title: Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries.
abstract: Cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid, has been bred for distinct market classes, including fresh market, pigmented, and processing varieties. Breeding efforts have relied on phenotypic selection of populations developed from intra- and intermarket class crosses and introgressions of wild and cultivated Solanum relatives. To retrospectively explore the effects of potato breeding at the genome level, we used 8303 single-nucleotide polymorphism markers to genotype a 250-line diversity panel composed of wild species, genetic stocks, and cultivated potato lines with release dates ranging from 1857 to 2011. Population structure analysis revealed four subpopulations within the panel, with cultivated potato lines grouping together and separate from wild species and genetic stocks. With pairwise kinship estimates clear separation between potato market classes was observed. Modern breeding efforts have scarcely changed the percentage of heterozygous loci or the frequency of homozygous, single-dose, and duplex loci on a genome level, despite concerted efforts by breeders. In contrast, clear selection in less than 50 years of breeding was observed for alleles in biosynthetic pathways important for market class-specific traits such as pigmentation and carbohydrate composition. Although improvement and diversification for distinct market classes was observed through whole-genome analysis of historic and current potato lines, an increased rate of gain from selection will be required to meet growing global food demands and challenges due to climate change. Understanding the genetic basis of diversification and trait improvement will allow for more rapid genome-guided improvement of potato in future breeding efforts.
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA.
authors.forename: Candice N
authors.initials: CN
authors.lastname: Hirsch
authors.forename: Cory D
authors.initials: CD
authors.lastname: Hirsch
authors.forename: Kimberly
authors.initials: K
authors.lastname: Felcher
authors.forename: Joseph
authors.initials: J
authors.lastname: Coombs
authors.forename: Dan
authors.initials: D
authors.lastname: Zarka
authors.forename: Allen
authors.initials: A
authors.lastname: Van Deynze
authors.forename: Walter
authors.initials: W
authors.lastname: De Jong
authors.forename: Richard E
authors.initials: RE
authors.lastname: Veilleux
authors.forename: Shelley
authors.initials: S
authors.lastname: Jansky
authors.forename: Paul
authors.initials: P
authors.lastname: Bethke
authors.forename: David S
authors.initials: DS
authors.lastname: Douches
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
mesh_terms: D000383:Agriculture; D053898:Biosynthetic Pathways / Q000235:genetics; D001947:Breeding / Q000266:history*; D002338:Carotenoids / Q000378:metabolism; D005787:Gene Frequency / Q000235:genetics; D005843:Geography; D006579:Heterozygote; D049673:History, 20th Century; D049674:History, 21st Century; D040541:Marketing; D009656:North America; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012639:Seeds / Q000235:genetics; D012641:Selection, Genetic; D011198:Solanum tuberosum / Q000191:economics / Q000235:genetics / Q000254:growth & development* / Q000266:history*
chemical_list: D002338:Carotenoids
keywords: Solanum tuberosum; genomics; genotypic diversity; phenotypic diversity