%0 Journal Article
%T High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response
%A Yongle Li
%A Grit Haseneyer
%A Chris-Carolin Sch£¿n
%A Donna Ankerst
%A Viktor Korzun
%A Peer Wilde
%A Eva Bauer
%J BMC Plant Biology
%D 2011
%I BioMed Central
%R 10.1186/1471-2229-11-6
%X A 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 ¦Ð = 5.6 ¡Á 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.The 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.Rye (Secale cereale L.) is a cross-pollinated cereal with a diploid genome. It is grown on approximately 6 million hectares in Europe for bread-making, animal feed, forage feeding, and vodka production (FAO, 2010). As the most frost tolerant small grain cereal [1] it is well-suited for investigations of frost tolerance. Findings in rye are of interest for less frost tolerant cereals such as wheat and barley.Cold and frost stress, namely chilling injury at temperatures lower than 10¡ãC and freezing injury at temperatures lower than 0¡ãC, adversely affect plant growth and productivity via cellular damage, dehydration and metabolic reaction slow-down. A major fo
%U http://www.biomedcentral.com/1471-2229/11/6