scholarly journals Genomic and Transcriptomic Resources for Marker Development in Synchytrium endobioticum, an Elusive but Severe Potato Pathogen

2017 ◽  
Vol 107 (3) ◽  
pp. 322-328 ◽  
Author(s):  
Friederike Busse ◽  
Annette Bartkiewicz ◽  
Diro Terefe-Ayana ◽  
Frank Niepold ◽  
Yvonne Schleusner ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Synchytrium Endobioticum ◽  
Sequence Characterized Amplified Region ◽  
Ssr Loci ◽  
Polymerase Chain ◽  
Low Levels ◽  
Taxonomic Studies ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Open Access Article

Synchytrium endobioticum is an obligate biotrophic fungus that causes wart diseases in potato. Like other species of the class Chytridiomycetes, it does not form mycelia and its zoospores are small, approximately 3 μm in diameter, which complicates the detection of early stages of infection. Furthermore, potato wart disease is difficult to control because belowground organs are infected and resting spores of the fungus are extremely durable. Thus, S. endobioticum is classified as a quarantine organism. More than 40 S. endobioticum pathotypes have been reported, of which pathotypes 1(D1), 2(G1), 6(O1), 8(F1), and 18(T1) are the most important in Germany. No molecular methods for the differentiation of pathotypes are available to date. In this work, we sequenced both genomic DNA and cDNA of the German pathotype 18(T1) from infected potato tissue and generated 5,422 expressed sequence tags (EST) and 423 genomic contigs. Comparative sequencing of 33 genes, single-stranded confirmation polymorphism (SSCP) analysis with polymerase chain reaction fragments of 27 additional genes, as well as the analysis of 41 simple sequence repeat (SSR) loci revealed extremely low levels of variation among five German pathotypes. From these markers, one sequence-characterized amplified region marker and five SSR markers revealed polymorphisms among the German pathotypes and an extended set of 11 additional European isolates. Pathotypes 8(F1) and 18(T1) displayed discrete polymorphisms which allow their differentiation from other pathotypes. Overall, using the information of the six markers, the 16 isolates could be differentiated into three distinct genotype groups. In addition to the presented markers, the new collection of EST from genus Synchytrium might serve in the future for molecular taxonomic studies as well as for analyses of the host–pathogen interactions in this difficult pathosystem. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Study of simple sequence repeat markers from coffee expressed sequences associated to leaf miner resistance

2007 ◽  
Vol 42 (3) ◽  
pp. 377-384 ◽  
Author(s):  
Fernanda de Oliveira Pinto ◽  
Mirian Perez Maluf ◽  
Oliveiro Guerreiro-Filho
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Defense Mechanisms ◽  
Leaf Miner ◽  
Gene Transcript ◽  
Est Database ◽  
Hybrid Frequency ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

The objective of this work was to identify expressed simple sequence repeats (SSR) markers associated to leaf miner resistance in coffee progenies. Identification of SSR markers was accomplished by directed searches on the Brazilian Coffee Expressed Sequence Tags (EST) database. Sequence analysis of 32 selected SSR loci showed that 65% repeats are of tetra-, 21% of tri- and 14% of dinucleotides. Also, expressed SSR are localized frequently in the 5'-UTR of gene transcript. Moreover, most of the genes containing SSR are associated with defense mechanisms. Polymorphisms were analyzed in progenies segregating for resistance to the leaf miner and corresponding to advanced generations of a Coffea arabica x Coffea racemosa hybrid. Frequency of SSR alleles was 2.1 per locus. However, no polymorphism associated with leaf miner resistance was identified. These results suggest that marker-assisted selection in coffee breeding should be performed on the initial cross, in which genetic variability is still significant.

Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 277-290 ◽  
Author(s):  
Eline van Zijll de Jong ◽  
Kathryn M Guthridge ◽  
German C Spangenberg ◽  
John W Forster
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
Sequence Repeat ◽  
Pasture Grass ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Key words: Neotyphodium, simple sequence repeats, expressed sequence tags, amplified fragment length polymorphism, genetic diversity.

Analyses of Thinopyrum bessarabicum, T. elongatum, and T. junceum chromosomes using EST-SSR markers

Genome ◽  
2010 ◽  
Vol 53 (12) ◽  
pp. 1083-1089 ◽  
Author(s):  
Richard R.-C. Wang ◽  
Steven R. Larson ◽  
Kevin B. Jensen
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Cereal Crops ◽  
Gene Pools ◽  
Addition Lines ◽  
Comparative Gene Mapping ◽  
Thinopyrum Bessarabicum ◽  
Taxonomic Studies ◽  
Expressed Sequence ◽  
Simple Sequence

Wild Thinopyrum grasses are important gene pools for forage and cereal crops. Knowledge of their chromosome organizations is pivotal for efficient utilization of this important gene pool in germplasm enhancement programs. Expressed sequence tags derived simple sequence repeat (EST-SSR) markers for Thinopyrum bessarabicum , T. elongatum , and T. junceum chromosomes were identified among amplicons produced from three series of wheat-Thinopyrum addition lines using 193 primer pairs designed from the Leymus EST unigenes. The homology of T. junceum chromosomes in 13 wheat addition lines was tentatively established to reveal that homologous groups 3, 4, 5, 6, and 7 were represented by HD3515, HD3505, AJDAj11, AJDAj1, and HD3508, whereas groups 1 and 2 were represented by AJADj7–AJDAj9 and AJDAj2–AJDAj4, respectively. AJDAj5 and AJDAj6 had complexly reconstituted T. junceum chromosomes that might have resulted from fusion or translocations of large chromosomal segments from two or more chromosomes, that is (1+5) and (2+5+1), respectively. The identified EST-SSR markers will be useful in comparative gene mapping, chromosome tracing, taxonomic studies, gene introgression, and cultivar identification.

