Location: Vegetable Crops ResearchTitle: The contribution of the “SolCAP” project to potato breeding) Author
Submitted to: Potato Research
Publication Type: Proceedings
Publication Acceptance Date: 5/12/2014
Publication Date: 7/8/2014
Citation: Douches, D., Hirsch, C., Felcher, K., Manrique, N., Massa, A., Coombs, J., Hardigan, M., Bisognin, D., Jansky, S.H., Dejong, W., Buell, C.R. 2014. The contribution of the “SolCAP” project to potato breeding. Potato Research. Paper No. KNL 5. Interpretive Summary:
Technical Abstract: Potato variety development in the US is driven by public sector scientists interacting with state and national grower organizations to test and commercialize new varieties. The processing market drives the breeding focus while disease and insect resistances may have regional importance. Based upon stakeholder priorities, variety development is a key component to make positive changes for the overall potato industry in the United States. Historically, the breeding, genetic studies and germplasm development efforts have relied on phenotypic analysis to evaluate, select and advance germplasm because we have been limited by the availability of quality genetic markers. The goal of the USDA-funded SolCAP Coordinated Agricultural Project was to translate genomic resources into tools that can be used by breeders and geneticists. A major outcome of this project was the development of a genome-wide potato single nucleotide polymorphism (SNP) array that can be used in elite breeding germplasm. The SolCAP 8303 Infinium Potato SNP array was utilized to genotype numerous biparental tetraploid and diploid populations, a diversity panel and a core collection of Solanum species. In addition, replicated phenotypic data was collected on the diversity panel and the mapping populations for QTL and GWAS analysis. The SNP array provides a SNP marker density sufficient to generate genetic maps to identify numerous QTL for agronomic, quality and disease resistance traits. We have constructed many new diploid and tetraploid genetic maps and have identified numerous major QTL linked to these traits that are now candidates for marker-assisted breeding. Tetraploid clones were genotyped with over 5000 of the SNPs for five genotypic classes. We examined the occurrence and frequency of double reduction along the chromosome arms, germplasm relationships, varietal fingerprinting and candidate gene enrichment. The codominant SNP markers also help us clearly separate conventionally bred potato varieties and evaluate population structure. Using SNP markers that are physically mapped allows us to compare regions of distorted segregation and marker gaps between populations at the diploid and tetraploid level as well as recombination rates throughout the genome. Mapping traits and better understanding the cultivated tetraploid genome provides opportunities for breeders to more efficiently develop new cultivars. The SolCAP 8303 Infinium Potato SNP array provides a common set of markers that the breeders and geneticists can reliably use and reference for mapping, germplasm assessment and fingerprinting. This array has also been a useful tool to advance our understanding of the potato genome. Furthermore, breeders are mapping QTL across numerous populations that will expand our understanding of economically important traits and lead to marker-assisted selection and breeding.