Geographical distribution of genetic diversity in Secale landrace and wild accessions

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.

Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping‐by‐sequencing

“…Similar results were obtained by Hagenblad et al. () who found limited genetic clustering according to taxonomy below the species level. All our samples have been maintained in ex situ genebank collections for at least one decade, some even since the 1940s.…”

“…Hagenblad et al. () used a SNP array with 576 features to genotype a panel of S. cereale , S. cereale subsp. vavilovii , and S. strictum genebank accessions and found that they likely underestimated diversity in S. strictum because the discovery panel comprised only domesticated rye.…”

“…() designed a SNP array with 5,234 features. A subset of these were used to genotype a diversity panel of rye and wild relatives by Hagenblad, Oliveira, Forsberg, and Leino (). Compared to SNP arrays, reduced‐representation sequencing methods based on digestion with restriction enzymes have the advantage of joint discovery and genotyping of sequence variant without the requirement for ascertaining polymorphic markers in a discovery panel, which may lead to underestimation of genetic diversity of diverse genetic material.…”

Genetic Distinctiveness of Rye In situ Accessions from Portugal Unveils a New Hotspot of Unexplored Genetic Resources

“…Hagenblad et al (2016) linked its distinctiveness with historical human migrations, since Finnish farmers settled after leaving their native country in the sixteenth century (Ahokas, 2008). Considering Portuguese historic trading markets it cannot be ruled out a scenario of multiple rye introductions into Portuguese territory, especially from Northern Europe (i.e., Sweden).…”

Genetic diversity of maize accessions for maizelethal necrosis disease resistance

“…Landraces are plant populations which are cultivated by local farmers that have historic origin, unique identity with no any formal crop improvement (Prasanna, 2012;Hagenblad et al, 2016). They are often endowed with diverse genetic inheritance (Zeven, 1998) as well as local adaption and strong connection to traditional farming systems (Camacho-Villa et al, 2005).…”