RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars ‘TAM 111’ and ‘TAM 112’

Authors: Chu, Chenggen; WANG, SHICHEN - Texas Agrilife Research; PAETZOLD, LI - Texas Agrilife Research; WANG, ZHEN - Texas Agrilife Research; HUI, KELE - Texas Agrilife Research; RUDD, JACKIE - Texas Agrilife Research; XUE, QINGWU - Texas Agrilife Research; IBRAHIM, AMIR - Texas A&M University; METZ, RICHARD - Texas Agrilife Research; JOHNSON, CHARLES - Texas Agrilife Research

Submitted to: Nature Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/27/2021
Publication Date: 2/22/2021
Citation: Chu, C.N., Wang, S., Paetzold, L., Wang, Z., Hui, K., Rudd, J.C., Xue, Q., Ibrahim, A.M., Metz, R., Johnson, C.D. 2021. RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars ‘TAM 111’ and ‘TAM 112’. Nature Scientific Reports. 11. Article e4301. https://doi.org/10.1038/s41598-021-83372-0.
DOI: https://doi.org/10.1038/s41598-021-83372-0

Interpretive Summary: Drought has become a major environmental stress threatening wheat production in the Southern Great Plains area of the U.S. Increasing resilience to water stresses through genetic improvement, therefore, becomes a critical component of wheat breeding. Two wheat varieties, ‘TAM 111’ and ‘TAM 112’, have been dominantly grown in the Southern Great Plains for many years due to their high yield and excellent drought tolerance. This research compared the gene expression level in two varieties under conditions of drought and irrigation during periods of flowering and seed formation, and identified genes involved in response to drought that were either commonly shared by two varieties or specifically carried in each of them. According to their different patterns of gene expression under drought and wet condition, TAM 112 showed more active response to drought which agreed with its high yield performance under long-lasting drought. In contrast, TAM 111 tended to turn off expression of some genes under drought to maintain its yield level explaining its better adaption to intermittent drought. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified drought tolerance genes that can be used for improving wheat adaption to drought condition. This research thus provided information for genetically improving wheat adaption to drought which will benefit wheat growers in the Southern Great Plains.

Technical Abstract: Wheat cultivars ‘TAM 111’ and ‘TAM 112’ have been dominantly grown in the Southern U.S. Great Plains for many years due to their high yield and 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. A total of 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 has a specific mechanism to cope with drought. Annotations of all 2,254 genes showed 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. TAM 112 showed more active than TAM 111 in response to drought and carried more specific genes with most of them were up regulated in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation. In addition, 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases 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. Data of gene sequence and expression regulation from this study also provided useful information of annotating novel genes associated with drought tolerance in the wheat genome.