Jeffrey Endelman
This R package was designed to facilitate the use of genome-wide markers for breeding autotetraploid (4x) species, but it is also works for diploids. The software has been developed and tested using data from the University of Wisconsin-Madison potato breeding program.
To install and load the package:
install.packages("devtools")
library(devtools)
install_github("jendelman/polyBreedR", build_vignettes=FALSE)
library(polyBreedR)Vignette 1 covers the making of tetraploid genotype calls and their utility for pedigree curation. The pedigree functionality is based on Endelman et al. (2017). Financial support has come from USDA NIFA Hatch Projects 1002731 and 1013047, administered through the Wisconsin Agricultural Experiment Station at UW-Madison.
Vignette 2 covers the analysis of marker data for dihaploids, including checking ploidy and parentage. Financial support has come from USDA NIFA Awards 2014-67013-22434 (AFRI) and 2019-51181-30021 (SCRI).
Vignette 3 introduces functions for representing DArTag GBS and SNP array data in Variant Call Format, and functions for imputing from low to high density markers. Financial support has come from USDA NIFA Awards 2019-51181-30021, 2020-51181-32156, and 2021-34141-35447.
For a complete specification of the package functions, consult the reference manual.