Abstract
BackgroundRye, Secale cereale L., has historically been a crop of major importance and is still a key cereal in many parts of Europe. Single populations of cultivated rye have been shown to capture a large proportion of the genetic diversity present in the species, but the distribution of genetic diversity in subspecies and across geographical areas is largely unknown. Here we explore the structure of genetic diversity in landrace rye and relate it to that of wild and feral relatives.ResultsA total of 567 SNPs were analysed in 434 individuals from 76 accessions of wild, feral and cultivated rye. Genetic diversity 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 in S. strictum and S. africanum. Levels of ascertainment bias, STRUCTURE and principal component analyses all supported the 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, in contrast, to share the same gene pool as S. cereale and their genetic clustering was more dependent on geographical origin than taxonomic classification. S. vavilovii was found to be the most likely wild ancestor of cultivated rye. Among cultivated 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 Scandinavia formed a distinct cluster with little similarity to other landrace ryes. Regional studies of Northern and South-West Europe demonstrate different genetic distribution patterns as a result of varying cultivation intensity.ConclusionsWith the exception of S. strictum and S. africanum different rye taxa share the majority of the genetic variation. Due to the vast sharing of genetic diversity within the S. cereale clade, ascertainment bias seems to be a lesser problem in rye than in predominantly selfing species. By exploiting within accession diversity geographic structure can be shown on a much finer scale than previously reported.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0710-y) contains supplementary material, which is available to authorized users.
Highlights
Rye, Secale cereale L., has historically been a crop of major importance and is still a key cereal in many parts of Europe
Population structure We investigated our data for genetic structure by initially running STRUCTURE for the full final data set
Genetic diversity in the genus Secale In this study we demonstrate that SNP markers developed for rye elite cultivars can be applied to landrace varieties as well as feral and wild ryes
Summary
Secale cereale L., has historically been a crop of major importance and is still a key cereal in many parts of Europe. Rye (Secale cereale L.) has the ability to thrive and to produce high yields under adverse environmental conditions [1, 2]. It is unique amongst old-world graminoid cereals for being an out-breeder (wind cross-pollinated). In this paper we follow the Sencer and Hawkes [8] classification with cultivated rye classified as the species Secale cereale subsp. These weedy forms, here called feral, occur as weeds in cereal fields, mostly in the Near East and Central Asia and are fully inter-fertile with cultivated rye [17]
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