title: Doubled Haploid 'CUDH2107' as a Reference for Bulb Onion (Allium cepa L.) Research: Development of a Transcriptome Catalogue and Identification of Transcripts Associated with Male Fertility.
abstract: Researchers working on model plants have derived great benefit from developing genomic and genetic resources using 'reference' genotypes. Onion has a large and highly heterozygous genome making the sharing of germplasm and analysis of sequencing data complicated. To simplify the discovery and analysis of genes underlying important onion traits, we are promoting the use of the homozygous double haploid line 'CUDH2107' by the onion research community. In the present investigation, we performed transcriptome sequencing on vegetative and reproductive tissues of CUDH2107 to develop a multi-organ reference transcriptome catalogue. A total of 396 million 100 base pair paired reads was assembled using the Trinity pipeline, resulting in 271,665 transcript contigs. This dataset was analysed for gene ontology and transcripts were classified on the basis of putative biological processes, molecular function and cellular localization. Significant differences were observed in transcript expression profiles between different tissues. To demonstrate the utility of our CUDH2107 transcriptome catalogue for understanding the genetic and molecular basis of various traits, we identified orthologues of rice genes involved in male fertility and flower development. These genes provide an excellent starting point for studying the molecular regulation, and the engineering of reproductive traits.
authors.affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.
authors.forename: Jiffinvir S
authors.initials: JS
authors.lastname: Khosa
authors.affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.
authors.forename: Robyn
authors.initials: R
authors.lastname: Lee
authors.affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.|Department of Botany, University of Otago, Dunedin, New Zealand.
authors.forename: Sophia
authors.initials: S
authors.lastname: Bräuning
authors.affiliation: Department of Botany, University of Otago, Dunedin, New Zealand.
authors.forename: Janice
authors.initials: J
authors.lastname: Lord
authors.affiliation: New Zealand Institute for Plant & Food Research, Lincoln, New Zealand.
authors.forename: Meeghan
authors.initials: M
authors.lastname: Pither-Joyce
authors.affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.|New Zealand Institute for Plant & Food Research, Lincoln, New Zealand.
authors.forename: John
authors.initials: J
authors.lastname: McCallum
authors.affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.|New Zealand Institute for Plant & Food Research, Lincoln, New Zealand.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Macknight
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D006238:Haploidy; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D019697:Onions / Q000235:genetics*; D009928:Organ Specificity / Q000235:genetics; D059467:Transcriptome