽  
Discrimination Power ◽  
Prairie Grass

Prairie grass (Bromus catharticus Vahl) is an important grass species that could be used in the production systems of certified seed and high-quality forage for grazing ruminants. In the present research, a sequence-related amplified polymorphism (SRAP) marker was employed to detect the genetic variability and structure of 80 prairie grass accessions from all over the world. Altogether, 460 reliable bands were amplified from 47 SRAP primer pairs with 345 (75%) polymorphic bands. The average values of discrimination power (DP) and polymorphic information content (PIC) were 0.753 and 0.317, respectively. Both the UPGMA clustering and PCoA analyses grouped the 80 accessions into five clusters, whereas the STRUCTURE analysis showed that 80 prairie grass accessions possessed three genetic memberships (K = 3). The results of the Mantel test showed that the distance matrix has a moderately positive correlation between the morphological and molecular data sets (r = 0.524). A poor genetic differentiation (Fst = 0.045) was discovered among the six geo-groups of accessions. Besides, the highest intragroup genetic diversity was found in the North America group (He = 0.335). This study provides a genetic structure and diversity case for prairie grass, and supplies new clues for the study and utilization of prairie grass.

scholarly journals Genetic diversity of Salvia tomentosa Miller (Lamiaceae) species using Touch-down Directed Amplification of Minisatellite DNA (Td-DAMD) molecular markers

2020 ◽  
Vol 63 (2) ◽  
pp. 135-141
Author(s):  
Basel Saleh
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Sea Level ◽  
Natural Population ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Mediterranean Species ◽  
Marker Index ◽  
Minisatellite Dna

Salvia tomentosa Miller (Lamiaceae) a Mediterranean species has an important role in various pharmacological applications. To reveal genetic relationships among S. tomentosa natural populations, 35 samples were collected from different regions of Syria. Touch-down Directed Amplification of Minisatellite DNA (Td-DAMD) markers have been investigated for this goal. Td-DAMD assay produced 158 total bands of which 131 (82.911%) were polymorphic with a mean polymorphic information content (PIC) value of 0.264 and a mean marker index (MI) value of 2.269. Clustering profile based on TdDAMD data showed that samples were grouped into two main clusters; the first cluster included Lattakia samples which split into two subclusters regardless their altitudes over the sea level. Whereas, the second cluster included Tartous and Hama samples. Td-DAMD assay successfully discriminate among the tested 35 samples belonged to the S. tomentosa natural population.

scholarly journals Genetic Diversity Among Accessions of Cucurbita pepo Resistant to Phytophthora Crown Rot

HortScience ◽  
2019 ◽  
Vol 54 (1) ◽  
pp. 17-22
Author(s):  
Njung’e Vincent Michael ◽  
Pamela Moon ◽  
Yuqing Fu ◽  
Geoffrey Meru
Keyword(s):  
Genetic Diversity ◽  
Cucurbita Pepo ◽  
Genetic Relatedness ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Phytophthora Capsici ◽  
Crown Rot ◽  
Sources Of Resistance ◽  
Plant Introductions

Phytophthora capsici Leonian, the causal agent of Phytophthora crown rot in squash (Cucurbita pepo L.), is an economically important pathogen worldwide. Currently, no C. pepo cultivars immune to the pathogen are commercially available, but sources of resistance to Phytophthora crown rot have been identified in a set of 16 C. pepo plant introductions (PIs). Knowledge of the genetic relationships among these accessions and their relatedness to economically important morphotypes of C. pepo would inform breeders’ best strategies for introgressing resistance; however, this information is currently lacking. The goal of the current study was to determine genetic diversity among the resistant accessions and their genetic relatedness to susceptible morphotypes of subspecies pepo (Zucchini and Pumpkin) and texana (Acorn, Straightneck, and Crookneck) using 39 SSR markers. The markers revealed 132 alleles averaging 4.40 alleles per locus and had a mean polymorphic information content (PIC) and gene diversity of 0.44 and 0.49, respectively. CMTp235 had the highest PIC and gene diversity of 0.80 and 0.82, respectively. Hierarchical clustering by UPGMA and principal coordinate analysis (PCOA) revealed grouping into two major C. pepo subspecies, texana and pepo, with all the resistant accessions grouping in the latter. In order of increasing genetic distance (GD), the resistant accessions were least distant to Zucchini (GD = 0.34), followed by Pumpkin (GD = 0.40), Crookneck (GD = 0.56), Acorn (GD = 0.60), and Straightneck (GD = 0.61) morphotypes. Mean GD among the resistant accessions was 0.31 and was highest between PIs 615142 and 615132 (0.61). Based on genetic similarity, PIs 174185 and 181761 (disease severity ≤1.4) would be the best sources of resistance for transfer into subspecies texana and pepo, respectively. Overall, the results presented here support a closer genetic relationship between the resistant accessions and morphotypes of subspecies pepo than those of subspecies texana.

Molecular marker diversity of SCN-resistant sources in soybean

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 938-949 ◽  
Author(s):  
Yiwu Chen ◽  
Dechun Wang ◽  
Prakash Arelli ◽  
Mohsen Ebrahimi ◽  
Randall L Nelson
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Soybean Cyst Nematode ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Nematode Resistance ◽  
The United States ◽  
Cyst Nematode ◽  
Clustering Methods

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe; HG) is one of the most destructive pests of soybean (Glycine max (L.) Merr.) in the United States. Over 100 SCN-resistant accessions within the USDA Soybean Germplasm Collection have been identified, but little is known about the genetic diversity of this SCN-resistant germplasm. The objective of this research was to evaluate the genetic variation and determine the genetic relationships among SCN-resistant accessions. One hundred twenty-two genotypes were evaluated by 85 simple sequence repeat (SSR) markers from 20 linkage groups. Non-hierarchical (VARCLUS) and hierarchical (Ward's) clustering were combined with multidimensional scaling (MDS) to determine relationships among tested lines. The 85 SSR markers produced 566 allelic fragments with a mean polymorphic information content (PIC) value of 0.35. The 122 lines were grouped into 7 clusters by 2 different clustering methods and the MDS results consistently corresponded to the assigned clusters. Assigned clusters were dominated by genotypes that possess one or more unique SCN resistance genes and were associated with geographical origins. The results of analysis of molecular variance (AMOVA) showed that the variation differences among clusters and individual lines were significant, but the differences among individuals within clusters were not significant.Key words: soybean cyst nematode resistance, genetic diversity, SSR markers, cluster analysis, soybean.

scholarly journals IMPROVED SSRs-BASED GENETIC DIVERSITY ASSESSMENT OF COCONUTS (COCOS NUCIFERA L) ALONG THE COAST OF KENYA

2021 ◽  
Author(s):  
Justus C. Masha ◽  
Najya Muhammed ◽  
Vincent Njung’e ◽  
Maurice E. Oyoo ◽  
Manfred Miheso
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Cocos Nucifera ◽  
Marker Gene ◽  
Ex Situ ◽  
Ssr Analysis ◽  
Diversity Assessment ◽  
Ssrs Markers ◽  
Important Cash Crop

ABSTRACTCoconut is the most important cash crop along the Coast of Kenya, yet its genetic diversity has not been fully established. A genetic diversity study of 48 coconut genotypes that were collected along the Coast of Kenya was conducted with 13 polymorphic short sequence repeats (SSRs) markers. SSR analysis was performed using GeneMapper while data analysis was done with PowerMarker and DARwin softwares.The results revealed a total of 68 alleles ranging from 2 to 11 per locus with a mean of 5.23 per marker. Gene diversity and polymorphic information content (PIC) ranged between 0.41 to 0.83 and 0.33 to 0.79, respectively. A neighbour-joining dendrogram grouped the genotypes into three major clusters containing distinct sub-clusters. This study underscored that capillary electrophoresis is a more accurate and informative technique for SSRs allele scoring than agarose gels, which was reported in a previous study with the same SSRs markers and coconut genotypes in Kenya. The clusters observed forms the basis to isolate conservation blocks, which are the key to establishing a genebank, since there is no documented coconut genebank for ex-situ conservation in Kenya.

scholarly journals Geographical patterns of genetic diversity in cultivated chickpea (Cicer arietinum L.) characterized by amplified fragment length polymorphism

2008 ◽  
Vol 54 (No. 10) ◽  
pp. 447-452 ◽  
Author(s):  
R. Talebi ◽  
A.M. Naji ◽  
F. Fayaz
Keyword(s):  
Genetic Diversity ◽  
Fragment Length Polymorphism ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Aflp Analysis ◽  
Geographical Patterns ◽  
Upgma Dendrogram ◽  
Secondary Center ◽  
Center Of Diversity ◽  
Diverse Origin

