scholarly journals Development and annotation of perennial Triticeae ESTs and SSR markers

Genome ◽  
2008 ◽  
Vol 51 (10) ◽  
pp. 779-788 ◽  
Author(s):  
B. Shaun Bushman ◽  
Steve R. Larson ◽  
Ivan W. Mott ◽  
Paul F. Cliften ◽  
Richard R.-C. Wang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Rice Genome ◽  
Rice Chromosome ◽  
Sequence Information ◽  
Chromosome 2 ◽  
Annotation Database ◽  
Genomic Tools ◽  
Leymus Cinereus ◽  
Expressed Sequence

Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata , a mixture of both Elymus wawawaiensis and E. lanceolatus , and a Leymus cinereus  × L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8 780 unigenes for P. spicata, 11 281 unigenes for Leymus, and 7 212 unigenes for Elymus. Unigenes were annotated based on putative orthology to genes from rice, wheat, barley, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Simple sequence repeat (SSR) markers were developed, tested for amplification and polymorphism, and aligned to the rice genome. Leymus EST markers homologous to rice chromosome 2 genes were syntenous on Leymus homeologous groups 6a and 6b (previously 1b), demonstrating promise for in silico comparative mapping. All ESTs and SSR markers are available on an EST information management and annotation database ( http://titan.biotec.uiuc.edu/triticeae/ ).

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.

A comparative assessment of genetic diversity in cultivated barley collected in different decades of the last century in Austria, Albania and India by using genomic and genic simple sequence repeat (SSR) markers

2006 ◽  
Vol 4 (2) ◽  
pp. 125-133 ◽  
Author(s):  
Elena K. Khlestkina ◽  
Rajeev K. Varshney ◽  
Marion S. Röder ◽  
Andreas Graner ◽  
Andreas Börner
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Polymorphic Information Content ◽  
Time Interval ◽  
Slight Reduction ◽  
Geographical Regions ◽  
Cultivated Barley ◽  
Quantitative Changes ◽  
Expressed Sequence

Molecular investigations of qualitative and quantitative changes in the genetic diversity of cultivated crops are useful for plant breeding and the management of crop genetic resources. A genotyping study, based on 28 genomic (g-SSR) and 13 expressed sequence tag-derived (e-SSR) microsatellite markers uniformly distributed across the barley genome, was conducted on samples of cultivated barley (Hordeum vulgare L.) collected at intervals of 40–50 years in three comparable geographical regions in Austria, Albania and India. The analysis indicated an absence of any significant differences either in the total number of alleles per locus or in g-SSR and e-SSR polymorphic information content (PIC) values from the Indian and Austrian materials. However, a slight reduction in genetic diversity was noted among the materials collected in Albania. The trend in numbers of collection mission-specific SSR alleles suggests significant allele flow over the time interval sampled. The g-SSRs yielded a higher mean number of alleles per locus and a superior PIC than the e-SSR markers. We conclude that a qualitative, rather than a quantitative shift in diversity has taken place over time, and that g-SSR markers detect more diversity than do e-SSR markers.

scholarly journals Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars

2021 ◽  
Vol 12 ◽  
Author(s):  
Haftom Brhane ◽  
Teklehaimanot Haileselassie ◽  
Kassahun Tesfaye ◽  
Cecilia Hammenhag ◽  
Rodomiro Ortiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Finger Millet ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
Geographic Regions ◽  
Landrace Accessions ◽  
Expressed Sequence ◽  
Simple Sequence

Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.

scholarly journals Genetic Diversity Analysis and Single-nucleotide Polymorphism Marker Development in Cultivated Bulb Onion Based on Expressed Sequence Tag–Simple Sequence Repeat Markers

2008 ◽  
Vol 133 (6) ◽  
pp. 810-818 ◽  
Author(s):  
John McCallum ◽  
Susan Thomson ◽  
Meeghan Pither-Joyce ◽  
Fernand Kenel ◽  
Andrew Clarke ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Snp Markers ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Bulb Onion ◽  
Expressed Sequence ◽  
Simple Sequence

Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (SSR) markers and sequenced regions flanking expressed sequence tag (EST)-SSRs to develop single-nucleotide polymorphism (SNP) markers. Samples from 89 inbred and open-pollinated (OP) bulb onion populations of wide geographical adaptation and four related Allium L. accessions were genotyped with 56 EST-SSR and four genomic SSR markers. Multivariate analysis of genetic distances among populations resolved long-day, short-day, and Indian populations. EST-SSR markers frequently revealed two major alleles at high frequency in OP populations. The median proportion of single-locus polymorphic loci was 0.70 in OP and landrace populations compared with 0.43 in inbred lines. Resequencing of 24 marker amplicons revealed additional SNPs in 17 (68%) and five SNP assays were developed from these, suggesting that resequencing of EST markers can readily provide SNP markers for purity testing of inbreds and other applications in Allium genetics.

scholarly journals Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana

2001 ◽  
Vol 11 (7) ◽  
pp. 1167-1174
Author(s):  
Klaus Mayer ◽  
George Murphy ◽  
Renato Tarchini ◽  
Rolf Wambutt ◽  
Guido Volckaert ◽  
...  
Keyword(s):  
Sequence Data ◽  
Rice Genome ◽  
Rice Chromosome ◽  
Gene Content ◽  
Chromosome 2 ◽  
Chromosome 4 ◽  
Orthologous Genes ◽  
Protein Coding ◽  
Duplication Events ◽  
Conserved Gene

The nucleotide sequence was determined for a 340-kb segment of rice chromosome 2, revealing 56 putative protein-coding genes. This represents a density of one gene per 6.1 kb, which is higher than was reported for a previously sequenced segment of the rice genome. Sixteen of the putative genes were supported by matches to ESTs. The predicted products of 29 of the putative genes showed similarity to known proteins, and a further 17 genes showed similarity only to predicted or hypothetical proteins identified in genome sequence data. The region contains a few transposable elements: one retrotransposon, and one transposon. The segment of the rice genome studied had previously been identified as representing a part of rice chromosome 2 that may be homologous to a segment of Arabidopsis chromosome 4. We confirmed the conservation of gene content and order between the two genome segments. In addition, we identified a further four segments of the Arabidopsis genome that contain conserved gene content and order. In total, 22 of the 56 genes identified in the rice genome segment were represented in this set of Arabidopsis genome segments, with at least five genes present, in conserved order, in each segment. These data are consistent with the hypothesis that theArabidopsis genome has undergone multiple duplication events. Our results demonstrate that conservation of the genome microstructure can be identified even between monocot and dicot species. However, the frequent occurrence of duplication, and subsequent microstructure divergence, within plant genomes may necessitate the integration of subsets of genes present in multiple redundant segments to deduce evolutionary relationships and identify orthologous genes.

Development of EST–SSR markers in castor bean (Ricinus communis L.) and their utilization for genetic purity testing of hybrids

Genome ◽  
2011 ◽  
Vol 54 (8) ◽  
pp. 684-691 ◽  
Author(s):  
B. Pranavi ◽  
G. Sitaram ◽  
K.N. Yamini ◽  
V. Dinesh Kumar
Keyword(s):  
Ssr Markers ◽  
Castor Bean ◽  
Expressed Sequence Tag ◽  
Ricinus Communis ◽  
Rapid Development ◽  
Genetic Purity ◽  
Ricinus Communis L ◽  
Purity Testing ◽  
Expressed Sequence ◽  
Simple Sequence

Expressed sequence tag (EST) databases offer opportunity for the rapid development of simple sequence repeat (SSR) markers in crops. Sequence assembly and clustering of 57 895 ESTs of castor bean resulted in the identification of 10 960 unigenes (6459 singletons and 4501 contigs) having 7429 SSRs. On an average, the unigenes contained 1 SSR for every 1.23 kb of unigene sequence. The identified SSRs mostly consisted of dinucleotide (62.4%) and trinucleotide (33.5%) repeats. The AG class was the most common among the dinucleotide motifs (68.9%), whereas the AAG class (25.9%) was predominant among the trinucleotide motifs. A total of 611 primer pairs were designed for the SSRs, having repeat length more than or equal to 20 nucleotides, of which a set of 130 markers were tested and 92 of these yielding robust amplicons were analyzed for their utility in genetic purity assessment of castor bean hybrids. Nine markers were able to detect polymorphism between the parental lines of nine commercial castor bean hybrids (DCH-32, DCH-177, DCH-519, GCH-2, GCH-4, GCH-5, GCH-6, GCH-7, and RHC-1), and their utility in genetic purity testing was demonstrated. These novel EST–SSR markers would be a valuable addition to the growing molecular marker resources that could be used in genetic improvement programmes of castor bean.

