The Central Region Agricultural Research Center (CARC) is one of five core research institute of NARO, which works in farm management research, crop production systems especially in lowland farming, soil science & plant nutrition, plant disease management, applied entomology and zoology, and breeding in rice and barley. CARC lays emphasis on the technology for low-cost, stable and high-yield production systems of crop rotation on paddy field with rice, wheat and soybean. Environmentally friendly farming using integrated control system of pests, diseases and weeds is also a major research focus. CARC is mainly resolving domestic agricultural problems in the Kanto, Tokai and Hokuriku areas, located in the central region of Honshu island.
International competitiveness strengthen of farm products is indispensable for Japanese agriculture. So a further cost cut is demanded. Direct seeding of rice as a technique that is effective for a cost reduction. By using the technique, raising of seedling and transplanting, which account for approximately 26% among all rice growing work, become needless. Then this technique is paid attention as the effective technique that can reduce production cost and work force. The dry direct seeding is lower-cost method, but it is influenced by establish habit of seeding and growth properties of cultivars. Therefore we assumed early seeding cultivation and late seeding cultivation as the cropping system that introduction was expected. And we examined establishment of seeding, the growth, yield and quality using ten main paddy-rice cultivars of the Kanto area including some cultivars bred newly in late years.
The identification of cultivars is important for the protection of intellectual property rights of breeders, for the maintenance of crop prices for farmers, and for precise product information for consumers. In Japan, several PCR methods have been developed for crop discrimination. To distinguish rice cultivars in particular, several types of DNA markers have been used. Multiplex PCR methods were developed previously using STS markers to reduce labor, time, and cost. Although SNPs are the most abundant polymorphisms among cultivars, SNP marker sets for multiplex PCR have not been created for rice discrimination. The present study's results demonstrate that the agarose gel electrophoresis of multiplex PCR with SNP markers was as reliable as STS markers, and 114 Japanese rice cultivars including the 10 most produced cultivars in Japan in 2014 and other major cultivars from each Japanese prefecture were successfully discriminated using 15 SNP markers, six STS markers and one SSR marker.
In this study, we developed negative marker sets for multiplex PCR for 16 major Niigata rice cultivars including Koshihikari BLs using 14 SNP markers and two STS markers. Of these 14 SNP markers, 10 markers of which the 3 - end of primers were changed properly were used for one or more of negative marker sets, resulting in the effective construction of these marker sets. Each negative marker set was composed of one to four markers, and the 16 negative marker sets were composed of a total of 33 SNP markers and three STS markers. By using nine negative marker sets to discriminate hybrid seeds crossing between a target and contaminant cultivars, we found that these nine negative marker sets could detect outcrosses. Using a bulk DNA preparation method for seeds or rice powder including target and contaminant cultivars, these 16 negative marker sets could discriminate contaminated samples of which the contaminant cultivars were included in at the rate of 0.4% - 20%. These results confirmed that these negative marker sets will be a useful tool to certify pure seed strains by effectively detecting unexpected contamination and outcrosses.