Abstract
BackgroundSugarcane is an important sugar and energy crop that is widely planted in the world. Among the environmental stresses, the water-deficit stress is the most limiting to plant productivity. Some groups have used PCR-based and microarray technologies to investigate the gene expression changes of multiple sugarcane cultivars under water stress. Our knowledge about sugarcane genes in response to water deficit is still poor.ResultsA wild sugarcane type, Saccharum narenga, was selected and treated with drought stress for 22 days. Leaves from drought treated (DTS) and control (CK) plants were obtained for deep sequencing. Paired-end sequencing enabled us to assemble 104,644 genes (N50 = 1605 bp), of which 38,721 were aligned to other databases, such as UniProt, NR, GO, KEGG and Pfam. Single-end and paired-end sequencing identified 30,297 genes (> 5 TPM) in all samples. Compared to CK, 3389 differentially expressed genes (DEGs) were identified in DTS samples, comprising 1772 up-regulated and 1617 down-regulated genes. Functional analysis showed that the DEGs were involved in biological pathways like response to blue light, metabolic pathways and plant hormone signal transduction. We further observed the expression patterns of several important gene families, including aquaporins, late embryogenesis abundant proteins, auxin related proteins, transcription factors (TFs), heat shock proteins, light harvesting chlorophyll a-b binding proteins, disease resistance proteins, and ribosomal proteins. Interestingly, the regulation of genes varied among different subfamilies of aquaporin and ribosomal proteins. In addition, DIVARICATA and heat stress TFs were first reported in sugarcane leaves in response to water deficit. Further, we showed potential miRNAs that might be involved in the regulation of gene changes in sugarcane leaves under the water-deficit stress.ConclusionsThis is the first transcriptome study of Saccharum narenga and the assembled genes are a valuable resource for future research. Our findings will improve the understanding of the mechanism of gene regulation in sugarcane leaves under the water-deficit stress. The output of this study will also contribute to the sugarcane breeding program.
Highlights
Sugarcane is an important sugar and energy crop that is widely planted in the world
It is interesting that differentially expressed genes (DEGs) encoding auxin response factors (ARFs) and auxin-induced proteins (TRINITY_DN26758_c0_g1 and TRINITY_DN18434_c1_g4) were up-regulated in sugarcane leaves in response to water deficit, genes encoding IAAs were down-regulated, generally, in Drought treated sugarcane leaves (DTS) samples compared to Control sugarcane leaves (CK) (Fig. 5c)
59 light-harvesting chlorophyll a-b binding proteins (LHCB) genes were annotated in the assembled sugarcane transcriptome and 22 (37.29%) of them were down-regulated in DTS samples compared to CK (Table 3, Fig. 5f)
Summary
Sugarcane is an important sugar and energy crop that is widely planted in the world. Among the environmental stresses, the water-deficit stress is the most limiting to plant productivity. Sugarcane is a C4 grass that belongs to the family Poaceae, sub-family Panicoideae and tribe Andropogoneae It is an important industrial crop widely grown in tropical and subtropical areas, due to the highly yield of sugar [1]. Studies have been demonstrated to understand the gene expression changes under the water-deficit stress in several model species, such as Arabidopsis [3, 4], maize [5], rice [6], tomato [7], banana [8], soybean [9], and other plants [10,11,12,13] They have shown that abscisic acid (ABA)-dependent and ABA-independent regulatory systems are two major pathways for plants to defense against the water-deficit stress [14]. The second group of gene products in response to water deficit in plants is comprised of regulatory proteins that are involved in further regulation of signal transduction and stress-responsive gene expression, such as various TFs and dehydration-responsive elements [2, 14, 15]
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