Abstract
BackgroundRye (Secale cereale L.) is the most frost tolerant cereal species. As an outcrossing species, rye exhibits high levels of intraspecific diversity, which makes it well-suited for allele mining in genes involved in the frost responsive network. For investigating genetic diversity and the extent of linkage disequilibrium (LD) we analyzed eleven candidate genes and 37 microsatellite markers in 201 lines from five Eastern and Middle European rye populations.ResultsA total of 147 single nucleotide polymorphisms (SNPs) and nine insertion-deletion polymorphisms were found within 7,639 bp of DNA sequence from eleven candidate genes, resulting in an average SNP frequency of 1 SNP/52 bp. Nucleotide and haplotype diversity of candidate genes were high with average values π = 5.6 × 10-3 and Hd = 0.59, respectively. According to an analysis of molecular variance (AMOVA), most of the genetic variation was found between individuals within populations. Haplotype frequencies varied markedly between the candidate genes. ScCbf14, ScVrn1, and ScDhn1 were dominated by a single haplotype, while the other 8 genes (ScCbf2, ScCbf6, ScCbf9b, ScCbf11, ScCbf12, ScCbf15, ScIce2, and ScDhn3) had a more balanced haplotype frequency distribution. Intra-genic LD decayed rapidly, within approximately 520 bp on average. Genome-wide LD based on microsatellites was low.ConclusionsThe Middle European population did not differ substantially from the four Eastern European populations in terms of haplotype frequencies or in the level of nucleotide diversity. The low LD in rye compared to self-pollinating species promises a high resolution in genome-wide association mapping. SNPs discovered in the promoters or coding regions, which attribute to non-synonymous substitutions, are suitable candidates for association mapping.
Highlights
Rye (Secale cereale L.) is the most frost tolerant cereal species
Several studies in Arabidopsis provide evidence that allelic variation in the C-repeat Binding Factor (Cbf) gene family forms the molecular basis for the freezing tolerance quantitative trait loci (QTL) [10,11]
DNA sequence polymorphisms In total, 7,639 bp from eleven candidate genes in 201 rye lines were amplified resulting in 147 SNPs, nine insertion-deletion events (Indels), and an average SNP frequency of 1 SNP/52 bp (Table 1)
Summary
Rye (Secale cereale L.) is the most frost tolerant cereal species. As an outcrossing species, rye exhibits high levels of intraspecific diversity, which makes it well-suited for allele mining in genes involved in the frost responsive network. Diploid and hexaploid wheat several cereal Cbf homologs have been cloned and mapped to the Fr2 locus on homoeologous group 5, which coincides with a major QTL for frost tolerance [6,7,8]. Transcript levels of all cold-induced Cbf genes at the frost tolerance locus Fr-H2 in barley are significantly higher in lines harbouring the vrn winter allele than in lines harbouring the Vrn spring allele [19]. It remains unknown how the Cbf family members interact with Vrn under frost stress
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