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Sequence mining and transcript profiling to explore differentially expressed genes associated with lipid biosynthesis during soybean seed development

Huan Chen12, Fa-Wei Wang1, Yuan-Yuan Dong1, Nan Wang1, Ye-Peng Sun1, Xiao-Yan Li1, Liang Liu2, Xiu-Duo Fan2, Hai-Long Yin1, Yuan-Yuan Jing1, Xin-Yue Zhang1, Yu-Lin Li1, Guang Chen2* and Hai-Yan Li12*

Author affiliations

1 Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin, 130118, China

2 College of Life Sciences, Jilin Agricultural University, Changchun, Jilin, 130118, China

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Citation and License

BMC Plant Biology 2012, 12:122  doi:10.1186/1471-2229-12-122

Published: 31 July 2012



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.


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.


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.

Gene expression; Lipid; RNA-sequencing; Soybean; Unigene