Variation block-based genomics method for crop plants.

BACKGROUND: In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits. RESULTS: We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. CONCLUSIONS: We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding.

Panax ginseng protects against global ischemia injury in rat hippocampus.

Based on the use of Panax ginseng C.A. Meyer (Family Araliaceae) for the treatment of stroke in traditional Korean medicine, the present study was carried out to evaluate neuroprotective effects of P. ginseng after transient global cerebral ischemia using the four-vessel occlusion rat model. Nissl staining, lipid peroxidation (malondialdehyde [MDA] formation), and activities of superoxide dismutase (SOD) and glutathione peroxidase (GPx) of rat brain were assessed. Ethanolic P. ginseng extract (200 mg/kg, i.p.) significantly protected CA1 neurons against 10 minutes of transient forebrain ischemia as demonstrated by measuring the density of neuronal cells. P. ginseng also significantly decreased the level of MDA and increased the expression of GPx and SOD. These results suggest that P. ginseng might be neuroprotective against cerebral ischemia-induced injury in rat brain by decreasing lipid peroxides and increasing the expression of GPx and SOD.