Recent release of whole genome draft sequences in legume species have led comparative genome studies among legume plants including Glycine max, G. soja, Cajanus cajan and Medicago truncatula. The majority of comparative genomic researches have been conducted based on synteny of coding sequences and coding sequence variations may be one of major forces for speciation and evolution. However, non-coding sequences have been also reported to be important phenotypic regulators. Especially, since short sequence motifs in the promoter regions are highly conserved, they are suggested to be another resources of interests in comparative studies. In this study, we predicted the conserved short sequence motifs by BLASTN algorithm using dicot promoter database from Softberry (http://www.softberry.com). A total of 37,396 conserved short sequence motifs were identified onto 2 kb upstreams of 46,367 high confident gene model of G. max (cv. Williams 82). Meanwhile, whole genome of 7 soybean landraces (G. max) and 7 wild soybean genotypes (G. soja) were sequenced at low depth of less than ten using Illumina Hiseq 2000. Among these genotypes, nucleotide variations were identified in predicted conserved regulatory motifs by mapping of short reads to the reference genome sequence using the Samtools program (http://samtools.sourceforge.net/). Fifteen and two genes, which have SNPs in regulatory motifs and no SNP in coding sequence, were identified by comparisons of inter-species and intra-species, respectively. qRT-PCR experiments are in progress for investigating differences of these 17 genes expressions at transcriptional level.

As soybean (Glycine max) is known for its high nutritional value of oil and protein, soybean has been domesticated and cultivated by one specific character trait based on human selection. Importantly, tracing back in time where G. max and G. soja, the undomesticated ancestor of G. max have diverged plays an important role in studying of genetic diversity and in investigating the common ancestor of soybean. In this study, we sequenced 6 G. max and 6 G. soja using Illumina’s Hiseq 2000 with a low coverage sequencing technology to estimate the divergence of times between genotypes and populations. A total of the 12 genotypes were sequenced at the average depth of 6.5 and resulted 892.5 Mb and 903.3 MB consensus sequences with the coverage of 91.54% and 92.65% for G. max and G. soja, respectively. The whole genome SNP analysis showed that G. max had lower frequency levels of polymorphism (~0.1%) than G. soja (~0.25%). And, a high number of SNPs located in introns were found among 6 G. soja genotypes as SNPs were approximately twice than those found in 6 G max. The number of SNPs in G. max intronic regions was 53,134, whereas a total of 133,329 SNPs were discovered in G. soja introns. Almost an equal number of SNPs were discovered in 5’ UTR and exon regions; however, different numbers of SNP in CDS and 3′ UTR were identified. By the rate of nonsynonymous change, divergence of time between G. soja and G. max would be investigated.

Phytic acid, myo-inositol (1, 2, 3, 4, 5, 6)-hexakisphosphate, is a material that plants store phosphorus in seeds. Phytic acid is classified as an antinutrient because of indigestibility. Non-ruminant animals, such as human and swine, excrete unavailable phytic acid. The unavailable phytic acid run off to ground water, river, sea, causing eutrophication as a factor. Accordingly, low-phytic acid crops draw the attention due to both nutritional and environmental reasons. Using more than 900 Glycine accessions including G. max, G. soja and G. gracillis, colormetric method was applied for detecting low-phytic acid mutant. Two hundred fifty accessions were screened by the colormetric method so far, but no mutant was identified. Screening of mutants with the rest 710 accessions is in progress. MIPS1 (D-myo-inositol 3-phosphate synthase) is considered as gene related to phytic acid content in soybean. Also, lpa1 (Zea mays low phytic acid 1) known as controlling phytic acid content in maize was recently reported that homologs of lpa1 were responsible for phytic acid content in soybean and located on linkage groups L and N (Chromosomes 19 and 3). After primers were designed from these three candidate genes for phytic acid content, identification of genes responsible for low phytic acid and investigation of genetic variation among 960 accessions will be performed as further study.

A single recessive gene, rxp, controls bacterial leaf pustule (BLP) resistance in a soybean. The Rxp locus appears to be linked to the malate dehydrogenase (Mdh) locus and Satt372 on linkage group (LG) D2. Around the Rxp locus, four bacterial artificial chromosome (BAC) clones are anchored by Satt486, Satt498, BARC-022037-04263, and BARC-040963-07870. Using these BAC clone sequences, possible orthologous region of Rxp locus was identified: Medicago truncatula contig 962 at chromosome 3 and contig 283 and contig 1108 at chromosome 8. Sequence analysis of contig 962 had revealed microsynteny with three soybean BAC clones on LG A1, which are duplicated with other two soybean BAC clones anchored by Satt486 and Satt498. After BLAST search was performed with M. truncatula contig 962 against soybean ESTs, several soybean ESTs were identified. With developed single nucleotide polymorphism (SNP) markers and the RIL population from the cross of Pureunkong and Jinpumkong 2, SNP genotyping was able to locate twos oybean ESTs: CO979743 at 1 cM away from Satt195 on LG C1 and BE021935 at 5 cM away from Satt363 on LG C2. Thus, our results indicate that structure of soybean genome around Rxp locus is very complicated.

The effect of biofertilizer in enhancing nutrient quality and antioxidant property of rice grain was investigated. The experiment was carried out in a randomized complete block design with 3 replications and 7 treatments namely : RF = N-P2O5-K2O(11-5.5-4.8kg~;10a-1); half of the recommended fertilizer rate, HRF=N-P2O5-K2O(5.5-2.75-2.4kg~;10a-1): HRF+Bio 250=HRF combined with 250 kg Biofertilizer 10 a-1 ; HRF+Bio 500=HRF combined with 500 kg Biofertilizer 10 a-1; Bio 250=250 kg Biofertilizer 10 a-1; Bio 500=500 kg Biofertilizer 10 a-1; and NF=No Fertilizer. Results showed that HRF+Bio 500 obtained a significantly higher protein content but a significantly lower amylose content compared with RF and NF treatments. Highest phytic acid content was recorded in NF treatment while the lowest was observed in HRF+500 treatment. The highest values in both electron donating ability and reducing power were obtained in HRF+Bio 500 treatment. All treatments obtained higher reducing power than that of the RF treatment and that NF treatment showed comparable values in both electron donating ability and reducing power with those of the treated plots. Highest antimutagenicity property was also observed in HRF+Bio 500 treatment followed by Bio 500 treatment. This study showed the possibility of using biofertilizer to enhance nutritional quality and antioxidant property of rice.

The effect of osmotic condition on β-glucuronidase (GUS) transient expression was evaluated in microspore-derived embryos of wheat. Microspore explants were treated on medium containing various mannitol concentrations prior to and post bombardment with plasmid DNA pAHC25 containing uidA gene controlled by maize ubiquitin 1 (UBI1) promoter. GUS expression in the bombarded explants was examined by histochemical and fluorometric assays. Increased GUS expression was observed with mannitol treatment when compared to untreated explants. The histochemical study showed that the number of blue (GUS) foci were the highest in the bombarded explants treated with 0.6 M mannitol medium. The fluorometric assay of bombarded explants also proved 3.5-fold increase in GUS activity with 0.6 M mannitol treatment when compared to without mannitol treatment. These results indicate that 0.6 M mannitol is beneficial for improving transformation efficiency of wheat microspore-derived embryos or embryogenic calli through biolistic transformation.