scholarly journals Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection

2018 ◽  
Author(s):  
John Damien Platten ◽  
Joshua N. Cobb ◽  
Rochelle E. Zantua
Keyword(s):  
Molecular Markers ◽  
Marker Assisted Selection ◽  
Mapping Population ◽  
Allelic Diversity ◽  
Quantitative Measure ◽  
Weak Point ◽  
High Allelic Diversity ◽  
Core Metrics ◽  
Selection Of

AbstractDespite strong interest over many years, the usage of quantitative trait loci in plant breeding has often failed to live up to expectations. A key weak point in the utilisation of QTLs is the “quality” of markers used during marker-assisted selection (MAS): unreliable markers result in variable outcomes, leading to a perception that MAS products fail to achieve reliable improvement. Most reports of markers used for MAS focus on markers derived from the mapping population. There are very few studies that examine the reliability of these markers in other genetic backgrounds, and critically, no metrics exist to describe and quantify this reliability. To improve the MAS process, this work proposes five core metrics that fully describe the reliability of a marker. These metrics give a comprehensive and quantitative measure of the ability of a marker to correctly classify germplasm as QTL[+]/[-], particularly against a background of high allelic diversity. Markers that score well on these metrics will have far higher reliability in breeding, and deficiencies in specific metrics give information on circumstances under which a marker may not be reliable. The metrics are applicable across different marker types and platforms, allowing an objective comparison of the performance of different markers irrespective of the platform. Evaluating markers using these metrics demonstrates that trait-specific markers consistently out-perform markers designed for other purposes. These metrics also provide a superb set of criteria for designing superior marker systems for a target QTL, enabling the selection of an optimal marker set before committing to design.

scholarly journals Molecular Identification of Pm4 Powdery Mildew Resistant Gene in Oat

2018 ◽  
Vol 46 (2) ◽  
pp. 350-355 ◽  
Author(s):  
Sylwia Magdalena OKOŃ ◽  
Tomasz OCIEPA ◽  
Aleksandra NUCIA
Keyword(s):  
Molecular Markers ◽  
Powdery Mildew ◽  
Correlation Coefficient ◽  
Molecular Identification ◽  
Marker Assisted Selection ◽  
Mapping Population ◽  
Breeding Programs ◽  
Resistant Gene ◽  
Modern Breeding ◽  
Selection Of

The selection of specific plants with desirable traits supported by molecular markers is one of the most important tools in modern breeding programs, which lead to reduce time and cost of selection. The aim of presented study was identification of dominant markers associated with Pm4 powdery mildew resistant gene in oat. To identify dominant silicoDArT markers for Pm4 gene, F2 mapping population ‘Av1860’ × ‘Fuchs’ were analyzed using DArTseq methodology. Among obtained 46 230 silicoDArT markers, 126 markers were high correlated with resistance to powdery mildew in oat conditioned by Pm4 gene. Among selected markers, 48 sequences have been chosen for potential conversion into specific STS markers. Finally, only 20 were suitable for primer design. As a result, 5 converted markers amplified expected products in resistant bulks, 3 of them segregated according to resistance in the whole population and shoved high correlation coefficient between marker and phenotype observation. Converted markers based on PCR could be used for identification of Pm4 gene in oat. Obtained results confirm the possibility of converting silicoDArT markers into PCR-based technique, which can be used in marker assisted selection (MAS).

scholarly journals Improving cooking and eating quality of Xieyou57, an elite indica hybrid rice, by marker-assisted selection of the Wx locus

Euphytica ◽  
2011 ◽  
Vol 179 (2) ◽  
pp. 355-362 ◽  
Author(s):  
Dahu Ni ◽  
Shilu Zhang ◽  
Sheng Chen ◽  
Yong Xu ◽  
Li Li ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Hybrid Rice ◽  
Eating Quality ◽  
Wx Locus ◽  
Cooking And Eating Quality ◽  
Indica Hybrid Rice ◽  
Selection Of

DEVELOPING MOLECULAR MARKERS FOR MARKER ASSISTED SELECTION OF FIRE BLIGHT RESISTANT APPLE SEEDLINGS

2007 ◽  
pp. 117-122 ◽  
Author(s):  
A. Peil ◽  
M.-V. Hanke ◽  
H. Flachowsky ◽  
K. Richter ◽  
T. Garcia ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Marker Assisted Selection ◽  
Fire Blight ◽  
Selection Of

Mapping and validation of chromosome regions associated with high malt extract in barley (Hordeum vulgare L.)

2003 ◽  
Vol 54 (12) ◽  
pp. 1223 ◽  
Author(s):  
H. M. Collins ◽  
J. F. Panozzo ◽  
S. J. Logue ◽  
S. P. Jefferies ◽  
A. R. Barr
Keyword(s):  
Marker Assisted Selection ◽  
Mapping Population ◽  
Malt Extract ◽  
Hordeum Vulgare L ◽  
Breeding Populations ◽  
Single Region ◽  
Soluble Material ◽  
Chromosome Regions ◽  
Mapping Populations

