This repository contains the phenotypic and genotypic data and R scripts associated with the tetraploid blueberry QTL analysis presented in the accompanying publication.
Phenotypic data for 831 individuals across all families. The file contains data for seven traits:
- Brix
- Total acidity
- pH
- Firmness
- Leaf burn
- Fruit sunburn
- Tipburn
The phenotypic data are provided before the sample filtering applied for the final analysis. Missing observations are represented as NA.
Genotypic data for 1,580 individuals at 2,451 targeted biallelic SNP markers distributed across the 12 blueberry chromosomes (Chr01–Chr12).
The samples in this file had been filtered based on copy number but are provided before sample deduplication and subsequent genotypic quality-control filtering.
The number of individuals in the deposited genotype and phenotype files therefore differs from the number reported for the final analysis in the publication. Following the filtering steps described in the paper, 727 individuals were retained for the final analysis.
R script used for the single-location phenotypic analysis and estimation of genotype BLUEs.
R script used for the across-location analysis of the single-location BLUEs using ASReml-R.
R script for QTL analysis using the diaQTL package. The script provides an example of the QTL analysis using one family and one trait.
The phenotype analyses were performed using ASReml-R, and QTL analysis was performed using diaQTL. Additional R packages required for individual analyses are specified in the corresponding scripts.
The file paths in the example scripts should be updated to match the location of the data files on the user's system.