| Cultivated potato (Solanum tuberosum L.) is unique among the major, global food crops in that it is autotetraploid and clonally propagated. There is a strong tradition of potato breeding in the public sector in the US, at land-grant universities, including the University of Wisconsin-Madison, and the USDA Agricultural Research Service. The National Chip Processing Trial (NCPT) is an ongoing, multi-year, multi-location trial in which advanced selections from the major US public potato breeding programs are evaluated for a common set of agronomic and processing traits. This research makes use of historical data from the NCPT to characterize USA elite chipping potato germplasm, which is universally autotetraploid. To enable additional analysis of this historic data, a method for accurate scoring of tetraploid molecular marker array data was developed. Further, extensive pedigree records from all public US potato breeding programs were assembled. Thus, relationships among entries were quantified with both marker-based and pedigree-based methods. It was demonstrated that the accuracy of genomic prediction of traits within the breeding program was higher when accounting for allele dosage. Finally, an analysis across locations of the NCPT developed an understanding of genetic correlation of trial environments, showing similarity in the relationship patterns whether clonal or additive effects were modeled. Outcomes include a novel genotype calling software, an assessment of the prospects of genomic prediction for potato selections, and the first analysis of under-utilized historic data from the NCPT. The findings should be of interest not only to potato scientists but also scientists studying polyploid crops and those breeding clonally propagated species. |