The objective of this study was to evaluate the genetic relationships of 28 chickpea accessions from diverse origin using AFLP markers. On average, 13 polymorphic bands per primer were observed in AFLP analysis. The average polymorphic information content (PIC) was 0.71, ranging from 0.48 to 0.92. The lowest and the highest PIC value were recorded for primer P-GAG/M-GC and P-AT/M-GC, respectively. The average GD, based on Fst values among the 21 accessions was 0.42, ranging from 0.61 to 0.16. From the UPGMA dendrogram, it is discernible that material taken for the analysis can be divided in four clusters. The results indicate that the greatest genetic diversity occurs in Afghanistan, Iran and Lebanon. In many cases, the diversity between individuals of an accession is as great as between individuals of different accessions. Based on DNA markers it is concluded that there are three centers of diversity for chickpea: Pakistan-Afghanistan, Iran-Turkey and Syria-Lebanon. India and Ethiopia, which were previously considered as a secondary center of diversity for chickpea, showed lower diversity than the above regions.

scholarly journals Genetic diversity analysis in a mini core collection of Damask rose (Rosa damascena Mill.) germplasm from Iran using URP and SCoT markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Atefeh Sadat Mostafavi ◽  
Mansour Omidi ◽  
Reza Azizinezhad ◽  
Alireza Etminan ◽  
Hassanali Naghdi Badi
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Core Collection ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Resolving Power ◽  
Start Codon ◽  
Rosa Damascena ◽  
Mini Core Collection ◽  
Damask Rose

Abstract Background Rosa damascena Mill is a well-known species of the rose family. It is famous for its essential oil content. The aim of the present study was to assess the genetic diversity and population structure of a mini core collection of the Iranian Damask rose germplasm. This involved the use of universal rice primers (URP) and start codon targeted (SCoT) molecular markers. Results Fourteen URP and twelve SCoT primers amplified 268 and 216 loci, with an average of 19.21 and 18.18 polymorphic fragments per primer, respectively. The polymorphic information content for URR and SCoT primers ranged from 0.38 to 0.48 and 0.11 to 0.45, with the resolving power ranging from 8.75 to 13.05 and 9.9 to 14.59, respectively. Clustering was based on neighbor-joining (NJ). The mini core collection contained 40 accessions and was divided into three distinct clusters, centered on both markers and on the combination of data. Conclusion Cluster analysis and principal coordinate analysis were consistent with genetic relationships derived by STRUCTURE analysis. The findings showed that patterns of grouping did not correlate with geographical origin. Both molecular markers demonstrated that the accessions were not genetically diverse as expected, thereby highlighting the possibility that gene flow occurred between populations.

scholarly journals Analyses of genetic diversity and population structure of anchote (Coccinia abyssinica (Lam.) Cogn.) using newly developed EST-SSR markers

2021 ◽  
Author(s):  
Bekele Serbessa Tolera ◽  
Kifle Dagne Woldegebriel ◽  
Abel Teshome Gari ◽  
Mulatu Geleta Dida ◽  
Kassahun Tesfaye Geletu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Citrullus Lanatus ◽  
Wide Range ◽  
Minor Crop ◽  
Ssrs Markers ◽  
Expressed Sequence

AbstractAnchote (Coccinia abyssinica (Lam.) Cogn.) is a perennial root crop belonging to Cucurbitaceae family. It is endemic to Ethiopia and distributed over wide range of agro-ecologies. For further improvement and efficient conservation of this crop, characterization of its genetic diversity and its pattern of distribution is a vitally important step. Expressed sequence tags-simple sequence repeats (EST-SSRs) markers were developed from publicly available watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] ESTs in the GenBank database. Among those novel markers, eight were polymorphic and subsequently used for genetic diversity and population structure analyses of 30 anchote accessions collected from western Ethiopia. A total of 24 alleles were obtained across the eight polymorphic loci and 30 accessions that revealed moderate level of genetic diversity in this minor crop. Among the eight loci, locus CA_06 was the most informative with six alleles and polymorphic information content (PIC) of 0.76. The accessions showed about threefold variation in terms of genetic diversity, with expected heterozygosity (He) ranging from 0.15 (accession An) to 0.44 (accession Dg). Other accessions with higher genetic diversity include Ar and Gu (He = 0.43 and 0.41, respectively). Analysis of molecular variance (AMOVA) revealed that the variation within accessions and among accessions accounted for 84.7% and 15.3% of the total variation, respectively. The study revealed low but significant population differentiation in this crop with no clear pattern of population structure. The EST-SSR markers developed in this study are the first of their kind for anchote and can be used for characterization of its wider genetic resources for conservation and breeding purposes.

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