Transcriptional Responses of Chilean Quinoa (Chenopodium quinoa Willd.) Under Water Deficit Conditions Uncovers ABA-Independent Expression Patterns

Abstract

HIGHLIGHTS R49 genotype displayed best performance on selected physiological parameters and highest tolerance to drought.R49 drought over-represented transcripts has exhibited 19% of genes (306 contigs) that presented no homology to published databases.Expression pattern for canonical responses to drought such as ABA biosynthesis and other genes induced in response to drought were assessed by qPCR. Global freshwater shortage is one of the biggest challenges of our time, often associated to misuse, increased consumption demands and the effects of climate change, paralleled with the desertification of vast areas. Chenopodium quinoa (Willd.) represents a very promising species, due to both nutritional content and cultivation under water constraint. We characterized drought tolerance of three Chilean genotypes and selected Genotype R49 (Salares ecotype) based upon Relative Water Content (RWC), Electrolyte Leakage (EL) and maximum efficiency of photosystem II (F_v/F_m) after drought treatment, when compared to another two genotypes. Exploratory RNA-Seq of R49 was generated by Illumina paired-ends method comparing drought and control irrigation conditions. We obtained 104.8 million reads, with 54 million reads for control condition and 51 million reads for drought condition. Reads were assembled in 150,952 contigs, were 31,523 contigs have a reading frame of at least 300 nucleotides (100 aminoacids). BLAST2GO annotation showed a 15% of genes without homology to NCBI proteins, but increased to 19% (306 contigs) when focused into drought-induced genes. Expression pattern for canonical drought responses such as ABA biosynthesis and other genes induced were assessed by qPCR, suggesting novelty of R49 drought responses.

Keywords: Andean grain; RNA-Seq; Salares and coastal/lowlands genotypes; drought tolerance; qPCR.

Figure 1

Physiological performance of quinoa genotypes in days under drought conditions. (A) Percentage of Relative water content (RWC). (B) Percentage of Electrolytic leakage (EL). (C) Maximum efficiency of photosystem II (F_v/F_m). X-axis represents days under drought. RWC was measured based in the plant total weight that corresponded to water; EL represents the percentage of ions that were released compared to total amount present in the plant; F_v/F_m represents the capacity for photon energy absorbed by photosystem II (PSII) to be utilized in photochemistry under dark- and light-adapted conditions. Values and Bars represent averages and standard deviation (n = 3); ^** and different letters denote significant differences (p < 0.01 and p < 0.05 respectively).

Figure 2

Identity analysis of quinoa genes. (A) Contig size distribution (bp). (B) Blast hit sequence similarity distribution. (C) Blast hit sequence E-value distribution. Red line represents the accumulation rate from low value to high whereas green line represents the accumulation ratio from high value to low.

Figure 3

GO classification of genes with differential expression under drought conditions. Functional categories (A) Biological process; (B) Molecular function; (C) Cellular component. Red bars: over-represented genes; Blue bars: down-represented genes.

Figure 4

Gene expression levels measured by qPCR. (A) ABA transport and biosynthesis genes expression levels. (B) Genes that respond to drought. The expression levels are relative to the normalizer gene (Pre-mRNA splicing PRP18-interacting factor) that was identified from the in silico expression analysis. Bars represent the standard deviation of three replicates.