The further development of a minimal KASP marker panel for distinguishing genotypes within apple collections

Abstract

Crop breeders are facing new challenges every year, creating a drive for tools which can be used to decrease the time it takes to develop new varieties. In the case of vegetatively cultivated crops, such as apples, a new variety can take multiple years if not decades of developmental work. Furthermore, apple cultivar collections are particularly costly to maintain, both in terms of monetary value, but also with regard to resources and land use. It is therefore of paramount importance that breeders have access to accurately maintained germplasm collections for use in breeding programs. Morphological identification can be time consuming, costly to undertake and requires expert knowledge. Previous work by the research group has sought to develop a low cost, reliable and rapid method for successfully genotyping germplasm collections. This project sought to build upon these previous studies by 1) using the KASP marker panel developed and validated by Winfield et al. (1) to genotype a nationally important collection of cider apples (Marker Set A), 2) develop a secondary minimal SNP marker set to further validate the results of the original set (Marker Set B) and 3) create a combined marker set of the best performing markers that covered all seventeen chromosomes found within the M. domestica genome (Marker Set C). The results of this study were varied, although the main aims and objectives were achieved. Genotyping data was produced for a large collection of apples important to the cider industry, 1323 samples for Marker Set A, 1426 for Marker Set B and 1421 for Marker Set C. The collection is housed at Thatchers cider and this data will be used to develop accurate orchard maps, which in turn will allow them to reliably plant the correct varieties, as well as share varieties within the industry. Comparisons between marker sets were subject to some limitations, however both Marker Set B and Marker Set C provided reliable and accurate markers that may be considered for inclusion in the current panel. The study also highlights potential areas for future work and ways in which this project may develop.

Date of Award	3 Oct 2023
Original language	English
Awarding Institution	University of Bristol
Supervisor	Gary Barker (Supervisor) & Keith Edwards (Supervisor)