scholarly journals Short note: Development, characterization and cross-amplification of eight EST-derived microsatellites in Salix

2014 ◽  
Vol 63 (1-6) ◽  
pp. 113-115 ◽  
Author(s):  
X. He ◽  
J. Zheng ◽  
M. Serapiglia ◽  
L. Smart ◽  
S. Shi ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Polymorphic Information Content ◽  
Short Note ◽  
Functional Markers ◽  
Sequence Identity ◽  
Expected Heterozygosity ◽  
Wide Range ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract A set of eight simple sequence repeat (SSR) markers were developed from 707 Salix expressed sequence tags (ESTs) deposited in GenBank. Each of the EST-SSR amplicons was identical to the original EST, with sequence identity 60.90-96.03% and presence of the expected repeat motifs. Of the eight EST-SSR loci, five were polymorphic among 14 individuals of S. eriocephala, with the number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) being 2-7 (mean 4.8), 0.29-0.85 (mean 0.65), 0.25-0.84 (mean 0.65) and 0.21-0.78 (mean 0.58), respectively. High rates of crossspecies/ genus amplification were also observed within fourteen different species. The primer sequences for the eight EST-SSRs have been deposited in the Probe database of GenBank (IDs Pr031820546 - Pr031820553). The EST-SSRs developed herein would be a valuable addition of functional markers for genetics and breeding applications in a wide range of Salix species.

scholarly journals VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Morad M Mokhtar ◽  
Ebtissam H A Hussein ◽  
Salah El-Din S El-Assal ◽  
Mohamed A M Atia
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Expressed Sequence Tags ◽  
Genetic Linkage ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Microrna Target ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

scholarly journals Development and Application of EST-SSR Markers for DNA Fingerprinting and Genetic Diversity Analysis of the Main Cultivars of Black Locust (Robinia pseudoacacia L.) in China

Forests ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 644 ◽  
Author(s):  
Li Dong ◽  
Yuhan Sun ◽  
Keqi Zhao ◽  
Jing Zhang ◽  
Yuwei Zhang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Black Locust ◽  
Robinia Pseudoacacia ◽  
Diversity Analysis ◽  
Simple Method ◽  
Genetic Diversity Analysis ◽  
Ssr Loci ◽  
Robinia Pseudoacacia L ◽  
Expressed Sequence ◽  
Simple Sequence

Black locust (Robinia pseudoacacia L.) is an economically and ecologically important tree species which is used for pillar construction, honey production and soil improvement. More EST-SSR (Expressed sequence tag simple sequence repeat) markers of black locust can be used as a complement and improvement of Genomic-SSR markers for the identification of the function of gene and the construction of genetic map. Additionally, currently there is no simple method for identifying black locust cultivars. In this study, we obtained 2702 unigenes from 3095 expressed sequence tags (ESTs) from the National Center of Biotechnology Information (NCBI) database to identify simple sequence repeats (SSRs) in R. pseudoacacia samples. A total of 170 SSR loci were found to be distributed in 162 non-redundant sequences with a frequency of 6.29%. Dinucleotide repeats were the most predominant types among microsatellites (62.35%), followed by tri-nucleotide repeats (25.88%); the remaining SSRs accounted for less than 12%. The repeat motifs AG/TC (29.25%) and CT/GA (29.25%) were the most abundant among dinucleotides, and AAT/TTA (15.91%) was the most common among tri-nucleotides. A total of 62 primer pairs were designed to screen polymorphic and stable SSR loci. The resulting 25 EST-SSR markers capable of amplifying polymorphic, stable, and repeatable products. Eight newly developed EST-SSR markers and four published SSR markers were selected for DNA fingerprinting and genetic diversity analysis of the 123 main R. pseudoacacia cultivars in China. The 12 SSR loci amplified 102 alleles, with an average number of alleles per locus of 8.5 (range 4–15). The average polymorphism information content at the 12 SSR loci for the 123 cultivars was 0.670 (range 0.427–0.881). The 123 cultivars clustered into six main groups based on similarity coefficients, with most cultivars in one subgroup. Fingerprinting was performed using eight SSR markers; 110 black locust cultivars were distinguished. The results of this study increase the availability of EST-SSR markers in black locust and make it a simple method for checking the collection, the certification, and the correct attribution of clones and cultivars.

Development of an EST-SSR marker in Panax ginseng

2008 ◽  
Vol 5 (2) ◽  
pp. 175-181 ◽  
Author(s):  
Yang Cheng-Jun ◽  
Wang Jun ◽  
Mu Li-Qiang ◽  
Li Shao-Chen ◽  
Liu Guan-Jun ◽  
...  
Keyword(s):  
Panax Ginseng ◽  
Expressed Sequence Tags ◽  
Genomic Dna ◽  
Ssr Marker ◽  
Panax Quinquefolius ◽  
Chain Reaction ◽  
Acanthopanax Senticosus ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Expressed Sequence

AbstractA total of 791 microsatellites (SSRs) were isolated from 7055 Panax ginseng expressed sequence tags (ESTs). According to primer design criteria, 68 primer pairs for EST-SSR were designed. Under an appropriate polymerase chain reaction (PCR) system, all EST-SSR primer pairs were screened against genomic DNA of Ji'anchangbo and Fusong'ermaya from Panax ginseng, and 43 EST-SSR primer pairs out of the above 68 resulted in PCR products. Then, all 43 pairs were detected in nine P. ginseng, two Panax quinquefolius and two Acanthopanax senticosus cultivars for polymorphisms, and 26 pairs (60.47%) were found to be polymorphic, accounting for 38.23% of the total number of designed primer pairs. These results demonstrate the possibility of developing EST-SSR markers using P. ginseng ESTs.

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