DeltaGen: a comprehensive decision support tool for plant breeders

The objective of our paper is to introduce a new and unique plant breeding decision support software tool “DeltaGen”, implemented in R and its package Shiny. DeltaGen provides plant breeders with a single integrated solution for experimental design generation, data quality control, statistical and quantitative genetic analyses, breeding strategy evaluation/simulation and cost analysis, pattern analysis, index selection and underlying basic theory on quantitative genetics. Key analysis procedures in DeltaGen were demonstrated using three data sets generated from forage breeding trials in Australia, New Zealand and the USA. Analyses of the perennial ryegrass seasonal growth data in case study 1 was based on REML analysis and pattern analysis. A graphical summary of the performance of entries across locations was generated and entries with specific and broad adaptation were identified. The quantitative genetic analysis and breeding method simulation procedures applied to the perennial ryegrass half sib (HS) family data in case study 2, enabled estimation of quantitative genetic parameters, prediction of genetic gain (∆G) and calculation of costs ($) per selection cycle. These results enabled comparison of three breeding methods, which also included Genomic Selection (GS), and their simulation. Data from case study 3 were analysed to investigate a multivariate approach to identify HS families of switchgrass with breeding values that would enable increasing the traits biomass dry matter yield (DMY) and cell wall ethanol (CWE) and decreasing Klason lignin (KL). The Smith-Hazel (SH) index developed enabled identification of HS families with genetic worth for increasing DMY and CWE and reducing KL, in contrast to individual trait selection. Analysis of the data sets in all three case studies provided a snapshot of the key analyses available within DeltaGen. This software tool could also be used as a teaching resource in plant breeding courses. DeltaGen is available as Freeware on the link: http://agrubuntu.cloudapp.net/shiny-apps/PlantBreedingTool/