Document details for 'Linkage disequilibrium and evaluation of genome-wide association mapping models in tetraploid potato'

Authors Sharma, S.K., MacKenzie, K., Mclean, K., Dale, M.F.B. and Bryan, G.J.
Publication details G3: Genes, Genomes, Genetics 8(10), 3185-3202.
Keywords Linkage Disequilibrium, kinship, population structure, genome-wide association studies (GWAS), mixed models, tetraploid, potato
Abstract Genome-wide association studies (GWAS) have become a powerful tool for analysing complex traits in crop plants. The presence of significant population structure within the analysed germplasm can lead to the detection of spurious marker-trait associations, and can also mask true associations. Appropriate statistical models are needed to detect true marker-trait associations from GWAS. In most published GWAS analyses in potato to date, a 'one model fits all traits' approach has been adopted. The current study evaluates the efficacy of various GWAS models and methods of elucidating population structure in potato. Models were examined on an association panel comprising 341 diverse autotetraploid potato cultivars and advanced breeding lines genotyped with single nucleotide polymorphism (SNP) markers. The panel was phenotyped for 20 agronomic and processing traits assessed in different environments. Best Linear Unbiased Estimates (BLUEs) for these traits were obtained for use in assessing the GWAS models. Goodness of fit of GWAS models, derived using different combinations of kinship and population structure for all traits, was evaluated using Bayesian information criterion. Kinship was found to play a major role in correcting population confounding effects and results also advocate a 'trait-specific' fit of different GWAS models. A survey of genome-wide linkage disequilibrium, one of the critical factors affecting GWAS, in the examined germplasm is also presented.
Last updated 2018-10-04

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