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

PloS One
John Damien PlattenRochelle E Zantua

Abstract

Despite 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 a...Continue Reading

References

Jul 1, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Luping FuYonggui Xiao
Mar 3, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Joshua CobbEng Hwa Ng
Jun 6, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·M MakhoulC Obermeier

Citations

Aug 16, 2005·Nature·International Rice Genome Sequencing Project
Sep 13, 2005·Nature Genetics·Zhong-Hai RenHong-Xuan Lin
Jun 23, 2006·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·K HayashiI Ashikawa
Nov 30, 2006·Plant Biotechnology Journal·Louis M T BradburyDaniel L E Waters
Aug 24, 2007·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Bertrand Collard, David J Mackill
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng Li1000 Genome Project Data Processing Subgroup
Jul 15, 2009·Proceedings of the National Academy of Sciences of the United States of America·Kenneth L McNallyJan E Leach
Dec 2, 2010·Nature Communications·Taiichiro OokawaMakoto Matsuoka
Mar 1, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Shalabh DixitArvind Kumar
Dec 29, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·R Bernardo
Aug 7, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jennifer E SpindelSusan McCouch
Nov 19, 2013·International Journal of Molecular Sciences·Gous MiahMohammad Abdul Latif
May 30, 2014·GigaScience
Mar 17, 2015·The Plant Pathology Journal·A K SinghU S Singh
Apr 7, 2016·Phytopathology·Klaus Konrad Scheuermann, Yulin Jia

Related Concepts

Biological Markers
Study
Quantitative Trait Loci
Vitamin D Deficiency
Evaluation
Breeding
Alleles
Bioconductor caAffy MAS Probe Summary Method
Germ Plasm
Perception

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Synapse Loss as Therapeutic Target in MS

As we age, the number of synapses present in the human brain starts to decline, but in neurodegenerative diseases this occurs at an accelerated rate. In MS, it has been shown that there is a reduction in synaptic density, which presents a potential target for treatment. Here is the latest research on synapse loss as a therapeutic target in MS.

Artificial Intelligence in Cardiac Imaging

Artificial intelligence (ai) techniques are increasingly applied to cardiovascular (cv) medicine in cardiac imaging analysis. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

Social Learning

Social learning involves learning new behaviors through observation, imitation and modeling. Follow this feed to stay up to date on the latest research.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Single Cell Chromatin Profiling

Techniques like ATAC-seq and CUT&Tag have the potential to allow single cell profiling of chromatin accessibility, histones, and TFs. This will provide novel insight into cellular heterogeneity and cell states. Discover the latest research on single cell chromatin profiling here.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.