Comparative transcriptome profiling of a resistant vs susceptible bread wheat (Triticum aestivum L.) cultivar in response to water deficit and cold stress

Abstract

Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars.

Transcriptome Dynamics in Triticum aestivum Genotypes Associated with Resistance against the Wheat Dwarf Virus

“…Recently, plants with less ROS accumulation show better adaptation to virus infections and are linked to salicylic acid signal deficiency [ 63 ]. In agreement with previous reports, the expression patterns of cell wall- and chloroplast-related genes changed significantly in response to virus infection [ 25 , 40 ], including WDV [ 64 ].…”

“…The RNA sequencing (RNA-seq) technology has become a very popular tool for studying multiple interactions in biotic and abiotic stresses [ 24 , 25 ]. RNA-seq offers a complex view of comparative gene expression to elucidate the basal defence response during plant-virus interactions [ 26 , 27 ].…”

Genome-wide association study to identify genomic loci associated with early vigor in bread wheat under simulated water deficit complemented with quantitative trait loci meta-analysis

“…The accessible annotation of genes in rice ( https://funricegenes.github.io/ ) was used for identifying putative CGs based to orthologous genes of wheat in rice ( Huang et al ., 2022 ). Four studies ( Derakhshani et al ., 2020 ; Rahimi et al ., 2021 ; Konstantinov et al ., 2021 ; Nouraei et al ., 2022 ) related to the transcriptomics of wheat against water deficit conditions were used to compare the differential expressed genes with the genes retrieved from MQTL and GWAS analyses. The KOBAS software ( Xie et al ., 2011 ) was used to detect enriched pathways for the common genes between these three different databases.…”

Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses

“…The B. distachyon dehydrin genes differentially expressed in leaves of plants under W and D conditions in this work were compared to the wheat dehydrin genes differentially expressed under drought conditions in previous transcriptomics analyses. The wheat RNAseq analyses were carried out in flag leaves of individuals under field drought stress [40] and field rain shelter and greenhouse experiments [6,41,81]. The reported DE wheat dehydrins were used to perform the comparisons.…”