Enabling Molecular Breeding
Among the major global food crops, potato is unique for being autotetraploid and clonally propagated. Autotetraploid genomes are organized in groups of four homologous chromosomes, which gives rise to more complex patterns of inheritance than in diploid crops. One focus of the lab is developing new methods and practical software solutions to enable molecular breeding in potato and other autotetraploids, such as alfalfa and blueberry. In 2016 we released GWASpoly, an R package to conduct genome-wide association studies with allele dosage markers. In 2017 we released ClusterCall, an R package for making accurate allele dosage calls from SNP array data.
Schmitz Carley et al. (2017) Automated tetraploid genotype calling by hierarchical clustering
Endelman et al. (2017) Pedigree reconstruction with genome-wide markers in potato
Currently, new clones are selected to become parents in the UW potato breeding program after 4 years of field testing, which corresponds to a 6 year breeding cycle. By coupling historical crop data with molecular markers, breeding value predictions about new clones can be made earlier to shorten the cycle. We have begun implementing this genomic selection approach for the chip processing segment of the UW breeding program and are investigating how to design the program for optimal genetic gain.
One of the main drivers of genomic selection accuracy is the size of the population used to train the prediction model. At present, the cost of the potato SNP array is more limiting than the cost of phenotyping for increasing our training population size. One way to reduce genotyping costs is through multiplexing, in which many DNA samples are pooled into one library for sequencing. This genotyping-by-sequencing (GBS) approach is widely used in diploids but is less straightforward in tetraploids because of the high read depth needed to determine allele dosage. Research is underway on the use of GBS in potato.
Genetics of tuber skin set and appearance
The appearance and integrity of potato tuber skin has a major influence on marketability and disease resistance during storage, but there is much we do not understand about the genetics of these traits. We are currently using image analysis to quantify skin set and red color in several mapping populations.
Endelman and Jansky (2016) Genetic mapping with an inbred line-derived F2 population in potato