Polyploids have multiple sets of chromosomes and have arisen by extensive genomic alteration and genome duplication. Many agriculturally and horticulturally important crops are polyploid. Instead, use of continuous genotypes simplifies the analysis, saves computational time and results more potential markers. Genotype calling does not improve the association and shows no advantages in this study. ConclusionsĪssociation of various phenotypic traits with continuous genotypes is successful with both uni- and multivariate regression methods. A simulation study was used to successfully validate the number of associating markers. Association based on genotype classes resulted in similar values, but missed several significant probes. Linear and partial least squares regression led to numerous associating probes. Baysian regression was the most restrictive method, resulting in ten probes for one trait and none for the others. The identified probe sets were overlapping, but not identical between the methods. We were able to detect associating probes using continuous genotypes for multiple traits, using different regression methods. The data set consisted of 55,825 probes and 228 samples. A disease, a flowering and a growth trait with h 2 of 0.51, 0.78 and 0.91 were associated with a hexaploid chrysanthemum genotypes. Linear, Bayesian and partial least squares regression were applied, to determine if the use of continuous genotypes is limited to a specific method.
We associated continuous genotypes to three different traits and compared the results to the output of the genotype caller SuperMASSA. Alternatively, continuous genotype values can be used for association analysis in higher polyploids.
Eventually, the errors produced by misclassifications exceed the benefits of genotype classes. While genotype classification is an established noise reduction step in diploids, it gains complexity with increasing ploidy levels. Available methods are limited with respect to the ploidy level or data producing technologies. The increased number of possible genotype classes complicates the differentiation between them. Association studies are an essential part of modern plant breeding, but are limited for polyploid crops.
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