Comparison of genomic and EST-derived SSR markers in phylogenetic analysis of wheat

2011 ◽  
Vol 9 (2) ◽  
pp. 243-246 ◽  
Author(s):  
Agata Gadaleta ◽  
Angelica Giancaspro ◽  
Silvana Zacheo ◽  
Domenica Nigro ◽  
Stefania Lucia Giove ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Phylogenetic Trees ◽  
Plant Genome ◽  
Phylogenetic Relations ◽  
Diversity Assessment ◽  
Wide Range ◽  
Genomic Ssr ◽  
High Level ◽  
Expressed Sequence

Microsatellite markers (simple sequence repeats, SSRs) are used for a wide range of crop genetic and breeding applications, including genetic diversity assessment, phylogenetic analysis, genotypic profiling and marker-assisted selection. Genomic SSR (gSSR) have attracted more attention because of abundance in plant genome, reproducibility, high level of polymorphism and codominant inheritance. Recently, the availability of data for expressed sequence tags (EST), has given more emphasis to EST-derived SSRs, which belong to the transcribed regions of DNA, and are expected to be more conserved and have a higher transferability rate across species than gSSR markers. In the present study, several gSSR and EST-SSR markers were investigated for their transferability and level of DNA polymorphism in different ancestral tetraploid and diploid Triticum and Aegilops species. The same gSSR and EST-SSR markers were also evaluated for their applicability in the phylogenetic analysis of wheat. Both gSSR and EST-SSR markers showed differences for the average transferability rate and the number of alleles/locus. Phylogenetic trees based on gSSR and EST-SSR markers were in accordance with phylogenetic relations based on cytogenetic and molecular analyses.

Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 637-647 ◽  
Author(s):  
M A. Rouf Mian ◽  
Malay C Saha ◽  
Andrew A Hopkins ◽  
Zeng-Yu Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Tall Fescue ◽  
Related Species ◽  
Grass Species ◽  
Forage Grass ◽  
Forage Grasses ◽  
Cool Season ◽  
Phylogenetic Relations ◽  
Wide Range

Microsatellites or simple sequence repeats (SSRs) are highly useful molecular markers for plant improvement. Expressed sequence tag (EST)-SSR markers have a higher rate of transferability across species than genomic SSR markers and are thus well suited for application in cross-species phylogenetic studies. Our objectives were to examine the amplification of tall fescue EST-SSR markers in 12 grass species representing 8 genera of 4 tribes from 2 subfamilies of Poaceae and the applicability of these markers for phylogenetic analysis of grass species. About 43% of the 145 EST-SSR primer pairs produced PCR bands in all 12 grass species and had high levels of polymorphism in all forage grasses studied. Thus, these markers will be useful in a variety of forage grass species, including the ones tested in this study. SSR marker data were useful in grouping genotypes within each species. Lolium temulentum, a potential model species for cool-season forage grasses, showed a close relation with the major Festuca–Lolium species in the study. Tall wheatgrass was found to be closely related to hexaploid wheat, thereby confirming the known taxonomic relations between these species. While clustering of closely related species was found, the effectiveness of such data in evaluating distantly related species needs further investigations. The phylogenetic trees based on DNA sequences of selected SSR bands were in agreement with the phylogenetic relations based on length polymorphism of SSRs markers. Tall fescue EST-SSR markers depicted phylogenetic relations among a wide range of cool-season forage grass species and thus are an important resource for researchers working with such grass species.Key words: phylogeny, EST-SSR, forage grasses, tall fescue.

scholarly journals Development of EST-derived SSR Markers with Long-core Repeat in Olive and Their Use for Paternity Testing

2013 ◽  
Vol 138 (4) ◽  
pp. 290-296 ◽  
Author(s):  
Raúl De la Rosa ◽  
Angjelina Belaj ◽  
Antonio Muñoz-Mérida ◽  
Oswaldo Trelles ◽  
Inmaculada Ortíz-Martín ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tag ◽  
Paternity Testing ◽  
High Level ◽  
Repeated Motifs ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Olive Breeding ◽  
Genomic Project

In the present work, a set of eight new hexa-nucleotide simple sequence repeats (SSRs) is reported in olive (Olea europaea L). These SSRs loci were generated on the basis of expressed sequence tag (EST) sequences in the frame of an olive genomic project. The markers showed a high level of polymorphism when tested on a set of cultivars used as genitors in the olive breeding program of Córdoba, Spain. The long-core repeat motif of these markers allows a wider separation among alleles, thus permitting an accurate genotyping. Besides, these markers showed comparable levels of polymorphism to di-nucleotide SSRs, the only ones so far reported in olive. Selected on the basis of their discrimination capacity, four of the eight SSRs were used to test their ability for paternity testing in a total of 81 seedlings coming from 12 crosses. The paternity testing showed that seven crosses matched the alleged paternity and the remaining five were products of illicit pollinations. These results exactly matched with previous paternity testing performed with di-nucleotide SSR markers. These results demonstrate the usefulness of the developed hexa-nucleotide repeated motifs for checking the paternity of breeding progenies and suggest their use on variability studies.

