Abstract
BackgroundFrost is an important abiotic stress that limits cereal production in the temperate zone. As the most frost tolerant small grain cereal, rye (Secale cereale L.) is an ideal cereal model for investigating the genetic basis of frost tolerance (FT), a complex trait with polygenic inheritance. Using 201 genotypes from five Eastern and Middle European winter rye populations, this study reports a multi-platform candidate gene-based association analysis in rye using 161 single nucleotide polymorphisms (SNPs) and nine insertion-deletion (Indel) polymorphisms previously identified from twelve candidate genes with a putative role in the frost responsive network.ResultsPhenotypic data analyses of FT in three different phenotyping platforms, controlled, semi-controlled and field, revealed significant genetic variations in the plant material under study. Statistically significant (P < 0.05) associations between FT and SNPs/haplotypes of candidate genes were identified. Two SNPs in ScCbf15 and one in ScCbf12, all leading to amino acid exchanges, were significantly associated with FT over all three phenotyping platforms. Distribution of SNP effect sizes expressed as percentage of the genetic variance explained by individual SNPs was highly skewed towards zero with a few SNPs obtaining large effects. Two-way epistasis was found between 14 pairs of candidate genes. Relatively low to medium empirical correlations of SNP-FT associations were observed across the three platforms underlining the need for multi-level experimentation for dissecting complex associations between genotypes and FT in rye.ConclusionsCandidate gene based-association studies are a powerful tool for investigating the genetic basis of FT in rye. Results of this study support the findings of bi-parental linkage mapping and expression studies that the Cbf gene family plays an essential role in FT.
Highlights
Frost is an important abiotic stress that limits cereal production in the temperate zone
Genotypic variation for frost tolerance (FT) was significant at both temperatures for both years in the controlled platform (P < 0.001)
Based on phenotypic data from three different phenotyping platforms, including field trials, our study showed that the C-repeat binding factor (Cbf) gene family plays an important role in FT of rye
Summary
Frost is an important abiotic stress that limits cereal production in the temperate zone. One of the important abiotic stresses, limits the geographic distribution of crop production and adversely affects crop development and yield through cold-induced desiccation, cellular damage and inhibition of metabolic reactions [1,2]. Plant damage during winter is affected by low temperature stress per se, and by the interaction of a range of factors such as snow coverage, water supply, and wind. Frost tests in growth chambers allow for a better control of environmental variation and are not limited to one trial per year. They are limited in capacity and may not correlate well with field performance. It has been recommended to test FT under both natural and controlled conditions whenever possible [3]
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