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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #379721

Research Project: Potato Genetic Improvement for Enhanced Tuber Quality and Greater Productivity and Sustainability in Western U.S. Production

Location: Small Grains and Potato Germplasm Research

Title: Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA

item PANDY, JEEWAN - Texas A&M University
item SCHEURING, DOUGLAS - Texas A&M University
item KOYM, JEFFREY - Texas A&M University
item COOMBS, JOSEPH - Michigan State University
item Novy, Richard - Rich
item THOMPSON, ASUNTA - North Dakota State University
item HOLM, DAVID - Colorado State University
item DOUCHES, DAVID - Michigan State University
item MILLER JR, CREIGHTON - Texas A&M University
item VALES, ISABEL - Texas A&M University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/24/2021
Publication Date: 4/16/2021
Citation: Pandy, J., Scheuring, D.C., Koym, J.W., Coombs, J., Novy, R.G., Thompson, A.L., Holm, D.G., Douches, D.S., Miller Jr, C.J., Vales, I.M. 2021. Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA. Scientific Reports. 11. Article 8344.

Interpretive Summary: Knowing the relatedness and diversity within a potato breeding program's material is helpful to the breeder in selection of parents for hybridizations. Parents that are more unrelated can provide greater hybrid vigor in their progenies. This study used molecular markers to analyze 214 potato clones in the Texas A&M University potato breeding program that represent a diversity of clones from that program as well as clones that were originally derived from other potato breeding programs. The genetic analyses is useful for parent selection and could also be used for genetic fingerprinting and management of the breeding collection. rw

Technical Abstract: Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in vitro over a 40 years period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, we genotyped 214 potato clones with the Infinium Illumina 22K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones, primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components. The highest coefficient of differentiation observed between the groups was 0.14. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.