title: Transcriptome analysis of callus from Picea balfouriana.
abstract: BACKGROUND
  Picea likiangensis var. balfouriana (Rehd. et Wils.) Hillier ex Slavin (also known as Picea balfouriana) is an ecologically and economically important conifer that grows rapidly under optimum conditions and produces high-quality wood. It has a wide geographic distribution and is prevalent in southwest and eastern regions of China. Under suboptimal conditions, P. balfouriana grows slowly, which restricts its cultivation. Somatic embryogenesis has been used in the mass propagation of commercial species. However, low initiation rates are a common problem and the mechanisms involved in the induction of somatic embryogenesis are not fully understood. To understand the molecular mechanisms regulating somatic embryogenesis in P. balfouriana, high-throughput RNA-seq technology was used to investigate the transcriptomes of embryogenic and non-embryogenic tissues from three P. balfouriana genotypes. We compared the genes expressed in these tissues to identify molecular markers with embryogenic potential.
  
  
  RESULTS
  A total of 55,078,846 nucleotide sequence reads were obtained for the embryogenic and non-embryogenic tissues of P. balfouriana, and 49.56% of them uniquely matched 22,295 (84.3%) of the 26,437 genes in the Picea abies genome database (Nature 497: 579-584, 2013). Differential gene expression analysis identified 1,418 differentially expressed genes (false discovery rate <0.0001; fold change ≥2) in the embryogenic tissues relative to the non-embryogenic tissues, including 431 significantly upregulated and 987 significantly downregulated genes. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that the most significantly altered genes were involved in plant hormone signal transduction, metabolic pathways (starch and sucrose metabolism), and phenylalanine metabolism.
  
  
  CONCLUSIONS
  We found that the initiation of embryogenic tissues affected gene expression in many KEGG pathways, but predominantly in plant hormone signal transduction, plant-pathogen interaction, and starch and sucrose metabolism. The changes in multiple pathways related to induction in the P. balfouriana embryogenic tissues described here, will contribute to a more comprehensive understanding of the mechanisms involved in the initiation of somatic embryogenesis. Additionally, we found that somatic embryogenesis receptor kinase (SERK), arabinogalactan proteins, and members of the WUS-related homeobox protein family may play important roles and could act as molecular markers in the early stage of somatic embryogenesis, as reported previously.
authors.forename: Qingfen
authors.initials: Q
authors.lastname: Li
authors.forename: Shougong
authors.initials: S
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Forest Genetics and Tree Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Number 1 of Dongxiaofu in Haidian District, Beijing, China. wangjh@caf.ac.cn.
authors.forename: Junhui
authors.initials: J
authors.lastname: Wang
mesh_terms: D020869:Gene Expression Profiling / Q000592:standards; D020043:Genes, Essential; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D028222:Picea / Q000235:genetics / Q000378:metabolism*; D058439:Plant Somatic Embryogenesis Techniques; D012015:Reference Standards; D012639:Seeds / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome