Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress

Abstract

BackgroundDespite the importance of osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources.MethodsA curated set of osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants. To test the efficiency of the seed sequences, these were aligned against four HT-SuperSAGE contrasting libraries generated by our group using soybean tolerant and sensible plants against water deficit, considering only differentially expressed transcripts (p ≤ 0.05). Identified transcripts from soybean and their respective tags were aligned and anchored against the soybean virtual genome.ResultsThe workflow applied resulted in a set including 1,996 seed sequences that allowed the identification of 36 differentially expressed genes related to the biosynthesis of osmoprotectants [Proline (P5CS: 4, P5CR: 2), Trehalose (TPS1: 9, TPPB: 1), Glycine betaine (BADH: 4) and Myo-inositol (MIPS: 7, INPS1: 8)], also mapped in silico in the soybean genome (25 loci). Another approach considered matches using Arabidopsis full length sequences as seed sequences, and allowed the identification of 124 osmoprotectant-related sequences, matching ~10.500 tags anchored in the soybean virtual chromosomes. Osmoprotectant-related genes appeared clustered in all soybean chromosomes, with higher density in some subterminal regions and synteny among some chromosome pairs.ConclusionsSoybean presents all searched osmoprotectant categories with some important members differentially expressed among the comparisons considered (drought tolerant or sensible vs. control; tolerant vs. sensible), allowing the identification of interesting candidates for biotechnological inferences. The identified tags aligned to corresponding genes that matched 19 soybean chromosomes. Osmoprotectant-related genes are not regularly distributed in the soybean genome, but clustered in some regions near the chromosome terminals, with some redundant clusters in different chromosomes indicating their involvement in previous duplication and rearrangements events. The seed sequences, transcripts and map represent the first transversal evaluation for osmoprotectant-related genes and may be easily applied to other plants of interest.

Intertwined signatures of desiccation and drought tolerance in grasses

“…Using a comparative approach, we observed a similar pattern of seed-related pathway expression under water deficit in desiccation-tolerant and -sensitive grasses. This is not totally surprising as some seed-dehydration-associated pathways have well-characterized overlap with drought responses such as accumulation of osmoprotectants, LEA proteins, and ROS scavengers (41)(42)(43). For example, 22 of the 57 LEA genes in Arabidopsis have drought-induced expression but only 10 LEA genes have overlapping expression in drying seeds (44).…”

Identification of salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains by genomic analysis

“…These genes were involved in multi-component binding-proteindependent transport systems for glycine, betaine, and camitine, and accumulated to high levels in the cell in response to increased external osmolality (Huang et al 2010). Additionally, proline is essential for primary metabolism in salt stress and plays a molecular chaperone role in maintaining the pH of the cytosolic redox status of the cell (Kido et al 2013). Previous research has indicated that proABC genes are related to the accumulation of proline and enable bacteria to withstand high osmotic pressure (Mahan and Csonka 1983).…”

Transgenic Asiatic Grain Legumes for Salt Tolerance and Functional Genomics

“…Osmoprotectants, otherwise known as compatible osmolytes are non-toxic in nature, which play an important role in raising osmotic potential of cells under salt stress. In legumes, expression of osmolyte like trehalose, a non-reducing disaccharide has been detected in soybean (Kido et al, 2013), M. truncatula and common bean (López et al, 2008). Overexpression of genes encoding for compatible osmolytes have conferred transgenics tolerance to osmotic stress.…”