Document Detail


Simultaneously accounting for population structure, genotype by environment interaction, and spatial variation in marker-trait associations in sugarcane.
MedLine Citation:
PMID:  21076513     Owner:  NLM     Status:  In-Process    
Abstract/OtherAbstract:
Few association mapping studies have simultaneously accounted for population structure, genotype by environment interaction (GEI), and spatial variation. In this sugarcane association mapping study we tested models accounting for these factors and identified the impact that each model component had on the list of markers declared as being significantly associated with traits. About 480 genotypes were evaluated for cane yield and sugar content at three sites and scored with DArT markers. A mixed model was applied in analysis of the data to simultaneously account for the impacts of population structure, GEI, and spatial variation within a trial. Two forms of the DArT marker data were used in the analysis: the standard discrete data (0, 1) and a continuous DArT score, which is related to the marker dosage. A large number of markers were significantly associated with cane yield and sugar content. However, failure to account for population structure, GEI, and (or) spatial variation produced both type I and type II errors, which on the one hand substantially inflated the number of significant markers identified (especially true for failing to account for GEI) and on the other hand resulted in failure to detect markers that could be associated with cane yield or sugar content (especially when failing to account for population structure). We concluded that association mapping based on trials from one site or analysis that failed to account for GEI would produce many trial-specific associated markers that would have low value in breeding programs.
Authors:
Xianming Wei; Phillip A Jackson; Scott Hermann; Andrzej Kilian; Katarzyna Heller-Uszynska; Emily Deomano
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Genome / National Research Council Canada = Génome / Conseil national de recherches Canada     Volume:  53     ISSN:  1480-3321     ISO Abbreviation:  Genome     Publication Date:  2010 Nov 
Date Detail:
Created Date:  2010-11-15     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8704544     Medline TA:  Genome     Country:  Canada    
Other Details:
Languages:  eng     Pagination:  973-81     Citation Subset:  IM    
Affiliation:
BSES Limited, PMB 57, Mackay Mail Centre, QLD 4741, Australia. xwei@bses.org.au
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