Geographical distribution of genetic diversity in Secale landrace and wild accessions

• Published in: BMC Plant Biology
• Main Authors: Hagenblad, Jenny, Oliveira, Hugo R, Forsberg, Nils E. G., Leino, Matti W.
• Format: Article in Journal/Newspaper
• Language: English
• Published: Linköpings universitet, Biologi 2016
• Subjects: Rye; Population structure; SNP; Ascertainment bias; Genetic variation; Phylogeography; Genetics; Genetik; Finnmark
• Online Access: http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-124223; https://doi.org/10.1186/s12870-016-0710-y

Background: Rye, Secale cereale L., has historically been a crop of major importance and is still a key cereal in manyparts of Europe. Single populations of cultivated rye have been shown to capture a large proportion of the geneticdiversity present in the species, but the distribution of genetic diversity in subspecies and across geographical areasis largely unknown. Here we explore the structure of genetic diversity in landrace rye and relate it to that of wildand feral relatives.Results: A total of 567 SNPs were analysed in 434 individuals from 76 accessions of wild, feral and cultivated rye. Geneticdiversity was highest in cultivated rye, slightly lower in feral rye taxa and significantly lower in the wild S. strictum Presl.and S. africanum Stapf. Evaluation of effects from ascertainment bias suggests underestimation of diversity primarily inS. strictum and S. africanum. Levels of ascertainment bias, STRUCTURE and principal component analyses all supportedthe proposed classification of S. africanum and S. strictum as a separate species from S. cereale. S. afghanicum (Vav.)Roshev, S. ancestrale Zhuk., S. dighoricum(Vav.) Roshev, S. segetale (Zhuk.) Roshev and S. vavilovii Grossh. seemed, incontrast, to share the same gene pool as S. cereale and their genetic clustering was more dependent on geographicalorigin than taxonomic classification. S. vavilovii was found to be the most likely wild ancestor of cultivated rye. Amongcultivated rye landraces from Europe, Asia and North Africa five geographically discrete genetic clusters were identified.These had only limited overlap with major agro-climatic zones. Slash-and-burn rye from the Finnmark area in Scandinaviaformed a distinct cluster with little similarity to other landrace ryes. Regional studies of Northern and South-West Europedemonstrate different genetic distribution patterns as a result of varying cultivation intensity.Conclusions: With the exception of S. strictum and S. africanum different rye taxa share the majority of the geneticvariation. Due to the ...