Uncovering the differential molecular basis of adaptive diversity in three Echinochloa leaf transcriptomes.
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.
Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
Gyoungju
G
Nah
Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
Ji-Hoon
JH
Im
Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
Jin-Won
JW
Kim
Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
Hae-Rim
HR
Park
Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
Min-Jung
MJ
Yook
Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
Tae-Jin
TJ
Yang
Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, United States of America.
Albert J
AJ
Fischer
Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
Do-Soon
DS
Kim
D000222:Adaptation, Physiological / Q000235:genetics; D031747:Echinochloa / Q000235:genetics* / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D006540:Herbicides / Q000633:toxicity; D008969:Molecular Sequence Data; D018515:Plant Leaves / Q000235:genetics* / Q000254:growth & development; D010940:Plant Proteins / Q000096:biosynthesis* / Q000235:genetics; D056910:Republic of Korea; D059467:Transcriptome / Q000235:genetics
D006540:Herbicides; D010940:Plant Proteins