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Transcriptomics of water-deficit Stress Responses in TAM Wheat Cultivars

ABSTRACT: Water deficit stress between the booting and grain filling stages significantly affect grain yield and quality of hard red winter wheat. Several stress tolerant cultivars with different adaptation mechanisms have been released and are widely cultivated on the Southern Great Plains of the US. However, the physiological, molecular, and genetic basis of adaptation to drought stress for these cultivars remains unknown. Use of transcriptome profiling to identify drought responsive genes in hexaploid wheat is a challenging process given the quantitative nature of drought stress, genome complexity, and the intricacy of interaction effects. If the information generated from functional genomics studies is to be used in molecular breeding programs for cultivar development, it is highly desirable to use cultivars better adapted for the region. In the current study we used two well-adapted, drought-tolerant, high-yielding, cultivated varieties, TAM 111 and TAM 112, which appear to have different adaptation mechanisms, to identify drought stress induced transcripts during heading and early dough stages. A set of 24 Affymetrix GeneChip wheat genome arrays (2 cultivars; 2 water treatments; 2 sampling stages; 3 biological replicates) from plants subjected to water deficit stress under controlled glasshouse conditions. Differentially expressed genes were identified using a ANOVA (p<0.01) controlling false discovery rate (FDR, q<0.01) using Benjamini Hochberg approach.

ORGANISM(S): Triticum aestivum

PROVIDER: GSE45262 | GEO | 2022/01/01

REPOSITORIES: GEO

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Project description:Wheat cultivars ‘TAM 111’ and ‘TAM 112’ have been dominantly grown in the Southern U.S. Great Plains for many years due to their excellent, yet variable, drought tolerance. To identify the molecular basis and genetic control of drought tolerance in these two landmark cultivars, RNA-seq analysis was conducted to compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions. Of the 122,017 gene sequences assembled, 2,254 genes showed significantly altered expression patterns under dry and wet conditions in the two cultivars. TAM 111 had 593 and 1,532 dry-wet differentially expressed genes (DEGs), and TAM 112 had 777 and 1,670 at heading and grain-filling stages, respectively. The two cultivars have 1,214 (53.9%) dry-wet DEGs in common, which agreed with their excellent adaption to drought, but 438 and 602 dry-wet DEGs were respectively shown only in TAM 111 and TAM 112 suggested that each may have a specific mechanism to cope with drought. Annotation of all 2,254 genes with dry-wet expression difference found 1,855 have functions related to biosynthesis, stress responses, defense responses, transcription factors and cellular components related to ion or protein transportation and signal transduction. Comparing hierarchical structure of biological processes, molecule functions and cellular components revealed the significant regulation differences between TAM 111 and TAM 112, particularly for genes of phosphorylation and adenyl ribonucleotide binding, and proteins located in nucleus and plasma membrane. Comparing gene expressions involved in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation found TAM 112 have more specific dry-wet DEGs than TAM 111 with most of them up-regulated, indicating that TAM 112 is more active than TAM 111 in response to drought. In addition, 399 dry-wet DEGs with unknown functions included 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases. These may represent novel genes related to drought response in TAM 111 or TAM 112. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified useful drought tolerance genes for wheat adaption.

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Transcriptomics of water-deficit Stress Responses in TAM Wheat Cultivars

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