Genome-Wide Analysis of the Trehalose-6-Phosphate Synthase (TPS) Gene Family and Expression Profiling of ScTPS Genes in Sugarcane

Abstract

<jats:p>The trehalose-6-phosphate synthase (TPS) gene family plays important roles 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 is to document functional classification, evolutionary characterization, and expression profiling of sugarcane TPS gene (ScTPS) family. Nine putative ScTPS genes were identified and assigned to two distinct classes based on gene structure and phylogeny. Phylogenetic analysis showed that 31 TPS genes from Arabidopsis, rice and sugarcane could be divided into five distinct clades, suggesting that there were at least five orthologous groups in monocot and dicot plants. Evolution analysis of TPS genes revealed that TPS family members appeared to have undergone strong negative selection. The strength of the selective pressure differed in most clades, especially Class I TPS genes, experienced significantly stronger negative selection pressure than Class II TPS genes. There were also cis-regulatory elements related to phytohormones and abiotic stresses. Additionally, ScTPS genes were found to exhibit divergent expression in response to simulated drought, salinity, and ABA stresses. Since ScTPS genes function in sugarcane adaptation to environmental stimuli, it might be used as a molecular marker in screening sugarcane germplasm for increased stress resistance.</jats:p>

Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)

“…Genes encoding TPS have been identified in many plants in the form of a gene family (Avonce et al, 2004). Previous studies have found 11, 11, 11, 8, 20, 13, 12, 10, 9 and 53 TPS genes in Arabidopsis (Yang et al, 2012), rice (Zang et al, 2011), pepper (Wei et al, 2016), potato (Xu et al, 2017), soybean (Xie, Wang & Huang, 2014), apple (Du et al, 2017), winter wheat (Xie et al, 2015), tomato (Chen & Lou, 2017), sugarcane (Hu et al, 2020), and cotton (Mu et al, 2016), respectively. However, the TPS gene family in cucumber has not been well-studied.…”

Genetic manipulation of trehalose‐6‐phosphate synthase results in changes in the soluble sugar profile in transgenic sugarcane stems

“…650 μmol/g FW) in the stem (Bosch, 2005 ; Welbaum & Meinzer, 1990 ; Zhang et al, 2006 ). Additionally, transcripts of putative TPS and TPP genes in sugarcane have been confirmed in different tissue‐ and genotypes (Bosch, 2005 ; Hu et al, 2020 ; McCormick et al, 2008 ; Nicolau et al, 2013 ; Thirugnanasambandam et al, 2017 ). Furthermore, Zhang et al ( 2006 ) expressed a fungal trehalose synthase ( TSase ) gene, which encodes an enzyme that synthesizes trehalose directly from glucose and glucose 1‐phosphate, in sugarcane.…”

Peer Review #1 of "Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.) (v0.1)"

“…Genes encoding TPS have been identified in many plants in the form of a gene family (Avonce et al, 2014). Previous studies have found 11,11,11,8,20,13,12,10,9, and 53 TPS genes in Arabidopsis (Yang et al, 2012), rice (Zang et al, 2011), pepper (Wei et al, 2016), potato (Xu et al, 2017), soybean (Xie et al, 2014), apple (Du et al, 2017), winter wheat (Xie et al, 2015), tomato (Chen et al, 2017), sugarcane (Hu et al, 2020), and cotton (Mu et al, 2016), respectively. However, the TPS gene family in cucumber has not been well-studied.…”