Morphological and molecular identification of some species of nematode of the family Protostrongylidae Leiper, 1926

2016 ◽  
Vol 3 (4) ◽  
pp. 454-461
Author(s):  
Салахутдинов ◽  
I. Salakhutdinov ◽  
Рузиев ◽  
B. Ruziev ◽  
Каримова ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Digital Camera ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Genetic Identification ◽  
Mountain Area ◽  
Phylogenetic Relations ◽  
The Family

Objective of research: conducting morphological and molecular-genetic identification and studying phylogenetic relations between protostrongylids. Materials and methods: helminthological material was collected from wild (Capra sibirica, C. falconeri, Ovis vignei and O. ammon) and domestic hollow horned ruminants (C. hircus and O. aries), and land mollusks of the family Xeropicta in the piedmont and mountain area of Uzbekisan. The morphology of protostrongylids was studied using the methods of Boev (1975) and Anderson (1978). To identify the nematode type we used temporary preparations treated with glycerol. The first-stage larvae were investigated by examination of fecal samples from animals taking into account the length, tail form and body size. To study the morphology of the third-stage protostrongylid larvae the feet of infected mollusks Xeropicta candaсharica were separated and placed into the artificial gastric juice where the cap was destroyed and the infected larvae were eliminated. After determination of species belonging of mature and larval nematodes the material was stored in separate test-tubes with distilled water under the low temperature (- 20 ºС) or in 70 % Ethanol for the molecular analysis. We used microscopes ML 2000 with a digital camera and Olympus CX3. DNA extraction, amplification and sequencing were performed with an automated sequencer. Phylogenetic analysis was conducted using the software Clustal X 2.0. Phylogenetic trees were created by the Neighbor–Joining method. Nucleotide sequences ITS-2 regions of species Protostrongylus rufescens (EU018485), P. shiozawai (AB478249), Ortostrongylus macrotis (EU018483), Cystocaulus ocreatus (EU018481) and Umingmakstrongylus pallikuukensis (AY648409) received from the NCBI GenBank were used in phylogenetic analysis. Results and discussion: Four species of adult protostrongylid nematodes: Protostrongylus rufescens, P. hobmaieri, Spiculocaulus leuckarti and Cystocaulus ocreatus were determined. DNA from four species of mature protostrongylids and larvae was amplified by using ITS-2 regions. Amplificate dimension of nematodes P. rufescens and P. hobmaieri was 380 base pairs (b.p.), S. leuckarti – 388, C. ocreatus – 399 b.p. According to the results of phylogenetic analysis and comparison of nucleotide sequences, five protostrongylid species were found in animals of the Caprinae subfamily: P. rufescens, P. hobmaieri, Protostrongylus sp., S. leuckarti and C. ocreatus. The morphological and molecular-genetic analysis of detected nematodes enables the precise identification.

Genome-wide identification of SSR markers in the Brassica A genome and their utility in breeding

2016 ◽  
Vol 96 (5) ◽  
pp. 808-818 ◽  
Author(s):  
Neil Hobson ◽  
Habibur Rahman
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Low Cost ◽  
Pak Choi ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Genetic Pools ◽  
High Level ◽  
Simple Sequence

Simple sequence repeat (SSR) markers can be applied to genotyping projects at low cost with inexpensive equipment. The objective of this study was to develop SSR markers from the publically-available genome sequence of Brassica rapa and provide the physical position of these markers on the chromosomes for use in breeding and research. To assess the utility of these new markers, a subset of 60 markers were used to genotype 43 accessions of B. rapa. Fifty-five markers from the 10 chromosome scaffolds produced a total of 730 amplicons, which were then used to perform a phylogenetic analysis of the accessions, illustrating their utility in distinguishing between a wide range of germplasm. In agreement with similar studies of genetic diversity, our markers separated accessions into distinct genetic pools including Chinese cabbage, Chinese winter oilseed, European winter oilseed, Canadian spring oilseed, pak-choi, turnip, and yellow sarson. The results further illustrate the presence of a high level of genetic diversity in B. rapa, and demonstrate the potential of these SSR markers for use in breeding and research.

scholarly journals Phylogenetic Analysis Reveals Multiple Lateral Transfers of Adenosine-5′-Phosphosulfate Reductase Genes among Sulfate-Reducing Microorganisms

