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https://hdl.handle.net/2440/90316
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Type: | Journal article |
Title: | Association analysis of frost tolerance in rye using candidate genes and phenotypic data from controlled, semi-controlled, and field phenotyping platforms |
Author: | Li, Y. Böck, A. Haseneyer, G. Korzun, V. Wilde, P. Schön, C.-C. Ankerst, D. Bauer, E. |
Citation: | BMC Plant Biology, 2011; 11(1):146-1-146-14 |
Publisher: | BioMed Central |
Issue Date: | 2011 |
ISSN: | 1471-2229 1471-2229 |
Statement of Responsibility: | Yongle Li, Andreas Böck, Grit Haseneyer, Viktor Korzun, Peer Wilde, Chris-Carolin Schön, Donna P Ankerst, and Eva Bauer |
Abstract: | Background: Frost 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.Results: Phenotypic 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.Conclusions: Candidate 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. © 2011 Li et al; licensee BioMed Central Ltd. |
Keywords: | DNA, Plant Sequence Analysis, DNA Haplotypes Multifactorial Inheritance Phenotype Polymorphism, Single Nucleotide Genes, Plant INDEL Mutation Cold Temperature Genetic Association Studies Secale |
Rights: | © 2011 Li et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
DOI: | 10.1186/1471-2229-11-146 |
Published version: | http://dx.doi.org/10.1186/1471-2229-11-146 |
Appears in Collections: | Agriculture, Food and Wine publications Aurora harvest 2 |
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