Functional genomic resources for potato

2008 ◽  
Vol 88 (4) ◽  
pp. 573-581 ◽  
Author(s):  
Xiu-Qing Li ◽  
Rebecca Griffiths ◽  
David De Koeyer ◽  
Charlotte Rothwell ◽  
Vicki Gustafson ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Genetic Maps ◽  
Genomic Research ◽  
Functional Genomic ◽  
Entire Genome ◽  
Future Directions ◽  
Genomic Resources ◽  
Expressed Sequence ◽  
Selection Of ◽  
Made In

Considerable functional genomic resources have been developed by the potato research community in the past decade, including expressed sequence tag (EST) libraries, SAGE libraries, microarrays, molecular-function maps, and mutant populations. This article reviews the types, characteristics, strengths, limitations, and appropriate applications of these resources for genomic research and discusses perspectives on future directions. This wide selection of resources available to potato researchers complements efforts to sequence the entire genome and advances made in the development of saturated genetic maps. Key words: Solanum, potato, genomics, expressed sequence tag, microarray, longSAGE, data mining

scholarly journals New eSSR and gSSR markers added to Australian barley maps

2006 ◽  
Vol 57 (9) ◽  
pp. 953 ◽  
Author(s):  
Kerrie L. Willsmore ◽  
Paul Eckermann ◽  
Rajeev K. Varshney ◽  
Andreas Graner ◽  
Peter Langridge ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Genomic Library ◽  
Rice Genome ◽  
Genetic Maps ◽  
Net Blotch ◽  
Genomic Ssr ◽  
On Line ◽  
Good Coverage ◽  
Expressed Sequence ◽  
Simple Sequence

To enhance genetic maps of barley previously developed in Australia for identifying markers useable in molecular breeding, a new set of simple sequence repeat (SSR) and indel markers was added to the maps. These markers were developed through (i) database mining of barley expressed sequence tag (EST) sequences, (ii) comparative barley-rice genome analysis, and (iii) screening of a genomic library with SSR probes. The primer set selected for this study comprised 216 EST-SSR (eSSR) and 25 genomic SSR (gSSR) markers, which were screened for polymorphism on 4 doubled haploid (DH) or recombinant inbred line (RIL) populations. In total, 81 new markers were added to the maps, with good coverage on all 7 chromosomes, except 6H, which only had 2 new markers added. The marker order of previously published maps was re-evaluated by comparing recombination fractions calculated by 2 methods to discover the best position for each marker. The new SSR markers were then added to the updated maps. Several of these new markers are linked to important barley disease resistance genes such as those for cereal cyst nematode, spot form of net blotch, and leaf scald resistance, and are readily useable for marker-assisted barley breeding. The new maps are available on-line at www.genica.net.au.

scholarly journals Integration of EST-CAPS markers into genetic maps of Eucalyptus urophylla and E. tereticornis and their alignment with E. grandis genome sequence

2012 ◽  
Vol 61 (1-6) ◽  
pp. 247-255 ◽  
Author(s):  
X. Yu ◽  
Y. Guo ◽  
X. Zhang ◽  
F. Li ◽  
Q. Weng ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Rapd Markers ◽  
Expressed Sequence Tag ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Maps ◽  
Eucalyptus Urophylla ◽  
Linkage Groups ◽  
Caps Markers ◽  
Expressed Sequence ◽  
Genus Eucalyptus

AbstractA suite of 91 expressed sequence tag (EST) derived cleaved amplified polymorphic sequence (CAPS) markers were developed and used for enriching the genetic maps of Eucalyptus urophylla and E. tereticornis built previously based on random amplified polymorphic DNA (RAPD) markers. The EST-CAPS markers were highly similar to original ESTs, with sequence identity ranging from 92.5% to 100.0%. In linkage analysis, 48 and 42 EST-CAPSs were integrated into the genetic maps of E. urophylla and E. tereticornis, respectively, including 13 shared by both maps, while 14 were unmapped. For E. urophylla, the final map had a total length of 1789.5 cM and a mean interval between markers of 9.7 cM, being 284.9 cM larger and 1.3 cM less than those of the prior RAPD map, respectively. For E. tereticornis, the final map had a length of 1488.1 cM and a mean interval of 10.3 cM, being 452.4 and 0.2 cM more than the prior map, respectively. All the 77 newly mapped EST-CAPSs found each at least one homologue in the E. grandis genome sequence released recently, and conserved synteny and colinearity were observed between E. grandis genome and our linkage groups. The enriched maps would provide a set of useful markers for genome analysis, comparative mapping and fine-mapping of important genes located in conserved regions for the important tree genus Eucalyptus.

scholarly journals The genome of the warm-season turfgrass African bermudagrass (Cynodon transvaalensis)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Fengchao Cui ◽  
Geli Taier ◽  
Manli Li ◽  
Xiaoxia Dai ◽  
Nan Hang ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Agronomic Traits ◽  
Warm Season ◽  
Genomic Research ◽  
Functional Genomic ◽  
Evolutionary Analysis ◽  
Ecological Significance ◽  
Genomic Resources ◽  
Transcriptome Comparison ◽  
Genomic Basis

AbstractCynodon species can be used for multiple purposes and have high economic and ecological significance. However, the genetic basis of the favorable agronomic traits of Cynodon species is poorly understood, partially due to the limited availability of genomic resources. In this study, we report a chromosome-scale genome assembly of a diploid Cynodon species, C. transvaalensis, obtained by combining Illumina and Nanopore sequencing, BioNano, and Hi-C. The assembly contains 282 scaffolds (~423.42 Mb, N50 = 5.37 Mb), which cover ~93.2% of the estimated genome of C. transvaalensis (~454.4 Mb). Furthermore, 90.48% of the scaffolds (~383.08 Mb) were anchored to nine pseudomolecules, of which the largest was 60.78 Mb in length. Evolutionary analysis along with transcriptome comparison provided a preliminary genomic basis for the adaptation of this species to tropical and/or subtropical climates, typically with dry summers. The genomic resources generated in this study will not only facilitate evolutionary studies of the Chloridoideae subfamily, in particular, the Cynodonteae tribe, but also facilitate functional genomic research and genetic breeding in Cynodon species for new leading turfgrass cultivars in the future.

