Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids

  • Joyce Njuguna (Creator)
  • Lindsay Clark (Creator)
  • Alexander Edward Lipka (Creator)
  • Kossonou Anzoua (Creator)
  • Larisa Bagmet (Creator)
  • Pavel Chebukin (Creator)
  • Maria Dwiyanti (Creator)
  • Elena Dzyubenko (Creator)
  • Nicolay Dzyubenko (Creator)
  • Bimal Ghimire (Creator)
  • Xiaoli Jin (Creator)
  • Douglas Johnson (Creator)
  • Jens Kjeldsen (Creator)
  • Hironori Nagano (Creator)
  • Ivone Oliveira (Creator)
  • Junhua Peng (Creator)
  • Karen Petersen (Creator)
  • Andrey Sabitov (Creator)
  • Eun Seong (Creator)
  • Toshihiko Yamada (Creator)
  • Ji Yoo (Creator)
  • Chang Yu (Creator)
  • Hu Zhao (Creator)
  • Patricio Munoz (Creator)
  • Stephen P Long (Creator)
  • Erik J Sacks (Creator)

Dataset

Description

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.
Date made availableJul 5 2023
PublisherUniversity of Illinois Urbana-Champaign

Keywords

  • allelic dosage
  • Bayesian genotype-calling
  • Genome-wide association
  • Polyploid
  • Genomic prediction

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