Abstract
As sessile organisms, plants were constantly challenged with biotic and abiotic stresses. Transcriptional activation of stress-responsive genes is a crucial part of the plant adaptation to environmental changes. Here, early response of rice root to eight rhizotoxic stressors: arsenate, copper, cadmium, mercury, chromate, vanadate, ferulic acid and juglone, was analyzed using published microarray data. There were 539 general stress response (GSR) genes up-regulated under all eight treatments, including genes related to carbohydrate metabolism, phytohormone balance, and cell wall structure. Genes related to transcriptional coactivation showed higher Ka/Ks ratio compared to the other GSR genes. Network analysis discovered complicated interaction within GSR genes and the most connected signaling hubs were WRKY53, WRKY71, and MAPK5. Promoter analysis discovers enriched SCGCGCS cis-element in GSR genes. Moreover, GSR genes tend to be intronless and genes with shorter total intron length were induced in a higher level. Among genes uniquely up-regulated by a single stress, a phosphoenolpyruvate carboxylase kinase (PPCK) was identified as a candidate biomarker for detecting cadmium contamination. Our findings provide insights into the transcriptome dynamics of molecular response of rice to different rhizotoxic stress and also demonstrate potential use of comparative transcriptome analysis in identifying a novel potential early biomarker.
Highlights
Soil contamination by rhizotoxins is a threat to food security (Lobell et al, 2009)
Rice seedlings were submerged to six metal/metalloid stresses [5 μM CuCl2, 25 μM CdCl2, 25 μM HgCl2, 50 μM K2CrO4, 25 μM Na2AsO4·7H2O (arsenic, As(V)), 1 mM Na3VO4], and two allelochemicals [50 ppm Ferulic acid (FA) and 10 μM juglone]
There were 8737 differentially expressed genes (DEGs) with fold change (FC) value greater than two under at least one stress treatment. Among these DEGs, four sets of genes were defined based on their expression patter across eight rihizotoxin treatments: (1) 539 general stress response genes (GSR) that were up-regulated under all stress conditions; (2) 591 uniquely regulated genes with |FC| ≥ 2 under one stress treatment and |FC| ≤ 1.4 under the others; (3) 530 background genes with |FC| ≤ 1.2 under all eight stress treatments; (4) 66 low-regulated genes with 2 > FC > 1.2 under all eight stress treatments (Table 1)
Summary
Soil contamination by rhizotoxins is a threat to food security (Lobell et al, 2009). Rhizotoxins in agricultural soil, such as heavy metal, metalloid and organic pollutants from sewage water and industrial waste contamination, present problem for normal root function leading to reduced crop yields. The most common heavy metal pollutants found in soil for plants are Cd, Pb, Cr, Hg, As, Cu, Ni, and Zn (Schützendübel and Polle, 2002; Li et al, 2014; Ullah et al, 2015). The inhibitory effects of these heavy metals/metalloids on plant growth have been extensively studied. Accumulation of rhizotoxins in crops is a threat to food security to world populations (Tripathi et al, 2007; Meharg et al, 2013). Given the variety of rhizotoxins, it is important to understand the general stress response (GSR) to rhizotoxins in plants, especially in crops
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