Genome-Wide Analysis of the DREB Subfamily in Saccharum spontaneum Reveals Their Functional Divergence During Cold and Drought Stresses

Abstract

Drought and cold stresses are the main environmental factors that affect the yield of sugarcane, and DREB genes play very important roles in tolerance to drought, cold, and other environmental stresses. In this study, bioinformatics analysis was performed to characterize Saccharum spontaneum SsDREB genes. RNA sequencing (RNA-seq) was used to detect the expression profiles of SsDREBs induced by cold and drought stresses. According to our results, there are 110 SsDREB subfamily proteins in S. spontaneum, which can be classified into six groups; 106 of these genes are distributed among 29 chromosomes. Inter-and intraspecies synteny analyses suggested that all DREB groups have undergone gene duplication, highlighting the polyploid events that played an important role in the expansion of the DREB subfamily. Furthermore, RNA-seq results showed that 45 SsDREBs were up-or downregulated under cold stress; 35 of them were found to be involved in responding to drought stress. According to protein-protein interaction analysis, SsDREB100, SsDREB102, and SsDREB105 play key roles during the response to cold stress. These results reveal that functional divergence exists between collinear homologous genes or among common origin genes in the DREB subfamily of S. spontaneum. This study presents a comprehensive analysis and systematic understanding of the precise mechanism of SsDREBs in response to abiotic stress and will lead to improvements in sugarcane.

Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in Solanum tuberosum

“…The identified number of DREB genes in S. tuberosum (66) is greater than that in Arabidopsis (56) which may be due to the difference in their genome sizes. When compared to previous studies, greater numbers of DREB genes were reported in S. spontaneum (110) (Huang et al, 2020), P. trichocarpa (75) (Chen et al, 2013), soybean (73) (Zhou et al, 2020), and malus (68) (Zhao et al, 2012), but less DREB genes were found in sesame (41) (Dossa et al, 2016), maize (51) (Du et al, 2014), mulberry (30) (Liu et al, 2015), grape (38) (Zhao et al, 2014), common bean (54) (Konzen et al, 2019), Phyllostachys edulis (27), and pineapple (20) (Chai et al, 2020). In order to comprehend the potential functions of proteins, it is inevitable to compute the physiochemical characteristics of plant protein families (Salih et al, 2019).…”

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

“…Only in 2018, modern technologies enabled the assembly of a chromosome- and allele-level genome of an Ssp clone ( Zhang et al, 2018 ). This study paved the way for several comprehensive analyses of gene families in the species ( Hu et al, 2018 ; Shi et al, 2019 ; Wang et al, 2019a , b , c ; Zhang et al, 2019b ; Huang et al, 2020 ; Li et al, 2020 ; Su et al, 2020a ). Here, we analyzed the kinome of not only sugarcane but also sorghum, a close diploid relative.…”

The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

“…Members of the RAV group of the AP2/ERF family also have important functions in plant hormone signal transduction and the regulation of responses to biotic and abiotic stimuli [26,27]. Dehydration-responsive element-binding (DREB) members, as important plant-specific transcription factor, also belong to the AP2/ERF superfamily and are involved in response to abiotic stresses [28]. Furthermore, various studies have reported the involvement of DREBs and other ERF members in dealing with water deficit [29,30], cold, and oxidative [31] and salinity [32,33] stresses.…”