Tuber_bruising

R code for the publication:

Olivia Angelin-Bonnet, Susan Thomson, Matthieu Vignes, Patrick J. Biggs, Katrina Monaghan, Rebecca Bloomer, Kathryn Wright, Samantha Baldwin (2022). Investigating the genetic components of tuber bruising in a breeding population of tetraploid potatoes. Manuscript submitted for publication.

Folders

• genomics_data_preprocessing: variants filtering and dosage calling with polyRAD.

• genomics_population_structure: analysis of population structure with STRUCTURE and DAPC.

• genomics_gwas: pre-processing of tuber bruising data and GWAS with GWASpoly.

• transcriptomics_differential_expression: RNAseq data pre-processing, differential expression (DE) with DESeq2, and comparison of the GWAS and DE results.