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United States Department of Agriculture

Agricultural Research Service

Title: Populations structure in cultivated lettuce (Lactuca sativa L.) and its impact on assocation mapping.

Authors
item Simko, Ivan
item Hu, Jinguo

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 20, 2007
Publication Date: January 9, 2008
Citation: Simko, I., Hu, J. Populations structure in cultivated lettuce (Lactuca sativa L.) Journal of the American Society for Horticultural Science, Vol. 133, Pages 61-68, 2008.

Interpretive Summary: Association mapping is a novel method for detecting linkage between molecular markers and the traits of interest. The method is based on analysis of elite cultivars without the need of developing new mapping populations. However, to avoid detection of spurious associations, population structure in the analyzed set of cultivars needs to be assessed first. In the present work we have analyzed population structure in a set of 54 cultivars from five horticultural types that are representing diversity observed in the cultivated lettuce. Population structure and the presence of subpopulations were assessed with 388 TRAP (Target Region Amplified Polymorphism) molecular markers. Although clustering based on molecular markers was generally in good agreement with horticultural types, some cultivars were classified differently or showed mixed origin. To observe how population structure affects marker-trait association, we have analyzed four traits (lettuce dieback resistance, seed color, leaf margin undulation, and head height) with different relationships to the lettuce horticultural types for number of false positive associations. The traits that were strongly correlated with lettuce types displayed many false positive results when population structure was ignored in the analysis. But the spurious associations disappeared when structure was included into the statistical model. The identification of population structure in cultivated lettuce represent the first step towards use of association mapping in lettuce.

Technical Abstract: The association mapping technique is a useful tool for detecting markers linked to the genes underlying the variation of a trait among elite cultivars. To avoid false positive results due to unrecognized population structure in the analyzed set of individuals, the subpopulations need to be identified. Fifty-four lettuce cultivars representing diversity observed in five horticultural types important in North America, together with six accessions from two wild species (L. saligna and L. serriola), were assayed for polymorphism with 388 TRAP marker loci. The model-based clustering approach recognized three main subpopulations in cultivated lettuce that are well separated from wild species. Although the clustering based on molecular markers was generally in good agreement with horticultural types, some cultivars were classified differently or showed mixed origin. The effect of population structure on association mapping was tested on four traits (lettuce dieback resistance, seed color, leaf margin undulation, and head height) with different relationships to the lettuce horticultural types. The traits that were strongly correlated with lettuce types (lettuce dieback resistance and head height) displayed many false positive results when population structure was ignored, but the spurious associations disappeared when structure was included into the statistical model. The effect of population structure on number of false positive associations was notably less pronounced in seed color and leaf margin undulation that had weak correlation with horticultural types.

Last Modified: 10/31/2014
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