title: Root transcriptomes of two acidic soil adapted Indica rice genotypes suggest diverse and complex mechanism of low phosphorus tolerance.
abstract: Low phosphorus (P) tolerance in rice is a biologically and agronomically important character. Low P tolerant Indica-type rice genotypes, Sahbhagi Dhan (SD) and Chakhao Poreiton (CP), are adapted to acidic soils and show variable response to low P levels. Using RNAseq approach, transcriptome data was generated from roots of SD and CP after 15 days of low P treatment to understand differences and similarities at molecular level. In response to low P, number of genes up-regulated (1318) was more when compared with down-regulated genes (761). Eight hundred twenty-one genes found to be significantly regulated between SD and CP in response to low P. De novo assembly using plant database led to further identification of 1535 novel transcripts. Functional annotation of significantly expressed genes suggests two distinct methods of low P tolerance. While root system architecture in SD works through serine-threonine kinase PSTOL1, suberin-mediated cell wall modification seems to be key in CP. The transcription data indicated that CP relies more on releasing its internally bound Pi and coping with low P levels by transcriptional and translational modifications and using dehydration response-based signals. Role of P transporters seems to be vital in response to low P in CP while sugar- and auxin-mediated pathway seems to be preferred in SD. At least six small RNA clusters overlap with transcripts highly expressed under low P, suggesting role of RNA super clusters in nutrient response in plants. These results help us to understand and thereby devise better strategy to enhance low P tolerance in Indica-type rice.
authors.affiliation: School of Crop Improvement, College of Post-Graduate Studies, Central Agricultural University (Imphal), Umroi Road, Umiam, Meghalaya, 793103, India. wtyagi.cau@gmail.com.
authors.forename: Wricha
authors.initials: W
authors.lastname: Tyagi
authors.affiliation: School of Crop Improvement, College of Post-Graduate Studies, Central Agricultural University (Imphal), Umroi Road, Umiam, Meghalaya, 793103, India.
authors.forename: Mayank
authors.initials: M
authors.lastname: Rai
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D000143:Acids / Q000737:chemistry*; D000222:Adaptation, Physiological / Q000187:drug effects* / Q000235:genetics; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D018745:Genome, Plant; D005838:Genotype; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D010758:Phosphorus / Q000494:pharmacology*; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D036226:Seedlings / Q000187:drug effects / Q000235:genetics / Q000254:growth & development; D017422:Sequence Analysis, DNA; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D012987:Soil / Q000737:chemistry*; D024363:Transcription Initiation Site; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics*; D015854:Up-Regulation / Q000187:drug effects / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; D000143:Acids; D012333:RNA, Messenger; D012987:Soil; D010758:Phosphorus
keywords: Differentially expressed genes; Indica-type rice; Low phosphorus tolerance; RNAseq