RNA-Seq analysis of gene expression for floral development in crested wheatgrass (Agropyron cristatum L.)

PloS One
Fangqin ZengYong-Bi Fu

Abstract

Crested wheatgrass [Agropyron cristatum L. (Gaertn.)] is widely used for early spring grazing in western Canada and the development of late maturing cultivars which maintain forage quality for a longer period is desired. However, it is difficult to manipulate the timing of floral transition, as little is known about molecular mechanism of plant maturity in this species. In this study, RNA-Seq and differential gene expression analysis were performed to investigate gene expression for floral initiation and development in crested wheatgrass. Three cDNA libraries were generated and sequenced to represent three successive growth stages by sampling leaves at the stem elongation stage, spikes at boot and anthesis stages. The sequencing generated 25,568,846; 25,144,688 and 25,714,194 qualified Illumina reads for the three successive stages, respectively. De novo assembly of all the reads generated 311,671 transcripts with a mean length of 487 bp, and 152,849 genes with an average sequence length of 669 bp. A total of 48,574 (31.8%) and 105,222 (68.8%) genes were annotated in the Swiss-Prot and NCBI non-redundant (nr) protein databases, respectively. Based on the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database, 9,723 anno...Continue Reading

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Datasets Mentioned

BETA
SRP096782

Methods Mentioned

BETA
RNA-Seq
cDNA library construction
PCR

Software Mentioned

FASTQC
edgeR
TrinityStats
R Bioconductor
ClustalW
KEGG Automatic Annotation Server ( KAAS )
Blastx
Bowtie
PrimerQuest
Trimmomatic

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