Genome-wide analysis of the trehalose-6-phosphate synthase (TPS) gene family and expression profiling of ScTPS genes in sugarcane

Authors: HU, XIN - Yunnan Academy Of Agriculture Sciences; WU, ZHUAN-DI - Yunnan Academy Of Agriculture Sciences; LUO, ZHENG-YING - Yunnan Academy Of Agriculture Sciences; BURNER, DAVID - Yunnan Academy Of Agriculture Sciences; Pan, Yong-Bao; WU, CAI-WEN - Yunnan Academy Of Agriculture Sciences

Submitted to: Agronomy Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/1/2020
Publication Date: 7/5/2020
Citation: Hu, X., Wu, Z., Luo, Z., Burner, D., Pan, Y.-B., Wu, C. 2020. Genome-wide analysis of the trehalose-6-phosphate synthase (TPS) gene family and expression profiling of ScTPS genes in sugarcane. Agronomy Journal. 10(7):969. https://doi.org/10.3390/agronomy10070969.
DOI: https://doi.org/10.3390/agronomy10070969

Interpretive Summary: Due to urban development, sugarcane production areas have shifted to more stressful environments in higher latitudes, elevation, and lands with poorer soil fertility and less rainfall. To sustain sugarcane productivity in these environments, growers often ask for high yielding and disease resistant sugarcane cultivars that are also resistant to abiotic stresses. The objective of this research is to identify genes that play an important role in conferring plant stress resistance. Literature search was conducted to identify such a gene family called trehalose-6-phosphate synthase (TPS) gene family. Further research involved documentation, functional classification, evolutionary characterization, and gene-protein expression profiling of this gene family. One significant result was the identification of nine putative sugarcane TPS (ScTPS) genes with two domains, TPS and TPP. Gene structure and evolutionary analyses indicated that the nine ScTPS genes belonged to two distinct classes, I and II. Class I only contained ScTPS1 gene with 16 introns and five motifs, while Class II contained the other eight ScTPS genes with 2-3 introns and six motifs. In addition, several cis-regulatory genetic elements were also found to play roles in phytohormones and abiotic stresses. The ScTPS1 gene was predominantly expressed in sugarcane root and leaf tissues in response to simulated drought, salinity, and ABA stresses, which suggests that the ScTPS1 gene might be a good molecular marker in screening sugarcane germplasm for increased stress resistance.

Technical Abstract: The trehalose-6-phosphate synthase (TPS) gene family plays an important role in conferring plant stress resistance, but a comprehensive analysis of the gene family is lacking for sugarcane (Saccharum spp. hybrids). The objective of this study was to document functional classification, evolutionary characterization, and expression profiling of the sugarcane TPS gene (ScTPS) family. Nine putative ScTPS genes were identified by bioinformatics methods, and each contained one TPS and TPP domain. The ScTPS genes were assigned to two distinct classes I and II based on gene structure and phylogeny. ScTPS1 was assigned to Class I and contained 16 introns and five motifs. Eight other ScTPS genes were assigned to Class II with 2-3 introns and six motifs. There were also cis-regulatory elements related to phytohormones and abiotic stresses. The ScTPS1 was predominantly expressed in root and leaf tissues in response to simulated drought, salinity, and ABA stresses. Since ScTPS1 functions in sugarcane adaptation to environmental stimuli, it might be used as a molecular marker in screening sugarcane germplasm for increased stress resistance.