title: Transcriptome analysis of hexaploid hulless oat in response to salinity stress.
abstract: BACKGROUND
  Oat is a cereal crop of global importance used for food, feed, and forage. Understanding salinity stress tolerance mechanisms in plants is an important step towards generating crop varieties that can cope with environmental stresses. To date, little is known about the salt tolerance of oat at the molecular level. To better understand the molecular mechanisms underlying salt tolerance in oat, we investigated the transcriptomes of control and salt-treated oat using RNA-Seq.
  
  
  RESULTS
  Using Illumina HiSeq 4000 platform, we generated 72,291,032 and 356,891,432 reads from non-stressed control and salt-stressed oat, respectively. Assembly of 64 Gb raw sequence data yielded 128,414 putative unique transcripts with an average length of 1,189 bp. Analysis of the assembled unigenes from the salt stressed and control libraries indicated that about 65,000 unigenes were differentially expressed at different stages. Functional annotation showed that ABC transporters, plant hormone signal transduction, plant-pathogen interactions, starch and sucrose metabolism, arginine and proline metabolism, and other secondary metabolite pathways were enriched under salt stress. Based on the RPKM values of assembled unigenes, 24 differentially expressed genes under salt stress were selected for quantitative RT-PCR validation, which successfully confirmed the results of RNA-Seq. Furthermore, we identified 18,039 simple sequence repeats, which may help further elucidate salt tolerance mechanisms in oat.
  
  
  CONCLUSIONS
  Our global survey of transcriptome profiles of oat plants in response to salt stress provides useful insights into the molecular mechanisms underlying salt tolerance in this crop. These findings also represent a rich resource for further analysis of salt tolerance and for breeding oat with improved salt tolerance through the use of salt-related genes.
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Wu
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
authors.forename: Yani
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
authors.forename: Pengjie
authors.initials: P
authors.lastname: Huo
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
authors.forename: Zongwen
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D018554:Avena / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D063990:Gene Ontology; D058977:Molecular Sequence Annotation; D011123:Polyploidy; D020133:Reverse Transcriptase Polymerase Chain Reaction; D054712:Salinity; D055049:Salt Tolerance / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological
chemical_list: D012965:Sodium Chloride