title: Sequence mining and transcript profiling to explore differentially expressed genes associated with lipid biosynthesis during soybean seed development.
abstract: BACKGROUND
  Soybean (Glycine max L.) is one of the most important oil crops in the world. It is desirable to increase oil yields from soybean, and so this has been a major goal of oilseed engineering. However, it is still uncertain how many genes and which genes are involved in lipid biosynthesis.
  
  
  RESULTS
  Here, we evaluated changes in gene expression over the course of seed development using Illumina (formerly Solexa) RNA-sequencing. Tissues at 15 days after flowering (DAF) served as the control, and a total of 11592, 16594, and 16255 differentially expressed unigenes were identified at 35, 55, and 65 DAF, respectively. Gene Ontology analyses detected 113 co-expressed unigenes associated with lipid biosynthesis. Of these, 15 showed significant changes in expression levels (log2fold values ≥ 1) during seed development. Pathway analysis revealed 24 co-expressed transcripts involved in lipid biosynthesis and fatty acid biosynthesis pathways. We selected 12 differentially expressed genes and analyzed their expressions using qRT-PCR. The results were consistent with those obtained from Solexa sequencing.
  
  
  CONCLUSIONS
  These results provide a comprehensive molecular biology background for research on soybean seed development, particularly with respect to the process of oil accumulation. All of the genes identified in our research have significance for breeding soybeans with increased oil contents.
authors: Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, China.
authors: Huan
authors: H
authors: Chen
authors: Fa-Wei
authors: FW
authors: Wang
authors: Yuan-Yuan
authors: YY
authors: Dong
authors: Nan
authors: N
authors: Wang
authors: Ye-Peng
authors: YP
authors: Sun
authors: Xiao-Yan
authors: XY
authors: Li
authors: Liang
authors: L
authors: Liu
authors: Xiu-Duo
authors: XD
authors: Fan
authors: Hai-Long
authors: HL
authors: Yin
authors: Yuan-Yuan
authors: YY
authors: Jing
authors: Xin-Yue
authors: XY
authors: Zhang
authors: Yu-Lin
authors: YL
authors: Li
authors: Guang
authors: G
authors: Chen
authors: Hai-Yan
authors: HY
authors: Li
mesh_terms: D057225:Data Mining; D035264:Flowers / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D050356:Lipid Metabolism; D008055:Lipids / Q000096:biosynthesis* / Q000235:genetics; D058977:Molecular Sequence Annotation; D018749:RNA, Plant / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000254:growth & development* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013024:Soybean Oil / Q000235:genetics / Q000378:metabolism; D013025:Glycine max / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D013997:Time Factors
chemical_list: D008055:Lipids; D018749:RNA, Plant; D013024:Soybean Oil