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bioRxiv · 10.1101/050955

Efficiency of genome-wide association study in open-pollinated populations

José Marcelo Soriano Viana·Gabriel Borges Mundim·Fabyano Fonseca Silva·Antonio Augusto F Garcia
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Abstract

Genome-wide association studies (GWAS) with plant species have employed inbred lines panels. Thus, to our knowledge, no information is available on theory and efficiency of GWAS in open-pollinated populations. Our objectives are to present quantitative genetics theory for GWAS, evaluate the relative efficiency of GWAS in non-inbred and inbred populations and in an inbred lines panel, and assess factors affecting GWAS, such as linkage disequilibrium (LD), sample size, and quantitative trait locus (QTL) heritability. Fifty samples of 400 individuals from populations with LD were simulated. Individuals were genotyped for 10,000 single nucleotide polymorphisms (SNPs) and phenotyped for traits with different degrees of dominance controlled by 10 QTLs and 90 minor genes. The average SNP density was 0.1 centiMorgan and the trait heritabilities were 0.4 and 0.8. We assessed GWAS efficiency based on the power of QTL detection, number of false-positive associations, bias in the estimated QTL position, and range of the significant SNPs for the same QTL. When the LD between a QTL and one or more SNPs is restricted to markers very close to or within the QTL, GWAS in open-pollinated populations can be highly efficient, depending mainly on QTL heritability and sample size. GWAS achieved the highest power of QTL detection, the smallest number of false-positive associations, and the lowest bias in the estimated QTL position for the inbred lines panel correcting for population structure. Under low QTL heritability and reduced sample size, GWAS is ineffective for non-inbred and inbred populations and for inbred lines panel.

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José Marcelo Soriano Viana, Gabriel Borges Mundim, Fabyano Fonseca Silva, Antonio Augusto F Garcia. 2016-04-29. Efficiency of genome-wide association study in open-pollinated populations. https://doi.org/10.1101/050955

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