Expression Level of the DREB2-Type Gene, Identified with Amplifluor SNP Markers, Correlates with Performance, and Tolerance to Dehydration in Bread Wheat Cultivars from Northern Kazakhstan

Abstract

A panel of 89 local commercial cultivars of bread wheat was tested in field trials in the dry conditions of Northern Kazakhstan. Two distinct groups of cultivars (six cultivars in each group), which had the highest and the lowest grain yield under drought were selected for further experiments. A dehydration test conducted on detached leaves indicated a strong association between rates of water loss in plants from the first group with highest grain yield production in the dry environment relative to the second group. Modern high-throughput Amplifluor Single Nucleotide Polymorphism (SNP) technology was applied to study allelic variations in a series of drought-responsive genes using 19 SNP markers. Genotyping of an SNP in the TaDREB5 (DREB2-type) gene using the Amplifluor SNP marker KATU48 revealed clear allele distribution across the entire panel of wheat accessions, and distinguished between the two groups of cultivars with high and low yield under drought. Significant differences in expression levels of TaDREB5 were revealed by qRT-PCR. Most wheat plants from the first group of cultivars with high grain yield showed slight up-regulation in the TaDREB5 transcript in dehydrated leaves. In contrast, expression of TaDREB5 in plants from the second group of cultivars with low grain yield was significantly down-regulated. It was found that SNPs did not alter the amino acid sequence of TaDREB5 protein. Thus, a possible explanation is that alternative splicing and up-stream regulation of TaDREB5 may be affected by SNP, but these hypotheses require additional analysis (and will be the focus of future studies).

Peer Review #2 of "Two sugar beet chitinase genes, BvSP2 and BvSE2, analysed with SNP Amplifluor-like markers, are highly expressed after Fusarium root rot inoculations and field susceptibility trial (v0.1)"

“…Amplifluor-like SNP analysis, as described earlier (Shavrukov et al 2016;Jatayev et al 2017), was carried out using a QuantStudio-7 Real-Time PCR Cycler (ThermoFisher Scientific, USA).…”

“…Manuscript to be reviewed PCR cycling followed a program adjusted from those published earlier (Shavrukov et al 2016;Jatayev et al 2017), and included initial denaturation at 95 C for min; 26-28 cycles of C for 30 s, 55 0 C for s, and 0 C for 50 s; and final extension at 72 0 C for 5 min. Genotyping with SNP calling was determined automatically by software accompanying the instrument, but each SNP result was checked manually using amplification curves and allele discrimination.…”

“…Sugar beet chitinase IV gene BvSP2 when expressed in transgenic birch (Betula pendula) inhibited growth of the insect larvae of Orgyia antiqua L., Lymantriidae (Vihervuori et al 2013) but had no adverse effects on mammalian herbivores like roe deer (Capreolus capreolus L.) (Vihervuori et al 2012 Manuscript to be reviewed markers (He et al 2014). Amplifluor-like SNP markers have a simple design, employing a mixture of two universal probes carrying fluorescent labels and a quencher, and non-labelled gene-specific primers (Giancola et al 2006;Shavrukov et al 2016;Jatayev et al 2017). Based on our recent study in bread wheat (Shavrukov et al 2016), we extended our research to sugar beet via the development of primers targeting SNPs in an effort to identify candidate genes for RR resistance.…”

“…Amplifluor-like SNP markers have a simple design, employing a mixture of two universal probes carrying fluorescent labels and a quencher, and non-labelled gene-specific primers (Giancola et al 2006;Shavrukov et al 2016;Jatayev et al 2017). Based on our recent study in bread wheat (Shavrukov et al 2016), we extended our research to sugar beet via the development of primers targeting SNPs in an effort to identify candidate genes for RR resistance.…”

Genes Encoding Transcription Factors TaDREB5 and TaNFYC-A7 Are Differentially Expressed in Leaves of Bread Wheat in Response to Drought, Dehydration and ABA

“…Drought Responsive Element Binding ( DREB ) genes have been reported as regulatory components of abiotic stress responses and, particularly, drought response ( Zhu, 2002 ; Agarwal and Jha, 2010 ; Fujita et al, 2011 ; Kuromori et al, 2014 ; Rehman and Mahmood, 2015 ; Sah et al, 2016 ; Verma et al, 2016 ; Agarwal et al, 2017 ). Recently, we identified that expression levels of the TaDREB5 gene, which belongs to the DREB2 -type TFs, correlate with yields of wheat varieties grown in the dry conditions of Kazakhstan ( Shavrukov et al, 2016 ). Application of the Amplifluor-like SNP marker KATU-48, developed in our laboratory, showed a genetic polymorphism associated with two groups of Kazakh wheat genotypes.…”