2002 ◽  
Vol 184 (1) ◽  
pp. 278-289 ◽  
Author(s):  
Michael W. Friedrich
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
16S Rrna ◽  
Lateral Gene Transfer ◽  
Phylogenetic Trees ◽  
Gram Positive ◽  
Sulfate Reducing ◽  
Wide Range ◽  
Aps Reductase ◽  
Key Enzyme

ABSTRACT Lateral gene transfer affects the evolutionary path of key genes involved in ancient metabolic traits, such as sulfate respiration, even more than previously expected. In this study, the phylogeny of the adenosine-5′-phosphosulfate (APS) reductase was analyzed. APS reductase is a key enzyme in sulfate respiration present in all sulfate-respiring prokaryotes. A newly developed PCR assay was used to amplify and sequence a fragment (∼900 bp) of the APS reductase gene, apsA, from a taxonomically wide range of sulfate-reducing prokaryotes (n = 60). Comparative phylogenetic analysis of all obtained and available ApsA sequences indicated a high degree of sequence conservation in the region analyzed. However, a comparison of ApsA- and 16S rRNA-based phylogenetic trees revealed topological incongruences affecting seven members of the Syntrophobacteraceae and three members of the Nitrospinaceae, which were clearly monophyletic with gram-positive sulfate-reducing bacteria (SRB). In addition, Thermodesulfovibrio islandicus and Thermodesulfobacterium thermophilum, Thermodesulfobacterium commune, and Thermodesulfobacterium hveragerdense clearly branched off between the radiation of the δ-proteobacterial gram-negative SRB and the gram-positive SRB and not close to the root of the tree as expected from 16S rRNA phylogeny. The most parsimonious explanation for these discrepancies in tree topologies is lateral transfer of apsA genes across bacterial divisions. Similar patterns of insertions and deletions in ApsA sequences of donor and recipient lineages provide additional evidence for lateral gene transfer. From a subset of reference strains (n = 25), a fragment of the dissimilatory sulfite reductase genes (dsrAB), which have recently been proposed to have undergone multiple lateral gene transfers (M. Klein et al., J. Bacteriol. 183:6028–6035, 2001), was also amplified and sequenced. Phylogenetic comparison of DsrAB- and ApsA-based trees suggests a frequent involvement of gram-positive and thermophilic SRB in lateral gene transfer events among SRB.

scholarly journals Molecular Taxonomy and Phylogenetic Analysis of Dove and Pigeon Species (Aves: Columbidae) of Pakistan, Based on COI Region of Mitochondrial DNA

2020 ◽  
Vol 7 (3) ◽  
pp. 35-44
Author(s):  
Fakhar -i-Abbas ◽  
Fakhar -i-Abbas ◽  
Fakhra Nazir ◽  
Fida Muhammad Khan
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Molecular Taxonomy ◽  
Columba Livia ◽  
Taxonomic Diversity ◽  
Coi Gene ◽  
Maximum Parsimony Tree ◽  
Maximum Likelihood Tree ◽  
Wide Range ◽  
Parsimony Tree

Doves and Pigeons are the members of living family Columbidae (Order: Columbiformes) having a wide range of taxonomic diversity and geographic distribution. Seven species with one sample each of family Columbidae were collected via random sampling from different districts of Pakistan to carry out this study. The targeted gene region was sequenced and identified by using BLAST tool at National Center for Biotechnology Information (NCBI). CLUSTALW was used for sequence alignment and MEGA6 for reconstruction of phylogenetic trees to predict the effective ancestry of different Columbidae species. The following phylogenetic trees were obtained i.e. Maximum Likelihood tree, Neighborhood joining tree, Maximum parsimony tree and UPGMA tree. In the current study, COI gene barcoding and phylogenetic analysis of family Columbidae gave results of multiple alignment which showed that Columba livia livia and Columba eversmanni, closely resembled as well as Spilopelia senegalensis and Streptopelia decaocta. While Streptopelia tranquebarica and Spilopelia chinensis have great affinity due to small clade difference and Treron phoenicoptera was distinctly related to other species due to large clade difference.

