Uncovering the Differential Molecular Basis of Adaptive Diversity in Three Echinochloa Leaf Transcriptomes

Abstract

Echinochloa is a major weed that grows almost everywhere in farmed land. This high prevalence results from its high adaptability to various water conditions, including upland and paddy fields, and its ability to grow in a wide range of climates, ranging from tropical to temperate regions. Three Echinochloa crus-galli accessions (EC-SNU1, EC-SNU2, and EC-SNU3) collected in Korea have shown diversity in their responses to flooding, with EC-SNU1 exhibiting the greatest growth among three accessions. In the search for molecular components underlying adaptive diversity among the three Echinochloa crus-galli accessions, we performed de novo assembly of leaf transcriptomes and investigated the pattern of differentially expressed genes (DEGs). Although the overall composition of the three leaf transcriptomes was well-conserved, the gene expression patterns of particular gene ontology (GO) categories were notably different among the three accessions. Under non-submergence growing conditions, five protein categories (serine/threonine kinase, leucine-rich repeat kinase, signaling-related, glycoprotein, and glycosidase) were significantly (FDR, q < 0.05) enriched in up-regulated DEGs from EC-SNU1. These up-regulated DEGs include major components of signal transduction pathways, such as receptor-like kinase (RLK) and calcium-dependent protein kinase (CDPK) genes, as well as previously known abiotic stress-responsive genes. Our results therefore suggest that diversified gene expression regulation of upstream signaling components conferred the molecular basis of adaptive diversity in Echinochloa crus-galli.

Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress

“…β-glucosidase is known to be membrane-associated and is the key enzyme that mediates the conversion of cellobiose to glucose during cellulose hydrolysis [ 30 , 56 ], There has been little study of β-glucosidase related to abiotic stress, but the constitutive up-regulation of β-glucosidase in a flood-tolerant Echinochloa accession [ 57 ] and freezing tolerance in Arabidopsis transgenic lines of SRF2 ( SENSITIVE TO FREEZING2 ), which encodes β-glucosidase [ 58 ], have been reported.…”

Adaptive Diversity of Echinochloa Species to Osmotic Stress

“…Adaptive diversity of Echinochloa species to osmotic stress It is known that Echinochloa species have diverse ecological adaptability, which was recently investigated in transcriptome level (Nah et al, 2015a). Many of these studies have focused on adaptation to flooding stress (Kim, 1993;Im, 2016).…”

“…In ploidy level, E. oryzicola is tetraploid (2n=4X=36), while E. crus-galli is hexaploid (2n=6X=54) revealed by flow cytometric analysis and chromosome counting (Nah et al, 2015a). It is known that Echinochloa crus-galli is an allohexaploid produced by natural hybridization between tetraploid E. oryzicola and unknown diploid Echinochloa species and then subsequent chromosome doubling (Yabuno, 1966).…”

Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress

“…In contrast, flood-tolerant rice using an 'escape strategy' can tolerate deepwater flooding conditions, such as partial submergence (PS), by rapidly elongating their internodes when water levels rise [2,6]. Many studies on Arabidopsis (for example, see [5]), Oryza (for example, see [7,8]), Rumex [9][10][11][12], Rorippa [3,13,14], and Echinochloa [15,16] have investigated the molecular mechanisms for withstanding flooding.…”

“…The use of next-generation sequencing and microarray platforms led to the development of high-throughput transcript profiling (e.g., RNA-Seq) technologies as an efficient functional genomics tool [29,30]. In flash flood-tolerant rice, Rumex, Rorippa, and Echinochloa, large-scale transcriptome analyses using microarrays or RNA-Seq have been performed to attempt to identify the mechanism controlling flooding tolerance [11,16,31]. Comparative transcriptome analysis with two varieties, C9285 and T65, revealed differential expression patterns between the genotypes [32].…”