Rice-arsenate interactions in hydroponics: whole genome transcriptional analysis

Abstract

Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 muM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the BalaxAzucena mapping population.

Fig. 1.

(A) Azucena control conditions (top left), Azucena grown in 13.3 μM sodium arsenate (top right), Bala control conditions (bottom left), and Bala grown in 13.3 μM sodium arsenate (bottom right) for 1 week showing marked inhibition of root growth. (B) Length of the roots for the three replicates used in the gene expression experiment. Bar = SE.

Fig. 2.

Root lengths of plants grown in 13.3 μM sodium arsenate. Maximum root length was measured on days 2, 3, 5, and 7. Bar = SE.

Fig. 3.

Venn diagram of the number of probe sets up- and down-regulated in response to arsenate in Azucena and Bala. The number of probe sets which were up-regulated (bold) and the number of probe sets which were down-regulated (italic) with an adjusted P-value of ≤0.05 and a ≥2-fold change in gene expression.

Fig. 4.

Gene expression of GSTU5 (A) and GSTU19 (B) in response to 13.3 μM sodium arsenate over time as detected by quantitative real-time PCR (relative to actin expression). Bar = SE.