RT Journal Article
SR Electronic
T1 Genotyping-by-sequencing and microarrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 476598
DO 10.1101/476598
A1 Sandra Silvia Negro
A1 Emilie Millet
A1 Delphine Madur
A1 Cyril Bauland
A1 Valérie Combes
A1 Claude Welcker
A1 François Tardieu
A1 Alain Charcosset
A1 Stéphane Dimitri Nicolas
YR 2018
UL http://biorxiv.org/content/early/2018/11/23/476598.abstract
AB Background Single Nucleotide Polymorphism (SNP) array and re-sequencing technologies have different properties (e.g. calling rate, minor allele frequency profile) and drawback (e.g. ascertainment bias), which lead us to study the complementarity and consequences of using them separately or combined in diversity analyses and Genome-Wide Association Studies (GWAS). We performed GWAS on three traits (grain yield, plant height and male flowering time) measured in 22 environments on a panel of 247 diverse dent maize inbred lines using three genotyping technologies (Genotyping-By-Sequencing, Illumina Infinium 50K and Affymetrix Axiom 600K arrays).Results The effects of ascertainment bias of both arrays were negligible for deciphering global genetic trends of diversity in this panel and for estimating relatedness. We developed an original approach based on linkage disequilibrium (LD) extent in order to determine whether SNPs significantly associated with a trait and that are physically linked should be considered as a single QTL or several independent QTLs. Using this approach, we showed that the combination of the three technologies, which have different SNP distribution and density, allowed us to detect more Quantitative Trait Loci (QTLs, gain in power) and potentially refine the localization of the causal polymorphisms (gain in position).Conclusions Conceptually different technologies are complementary for detecting QTLs by tagging different haplotypes in association studies. Considering LD, marker density and the combination of different technologies (arrays and re-sequencing), the genotypic data presently available were most likely enough to well represent polymorphisms in the centromeric regions, whereas using more markers would be beneficial for telomeric regions.List of abreviationsDTADay to AnthesisGYGrain Yield adjusted at 15% moistureplantHTPlant HeightGBSGenotyping By SequencingLDLinkage disequilibriumGWASGenome-Wide Association StudiesMAFMinimum Allelic FrequencySNPSingle Nucleotide PolymorphismHRRHigh Recombinogenic RegionsLRRLow Recombinogenic RegionsQTLQuantitative Trait Locus