WINTER WHEAT DEVELOPED BY THE UDMURT RESEARCH INSTITUTE OF AGRICULTURE IN COMPETITIVE VARIETY TESTING

2020 ◽  
pp. 5-16
Author(s):  
I.V. TORBINA ◽  
◽  
I.R. FARDEYEVA ◽  
Keyword(s):  
Winter Wheat ◽  
Crop Rotation ◽  
Biological Characteristics ◽  
Commercial Use ◽  
Breeding Material ◽  
Rotation Pattern ◽  
Selection Of ◽  
Variety Testing ◽  
Made In ◽  
Research Institute

The paper assesses the promising varieties of winter wheat in a competitive variety test by the main economic and biological characteristics that determine the suitability of the variety for commercial use. The object of research was the authors’ own breeding material. The experiments on the selection of winter wheat were made in the experimental crop rotation pattern of the Institute.

Inflammatory Markers Associated With Diabetes Mellitus – Old and New Players

2020 ◽  
Vol 26 ◽  
Author(s):  
Emir Muzurović ◽  
Zoja Stanković ◽  
Zlata Kovačević ◽  
Benida Šahmanović Škrijelj ◽  
Dimitri P Mikhailidis
Keyword(s):  
Diabetes Mellitus ◽  
Inflammatory Markers ◽  
High Specificity ◽  
Future Directions ◽  
Effective Strategies ◽  
Advantages And Disadvantages ◽  
Type 2 Dm ◽  
Increased Risk ◽  
Made In

: Diabetes mellitus (DM) is a chronic and complex metabolic disorder, and also an important cause of cardiovascular (CV) diseases (CVDs). Subclinical inflammation, observed in patients with type 2 DM (T2DM), cannot be considered the sole or primary cause of T2DM in the absence of classical risk factors, but it represents an important mechanism that serves as a bridge between primary causes of T2DM and its manifestation. Progress has been made in the identification of effective strategies to prevent or delay the onset of T2DM. It is important to identify those at increased risk for DM by using specific biomarkers. Inflammatory markers correlate with insulin resistance (IR) and glycoregulation in patients with DM. Also, several inflammatory markers have been shown to be useful in assessing the risk of developing DM and its complications. However, the intertwining of pathophysiological processes and the not-quite-specificity of inflammatory markers for certain clinical entities limits their practical use. In this review we consider the advantages and disadvantages of various inflammatory biomarkers of DM that have been investigated to date as well as possible future directions. Key features of such biomarkers should be high specificity, non-invasiveness and cost-effectiveness.

Evidence-based Assessment

2010 ◽  
pp. 76-98
Author(s):  
John Hunsley ◽  
Eric J. Mash
Keyword(s):  
Decision Making ◽  
Clinical Assessment ◽  
Assessment Process ◽  
Evidence Based ◽  
The Past ◽  
Specific Assessment ◽  
The Many ◽  
Selection Of ◽  
Made In

Evidence-based assessment relies on research and theory to inform the selection of constructs to be assessed for a specific assessment purpose, the methods and measures to be used in the assessment, and the manner in which the assessment process unfolds. An evidence-based approach to clinical assessment necessitates the recognition that, even when evidence-based instruments are used, the assessment process is a decision-making task in which hypotheses must be iteratively formulated and tested. In this chapter, we review (a) the progress that has been made in developing an evidence-based approach to clinical assessment in the past decade and (b) the many challenges that lie ahead if clinical assessment is to be truly evidence-based.

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.

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

Interpreting testing and assessment: A state-of-the-art review

2021 ◽  
pp. 026553222110361
Author(s):  
Chao Han
Keyword(s):  
State Of The Art ◽  
Professional Certification ◽  
Automatic Assessment ◽  
Prospective Students ◽  
Assessment Practice ◽  
High Stakes ◽  
Future Directions ◽  
Assessment Tasks ◽  
Interpreter Education ◽  
Selection Of

Over the past decade, testing and assessing spoken-language interpreting has garnered an increasing amount of attention from stakeholders in interpreter education, professional certification, and interpreting research. This is because in these fields assessment results provide a critical evidential basis for high-stakes decisions, such as the selection of prospective students, the certification of interpreters, and the confirmation/refutation of research hypotheses. However, few reviews exist providing a comprehensive mapping of relevant practice and research. The present article therefore aims to offer a state-of-the-art review, summarizing the existing literature and discovering potential lacunae. In particular, the article first provides an overview of interpreting ability/competence and relevant research, followed by main testing and assessment practice (e.g., assessment tasks, assessment criteria, scoring methods, specificities of scoring operationalization), with a focus on operational diversity and psychometric properties. Second, the review describes a limited yet steadily growing body of empirical research that examines rater-mediated interpreting assessment, and casts light on automatic assessment as an emerging research topic. Third, the review discusses epistemological, psychometric, and practical challenges facing interpreting testers. Finally, it identifies future directions that could address the challenges arising from fast-changing pedagogical, educational, and professional landscapes.

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