GENOME WIDE STUDIES FOR FROST TOLERANCE IN WHEAT Abstract uri icon

abstract

  • In North America, North and Eastern Europe and Russia wheat production is exposed to low temperature and frost damage occurs frequently. In order to avoid high yield losses caused by frost stress it is necessary to understand cold stress response, identify genome regions and alleles, respectively involved in this response and introduce most efficient alleles into elite cultivars. Therefore, the aim of this study is to detect and validate QTL regions associated with frost tolerance (FT) by using genome wide association studies (GWAS) to genetically improve FT. In this respect, a diverse set of 276 winter wheat genotypes was tested in 2012, 2013 and 2014 at two and three locations in Germany and Russia, respectively. All wheat accessions were genotyped by the 90K iSelect chip. The raw marker data were mapped against the bread wheat reference genome of Chinese Spring (IWGSC, 2018) and resulted in a set of 24,247 SNPs uniquely mapped. This marker set was filtered for minor allele frequency (MAF, 3%), maximum percentage of missing values (10%) and maximum percentage of heterozygous SNPs (12.5%). Then, the resulting marker set was imputed for missing values. In total, 14,310 markers were used to perform GWAS together with 182 polymorphic sides for frost tolerance genes (Babben et al., 2018). Based on linkage disequilibrium (LD), 3,267 informative markers were selected to calculate kinship matrix. Linear mixed model (MLM) approach which corrected by kinship was used to conduct GWAS and to detect QTL which are involved in frost tolerance. GWAS for frost tolerance identified a total of 197 significant SNPs at threshold LOD 3 (–log10 (P-value) on 19 chromosomes. These SNPs were assigned to 90 distinct QTL regions based on LD (3.5 Mb, Lehnert et al.2018) which explained between 4.1% to 15.9% of the phenotypic variance. Significantly associated QTL regions were detected on all chromosomes with the exceptions of chromosome 3B and 6D. Thirty-eight significantly associated polymorphic sites for CBF (C-repeat binding factor) on chromosome 5A were identified by GWAS. Six candidate genes for frost tolerance i.e. CBF-A3, CBF-A10, CBF-A13, CBF-A14, CBF-A15 and VRN-B1 were co-localized with detected QTL on chromosome 5A and 5B, respectively. The peak marker on 5A (Excalibur_c2598_2052) could be a putative marker, which is located at a distance of 3 Mb from the CBF-A14 gene. The CBF-A14 gene at FR-A2 (frost resistance A2) locus is playing a critical role in frost tolerance.

publication date

  • July 2019