| Effect of population size and unbalanced data sets on QTL detection using genome-wide association mapping in barley breeding germplasm. | |
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MedLine Citation:
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PMID: 21898052 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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Over the past two decades many quantitative trait loci (QTL) have been detected; however, very few have been incorporated into breeding programs. The recent development of genome-wide association studies (GWAS) in plants provides the opportunity to detect QTL in germplasm collections such as unstructured populations from breeding programs. The overall goal of the barley Coordinated Agricultural Project was to conduct GWAS with the intent to couple QTL detection and breeding. The basic idea is that breeding programs generate a vast amount of phenotypic data and combined with cheap genotyping it should be possible to use GWAS to detect QTL that would be immediately accessible and used by breeding programs. There are several constraints to using breeding program-derived phenotype data for conducting GWAS namely: limited population size and unbalanced data sets. We chose the highly heritable trait heading date to study these two variables. We examined 766 spring barley breeding lines (panel #1) grown in balanced trials and a subset of 384 spring barley breeding lines (panel #2) grown in balanced and unbalanced trials. In panel #1, we detected three major QTL for heading date that have been detected in previous bi-parental mapping studies. Simulation studies showed that population sizes greater than 384 individuals are required to consistently detect QTL. We also showed that unbalanced data sets from panel #2 can be used to detect the three major QTL. However, unbalanced data sets resulted in an increase in the false-positive rate. Interestingly, one-step analysis performed better than two-step analysis in reducing the false-positive rate. The results of this work show that it is possible to use phenotypic data from breeding programs to detect QTL, but that careful consideration of population size and experimental design are required. |
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Authors:
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Hongyun Wang; Kevin P Smith; Emily Combs; Tom Blake; Richard D Horsley; Gary J Muehlbauer |
Publication Detail:
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Type: JOURNAL ARTICLE Date: 2011-9-7 |
Journal Detail:
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Title: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik Volume: - ISSN: 1432-2242 ISO Abbreviation: - Publication Date: 2011 Sep |
Date Detail:
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Created Date: 2011-9-7 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 0145600 Medline TA: Theor Appl Genet Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Affiliation:
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Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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