Development and transferability of EST-SSR and transferability of genomic SSR markers for genetic diversity assessment of Doritis

2012 ◽  
Vol 45 ◽  
pp. 57-65 ◽  
Author(s):  
Chatchawan Jantasuriyarat ◽  
Savitree Ritchuay ◽  
Pawat Pattarawat ◽  
Pattana Srifah Huehne ◽  
Sureeporn Kate-Ngam
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Diversity Assessment ◽  
Genomic Ssr

Assessment of the genetic diversity and population structure of apricot (Prunus armeniaca L.) germplasm of the Northwestern Himalaya using SSR markers

2021 ◽  
pp. 1-10
Author(s):  
Aijaz A. Wani ◽  
Khalid Hussain ◽  
Showkat A. Zargar ◽  
Faizan Ahmad ◽  
Reetika Mahajan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Geographical Location ◽  
Prunus Armeniaca ◽  
Resolving Power ◽  
Diversity Assessment ◽  
Prunus Armeniaca L ◽  
Genetic Pool ◽  
High Level

Abstract Apricot is considered an ecologically and economically important tree species of the stone-fruit crops that is widely grown in temperate regions of the world. Very few studies on apricot genetic diversity assessment have been carried out from the regions of Kashmir and Ladakh. In this backdrop, the present study was carried out to analyse the genetic diversity and population structure of 120 apricot genotypes collected from both the regions using 21 SSR markers. A total of 52 alleles were amplified with average values of marker index (MI) = 0.7084, resolving power (RP) = 2.8690, polymorphism information content (PIC) = 0.3132, Na = 2.317, Ne = 1.720, I = 0.572, Ho = 0.284, He = 0.360 and an average polymorphism of 91.2% per assay indicating high level of genetic diversity. The neighbour-joining (NJ) dendrogram generated three main clusters among selected apricot genotypes independent of their geographical locations. Interestingly, the result of the dendrogram coincides with the results of structure analysis which showed that the 120 apricot genotypes could be assigned to three (K = 3) sub-populations and the grouping of genotypes did not follow their geographical location suggesting that they share the same genetic pool. Moreover, analysis of molecular variance showed that 73% of the variation was attributed to differences within the individuals, 25% among individuals while only 2% of the variation was observed among the populations. The present study represents the most comprehensive analysis of the genetic diversity and population structure of apricot genotypes in Kashmir and Ladakh regions of India.

Genetic diversity of Crotalaria germplasm assessed through phylogenetic analysis of EST-SSR markers

Genome ◽  
2006 ◽  
Vol 49 (6) ◽  
pp. 707-715 ◽  
Author(s):  
M L Wang ◽  
J A Mosjidis ◽  
J B Morris ◽  
R E Dean ◽  
T M Jenkins ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Germplasm Collection ◽  
High Similarity ◽  
Ssr Primers ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Crotalaria Spectabilis

The genetic diversity of the genus Crotalaria is unknown even though many species in this genus are economically valuable. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago and soybean were used to assess the genetic diversity of the Crotalaria germplasm collection. This collection consisted of 26 accessions representing 4 morphologically characterized species. Phylogenetic analysis partitioned accessions into 4 main groups generally along species lines and revealed that 2 accessions were incorrectly identified as Crotalaria juncea and Crotalaria spectabilis instead of Crotalaria retusa. Morphological re-examination confirmed that these 2 accessions were misclassified during curation or conservation and were indeed C. retusa. Some amplicons from Crotalaria were sequenced and their sequences showed a high similarity (89% sequence identity) to Medicago truncatula from which the EST-SSR primers were designed; however, the SSRs were completely deleted in Crotalaria. Highly distinguishing markers or more sequences are required to further classify accessions within C. juncea.Key words: Crotalaria germplasm, EST-SSR, genetic diversity, phylogeny.

scholarly journals Genetic Diversity and Population Structure of Japanese Plum-Type (Hybrids of P. salicina) Accessions Assessed by SSR Markers

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1748
Author(s):  
Brenda I. Guerrero ◽  
M. Engracia Guerra ◽  
Sara Herrera ◽  
Patricia Irisarri ◽  
Ana Pina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Group Method ◽  
Japanese Plum ◽  
Pair Group ◽  
Prunus Salicina ◽  
Wide Range ◽  
High Level ◽  
Informative Content

Japanese plum (Prunus salicina Lindl.) is widely distributed in temperate zones across the world. Since its introduction to USA in the late 19th century, this species has been hybridized with up to 15 different diploid Prunus species. This high level of introgression has resulted in a wide range of traits and agronomic behaviors among currently grown cultivars. In this work, 161 Japanese plum-type accessions were genotyped using a set of eight Simple Sequence Repeats (SSR) markers to assess the current genetic diversity and population structure. A total of 104 alleles were detected, with an average of 13 alleles per locus. The overall Polymorphic Informative Content (PIC) value of SSR markers was 0.75, which indicates that these SSR markers are highly polymorphic. The Unweighted Pair Group Method with Arithmetic (UPGMA) dendrogram and the seven groups inferred by Discriminant Analysis of Principal Components (DAPC) revealed a strong correlation of the population structure to the parentage background of the accessions, supported by a moderate but highly significant genetic differentiation. The results reported herein provide useful information for breeders and for the preservation of germplasm resources.

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