BackgroundIn 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.ResultsWe 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.ConclusionsWe 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.
Tocochromanols are potent lipid-soluble antioxidants and essential nutrients for human health. Genetic engineering techniques were used to develop soybeans with enhanced vitamin E levels, including tocotrienols, which are not found in soybean. The gene encoding rice homogentisate geranylgeranyl transferase (HGGT) was overexpressed in soybeans using seed-specific and constitutive promoters. The association between abundance of vitamin E isomers and antioxidant activity was investigated during seed germination. With the exception of β-tocotrienol, all vitamin E isomers were detected in germinating seeds expressing OsHGGT. The antioxidant properties of germinating seed extracts were determined using 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radicals and lipid peroxidation (TBARS). Compared with intact wild-type seeds, transgenic seeds showed increases in radical scavenging of 5.4-17 and 23.2-35.3% in the DPPH and ABTS assays, respectively. Furthermore, the lipid peroxidation levels were 2.0-4.5-fold lower in germinating seeds from transgenic lines than in wild-type seeds. Therefore, it appears that the antioxidant potential of transgenic oil-producing plants such as soybean, sunflower, and corn may be enhanced by overexpressing OsHGGT during seed germination.
The microbial and physicochemical properties of brown and white cooked rice treated by atmospheric pressure plasma (APP). APP was produced (250 W, 15 kHz, ambient air) and applied to brown and white cooked rice for 5, 10, and 20 min. The 20-min plasma treatment reduced in bacterial counts by 2.01 log CFU/g when cooked rice were inoculated with or O157:H7. The pH of the brown cooked rice was decreased by the 5-min plasma. The hardness values of APP-treated brown and white cooked rice were lower than untreated samples. The reducing sugar contents of brown and white cooked rice were significantly higher than those in untreated samples. Lipid oxidation of APP-treated brown and white cooked rice were higher compared to untreated samples. These results indicate that APP improves microbial quality, although further studies should be conducted to change the physicochemical qualities of brown and white cooked rice induced by APP.
Total tocopherol content was higher in soybean landraces as compared with modern cultivars developed by cross-breeding. These results suggest that soybean breeding is necessary to increase tocopherol levels.
This study applied high hydrostatic pressure (HHP) and atmospheric pressure plasma (APP) treatments to rice and examined the effects of the treatments on the microbial contamination and physicochemical properties. The microbial population was 100% sterilized by HHP and reduced by up to 34% by APP. Color a values were increased by up to 285% and 33% in HHP and APP, respectively. HHP increased fructose (∼8,256%) but decreased glucose, sucrose, and maltose (∼97%, −100%, and −93%, respectively). APP only mildly modified sugar composition compared with HHP. Retrogradation factors were not changed remarkably by HHP or APP. In conclusion, HHP sterilized microorganisms, but the sterilization was accompanied by high modifications to color and sugar composition. APP had a lesser effect on the microbial population, but it only mildly changed the physicochemical properties of the rice. Therefore, application of either HHP or APP could be considered depending on the intended use of the rice.
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