Malt extract represents the soluble material extracted from malt during the mashing process of barley. The measurement of malt extract is used by maltsters and brewers to assess the quality of the barley they are purchasing and is therefore one of the most important parameters used by breeders to assess the quality of new barley varieties before release. This paper identifies and investigates several regions (quantitative trait loci, QTLs) found to be associated with malt extract and discusses the uses of these regions for marker assisted selection (MAS).Eight regions of the barley genome were found to be associated with malt extract in 3 mapping populations. Five regions were found in the Sloop/Alexis and Sloop-sib/Alexis mapping populations on chromosomes 1H, 2H, 3H, 4H, and 5H. Two regions were found in the Chebec/Harrington population on chromosomes 1H and 5H and a single region was found on chromosome 2H in the Galleon/Haruna Nijo mapping population. Markers from 6 of these regions were investigated using several breeding populations with a high malt extract variety as a parent. The 'allele' from the high malt extract parent was found to be associated with a significant increase in malt extract in 4 regions, 2 regions on chromosome 2H and 2 regions on chromosome 5H.

scholarly journals Selection of powdery mildew resistant and susceptible grapevine genotypes with molecular markers

2007 ◽  
pp. 100-104
Author(s):  
Stella Molnár ◽  
Zsuzsanna Galbács ◽  
Gábor Halász ◽  
Sarolta Hoffmann ◽  
Anikó Veres ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Powdery Mildew ◽  
Marker Assisted Selection ◽  
Powdery Mildew Resistance ◽  
Resistance Breeding ◽  
Breeding Programs ◽  
Pcr Rflp ◽  
Muscadinia Rotundifolia ◽  
Selection Of ◽  
Grape Breeding

Incorporation of competitive quality and resistance against the most important fungal diseases (powdery and downy mildew) in a cultivar is one of the most important aims of grapevine breeding. In the 20th century, the most advanced results in grapevine resistance breeding were achieved by French researchers. They used resistant cultivars in more than 30% of their growing areas. In these varieties, North American wild Vitisspecies were the resistance gene sources. The discovery of immunity-like resistance of Muscadinia rotundifolia opened new perspectives in resistance breeding. M. rotundifolia harbours a dominant powdery mildew gene, providing resistance in highquality cultivars after back-crosses with V. vinifera varieties. M. rotundifolia has been involved in the Hungarian grape breeding programs since 1996, thanks to a French-Hungarian variety exchange. In addition to traditional selection methods, application of MAS (Marker Assisted Selection) based on various types ofmolecular markers, can provide additional tools for these efforts. Run1 locus, responsible for powdery mildew resistance, was identified in Muscadinia rotundifolia. Molecular markers closely linked to this locus are very significant in screening progenies deriving from M. rotundifolia and V. vinifera crosses, making possible the discrimination between resistant and susceptible genotypes at DNA level. In our analyses BC5 progeny of {(M. rotundifola×V. vinifera) BC4}×Cardinal (V. vinifera) tested for powdery symptoms were analysed with PCR-RFLP (GLP1- 12P1P3) and microsatellite markers (VMC4f3.1, VMC8g9). Our results proved the applicability of the linked markers and reliability of marker assisted selection.

scholarly journals Application of molecular markers in sunflower breeding

Genetika ◽  
2007 ◽  
Vol 39 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Dejana Saftic-Pankovic
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Marker Assisted Selection ◽  
Rapd Markers ◽  
Inbred Lines ◽  
Vegetable Crops ◽  
Large Variability ◽  
Parental Lines ◽  
Early Phases ◽  
Selection Of

The results of the application of molecular markers in sunflower breeding obtained in the Institute of Field and Vegetable Crops in the last decade are reviewed. Our results on genetic distance (GD=7-75%) between sunflower inbred lines obtained with RAPD and SSR markers, indicate large variability and provide important information for the selection of parental lines for future crosses. Interspecific hybridization is often used in sunflower breeding. As only some populations of H. giganteus and H. maximiliani are resistant to sunflower diseases, the investigation of genetic variability in/between two species is of interest. The results obtained with SSR markers are presented. The successful hybridization between H. rigidus and H. annuus was confirmed with RAPD markers, and the variability between F1 and BC1F1 plants is discussed. Desirable alleles and haplotypes can be detected with molecular markers both in early phases of plant development and in early phases of the production of improved lines, which reduces or completely eliminates the large number of testing cycles for desirable phenotypes. CAPS markers for resistance to downy mildew, that can be used in marker assisted selection are presented. .

scholarly journals Application of molecular markers in livestock improvement

2010 ◽  
Vol 26 (3-4) ◽  
pp. 135-154 ◽  
Author(s):  
A. Teneva ◽  
M.P. Petrovic
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Biochemical Markers ◽  
Marker Assisted Selection ◽  
Distance Estimation ◽  
Breeding Strategies ◽  
New Class ◽  
Recent Developments ◽  
Selection Of ◽  
Synteny Mapping

With recent developments in DNA technologies, a large number of genetic polymorphisms at DNA sequence level has been introduced over the last decades as named DNA-based markers. The discovery of new class of DNA profiling markers has facilitated the development of marker-based gene tags, mapbased cloning of livestock important genes, variability studies, phylogenetic analysis, synteny mapping, marker-assisted selection of favourable genotypes, etc. The most commonly used DNA-based markers have advantages over the traditional phenotypic and biochemical markers since they provide data that can be analyzed objectively. In this article the main applications of molecular markers in present-day breeding strategies for livestock improvement - parentage determination, genetic distance estimation, genetic diversity, gene mapping and marker-assisted selection have been reviewed.

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