Open Access Open Badges Research article

Identification of genes associated with nitrogen-use efficiency by genome-wide transcriptional analysis of two soybean genotypes

Qing N Hao123, Xin A Zhou12*, Ai H Sha12, Cheng Wang14, Rong Zhou12 and Shui L Chen12

Author Affiliations

1 Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China

2 Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture, Wuhan 430062, China

3 Graduate School of Chinese Academy of Agriculture Sciences, Beijing 100081, China

4 Graduate School of Nanjing Agricultural University, Nanjing, 210095, China

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BMC Genomics 2011, 12:525  doi:10.1186/1471-2164-12-525

Published: 26 October 2011



Soybean is a valuable crop that provides protein and oil. Soybean requires a large amount of nitrogen (N) to accumulate high levels of N in the seed. The yield and protein content of soybean seeds are directly affected by the N-use efficiency (NUE) of the plant, and improvements in NUE will improve yields and quality of soybean products. Genetic engineering is one of the approaches to improve NUE, but at present, it is hampered by the lack of information on genes associated with NUE. Solexa sequencing is a new method for estimating gene expression in the transcription level. Here, the expression profiles were analyzed between two soybean varieties in N-limited conditions to identify genes related to NUE.


Two soybean genotypes were grown under N-limited conditions; a low-N-tolerant variety (No.116) and a low-N-sensitive variety (No.84-70). The shoots and roots of soybeans were used for sequencing. Eight libraries were generated for analysis: 2 genotypes × 2 tissues (roots and shoots) × 2 time periods [short-term (0.5 to 12 h) and long-term (3 to 12 d) responses] and compared the transcriptomes by high-throughput tag-sequencing analysis. 5,739,999, 5,846,807, 5,731,901, 5,970,775, 5,476,878, 5,900,343, 5,930,716, and 5,862,642 clean tags were obtained for the eight libraries: L1, 116-shoot short-term; L2 84-70-shoot short-term; L3 116-shoot long-term; L4 84-70-shoot long-term; L5 116-root short-term; L6 84-70-root short-term; L7 116-root long-term;L8 84-70-root long-term; these corresponded to 224,154, 162,415, 191,994, 181,792, 204,639, 206,998, 233,839 and 257,077 distinct tags, respectively. The clean tags were mapped to the reference sequences for annotation of expressed genes. Many genes showed substantial differences in expression among the libraries. In total, 3,231genes involved in twenty-two metabolic and signal transduction pathways were up- or down-regulated. Twenty-four genes were randomly selected and confirmed their expression patterns by quantitative RT-PCR; Twenty-one of the twenty-four genes showed expression patterns consistent with the Digital Gene Expression (DGE) data.


A number of soybean genes were differentially expressed between the low-N-tolerant and low-N-sensitive varieties under N-limited conditions. Some of these genes may be candidates for improving NUE. These findings will help to provide a detailed understanding of NUE mechanisms, and also provide a basis for breeding soybean varieties that are tolerant to low-N conditions.