Example breeder marker assisted seedling selection tools for streamlining DNA testing and presentation operations
This repository contains two tools, one of which has been used to facilitate timely delivery of marker-assisted seedling selection data to the Washington State University apple breeding program, the other to visualize the effects of marker culling decisions. One of these tools was recognized in a chapter by Evans, citing my original poster at the Rosaceae Genomics Conference in Italy. Data is entered onto one of the hidden sheets with the title of the DNA test. Plate information is entered into plates 1-4 (limit 4 per file = one 384-well PCR test). The Breeder can enter culling decision information on the Genetic Screening Inputs sheet and Master Decisions sheet to attach the DNA information to a final decision. These decisions will then be presented in two formats. A list format with the seedling information in the ABI data analysis sheet and a mapped 96-well format for easier location and removal of the seedlings arranged in a 96-well configuration in the greenhouse/glasshouse.
The second tool is an extension idea of the first that models the effects the marker-assisted culling decisions have on trait performance, for breeders to visualize the impact of these decisions. This tool called "Multi-Trait Family Planning". Further development will be to build into a small program, but Multi-Trait Family Planning for now is useful for breeders to get a visual idea of the effects of their decisions on the traits that they manage in a breeding program using the markers deployed by the Tree Fruit Genetics Laboratory at Washington State University under Dr. Cameron Peace's direction. Multitrait Family Planning was featured in the Washington Tree Fruit Research Commission Apple Horticulture/Postharvest final report for 2017 at https://treefruitresearch.org/wp-content/uploads/2019/12/2017-AHP-Continuing-and-Final-Reports.pdf, pages 16-25. Please cite this report and this github link for further development of this program.