Impact of Genotype-Calling Methodologies on Genome-Wide Association and Genomic Prediction in Polyploids

Njuguna, J.N., Clark, L.V., Lipka, A.E., Anzoua, K.G., Bagmet, L., Chebukin, P., Dwiyanti, M.S., Dzyubenko, E., Dzyubenko, N., Ghimire, B.K., Jin, X., Johnson, D.A., Kjeldsen, J.B., Nagano, H., Oliveira, I.B., Peng, J., Petersen, K.K., Sabitov, A., Seong, E.S., Yamada, T., Yoo, J.H., Yu, C.Y., Zhao, H., Munoz, P., Long, S.P., Sacks, E.J. Oct. 30, 2023. Data from: “Impact of Genotype-Calling Methodologies on Genome-Wide Association and Genomic Prediction in Polyploids.” University of Illinois Urbana-Champaign. DOI: 10.13012/B2IDB-4829913_V2.

This dataset contains all data used in the paper “Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids”. The dataset includes genotypes and phenotypic data from two autotetraploid species Miscanthus sacchariflorus and Vaccinium corymbosum that was used used for genome wide association studies and genomic prediction and the scripts used in the analysis.

In this V2, 2 files have the raw data are added:

“Miscanthus_sacchariflorus_RADSeq.vcf” is the VCF file with the raw SNP calls of the Miscanthus sacchariflorus data used for genotype calling using the 6 genotype calling methods.

“Blueberry_data_read_depths.RData” is the a RData file with the read depth data that was used for genotype calling in the Blueberry dataset.

Download (3.4MB) includes:

• Culm lengths
• Descriptive statistics
• Yields