Nucleotide Sequence Variation on Conserved Regulatory Sequence Motifs in Glycine max and Glycine soja

We predicted the conserved short sequence motifs regarding transcription factor binding sites in Glycine max (cv. Williams 82) by BLASTN program using dicot promoter database (http://linux1.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom). We found total 37,396 conserved short sequence motifs on to 2 kbp upstream sequences of 46,367 high confident genes. These results were evaluated using MAST algorithm and Jaspar core plant cis-element database with several demonstrated biological experiments. Furthermore, single nucleotide variations in the regulatory and genic regions were detected among 14 soybean genotypes including seven cultivated landraces and seven wild soybeans (Glycine soja). The Illumina HiSeq200 short reads of these 14 soybean genotypes were mapped to soybean reference genome to retrieve single nucleotide polymorphism (SNPs) by Samtools software. A total of 17 genes that were predicted to have the SNPs on the conserved short motifs were subject to the comparison of transcription levels by RT-PCR method; 15  with the inter-species variations  between G. max and G. soja and 2 with the intra-species variations. All of these 17 putative genes had no SNP in the genic regions. We could not observed any differences in the expression levels among the soybean genotypes. This result indicates that gene expression may controlled by more complex factors.