title: SNP diversity within and among Brassica rapa accessions reveals no geographic differentiation.
abstract: Genetic diversity was studied in a collection of 61 accessions of Brassica rapa, which were mostly oil-type turnip rapes but also included two oil-type subsp. dichotoma and five subsp. trilocularis accessions, as well as three leaf-type subspecies (subsp. japonica, pekinensis, and chinensis) and five turnip cultivars (subsp. rapa). Two-hundred and nine SNP markers, which had been discovered by amplicon resequencing, were used to genotype 893 plants from the B. rapa collection using Illumina BeadXpress. There was great variation in the diversity indices between accessions. With STRUCTURE analysis, the plant collection could be divided into three groups that seemed to correspond to morphotype and flowering habit but not to geography. According to AMOVA analysis, 65% of the variation was due to variation within accessions, 25% among accessions, and 10% among groups. A smaller subset of the plant collection, 12 accessions, was also studied with 5727 GBS-SNPs. Diversity indices obtained with GBS-SNPs correlated well with those obtained with Illumina BeadXpress SNPs. The developed SNP markers have already been used and will be used in future plant breeding programs as well as in mapping and diversity studies.
authors.affiliation: a Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.
authors.forename: P
authors.initials: P
authors.lastname: Tanhuanpää
authors.affiliation: b Internal Expert Services, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.
authors.forename: M
authors.initials: M
authors.lastname: Erkkilä
authors.affiliation: a Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.
authors.forename: T
authors.initials: T
authors.lastname: Tenhola-Roininen
authors.affiliation: a Green Technology, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.
authors.forename: J
authors.initials: J
authors.lastname: Tanskanen
authors.affiliation: c Boreal Plant Breeding Ltd., FI-31600 Jokioinen, Finland.
authors.forename: O
authors.initials: O
authors.lastname: Manninen
mesh_terms: D029688:Brassica napus / Q000235:genetics; D029741:Brassica rapa / Q000235:genetics* / Q000378:metabolism; D005227:Fatty Acids / Q000378:metabolism; D014644:Genetic Variation; D005961:Glucosinolates / Q000378:metabolism; D058974:Phylogeography; D000069600:Plant Breeding; D010935:Plant Diseases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide
chemical_list: D005227:Fatty Acids; D005961:Glucosinolates
keywords: Brassica rapa; GBS; SNP; STRUCTURE; diversité génétique; genetic diversity