scholarly journals Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5606 ◽  
Author(s):  
Jun Zeng ◽  
Jie Chen ◽  
Yixuan Kou ◽  
Yujin Wang
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Population Genetic Analysis ◽  
Protein Databases ◽  
Genetic Groups ◽  
Conifer Tree ◽  
Torreya Grandis ◽  
Expressed Sequence ◽  
Distribution Frequency

Torreya grandis (Taxaceae) is an ancient conifer species endemic to southeast China. Because of its nutrient-rich and delicious seeds, this species has been utilized for centuries by the Chinese. However, transcriptome data and transcriptome-derived microsatellite markers for population genetics studies are still insufficient for understanding of this species’ genetic basis. In this study, a transcriptome from T. grandis leaves was generated using Illumina sequencing. A total of 69,920 unigenes were generated after de novo assembly, and annotated by searching against seven protein databases. In addition, 2,065 expressed sequence tag–simple sequence repeats (EST-SSRs) were detected, with the distribution frequency of 2.75% of total unigenes and average number of 0.03 SSRs per unigene. Among these EST-SSRs, 1,339 primer pairs were successfully designed, and 106 primer pairs were randomly selected for the development of potential molecular markers. Among them, 11 EST-SSR markers revealed a moderate level of genetic diversity, and were used to investigate the population structure of T. grandis. Two different genetic groups within this species were revealed using these EST-SSR markers, indicating that these markers developed in this study can be effectively applied to the population genetic analysis of T. grandis.

scholarly journals Verification of Mandarin and Pummelo Somatic Hybrids by Expressed Sequence Tag–Simple Sequence Repeat Marker Analysis

2008 ◽  
Vol 133 (6) ◽  
pp. 794-800 ◽  
Author(s):  
Chunxian Chen ◽  
Jude W. Grosser ◽  
Milica Ćalović ◽  
Patricia Serrano ◽  
Gemma Pasquali ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Breeding System ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Somatic Hybrids ◽  
Poncirus Trifoliata ◽  
Sequence Repeat ◽  
Expressed Sequence ◽  
Simple Sequence

Somatic hybridization is a powerful tool for the genetic improvement of citrus rootstocks, and it is part of an efficient in vitro-based breeding system described here. An essential component of the system is the requirement of confirming tetraploidy and the combination of the two donor genomes. Expressed sequence tag–simple sequence repeat (EST-SSR) markers provide a means to accomplish both of these objectives, and their application to a population of pummelo [Citrus grandis (L.) Osbeck] + mandarin (C. reticulata Blanco) somatic hybrids developed for the specific purpose of providing alternative rootstocks for sour orange (Citrus aurantium L.) is detailed. Nineteen new somatic hybrids were produced from various mandarin and pummelo parents, and their ploidy level and the complementation of their nuclear genomes were confirmed using four EST-SSR markers. These markers were selected from markers previously mapped in sweet orange [C. sinensis (L.) Osbeck] and trifoliate orange [Poncirus trifoliata (L.) Raf.] and prescreened for suitable allelic polymorphism within the mandarin and pummelo lines used. After polymerase chain reaction amplification of sequences from the parents and putative hybrids, the products were separated on a genetic sequencer and visualized electronically. Additionally, EST-SSR markers identified the unexpected zygotic origin of a presumed nucellar embryogenic callus line. Integration of EST-SSR techniques for high-throughput genotyping with previously developed approaches to somatic hybrid creation increases substantially the effectiveness and efficiency of this in vitro-based breeding system for citrus rootstock improvement.

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