Takuya Wada

Detection of QTLs for white-back and basal-white grains caused by high temperature during ripening period in japonica rice

There is increasing evidence that global warming affects the development of rice. High temperatures during ripening increase the ratio of undesirable chalky grains followed by deteriorating grain appearance quality. In order to detect quantitative trait loci (QTLs) controlling the occurrence of white-back and basal-white chalky grains of brown rice, QTL analysis was performed using recombinant inbred lines derived from a cross between two strains, ‘Tsukushiroman’ (sensitive to heat stress) and ‘Chikushi 52’ (tolerant of heat stress). The F7 and F8 lines were exposed to heat stress during the ripening period in two locations, Fukuoka and Kagoshima, in Japan. QTLs for white-back grains and basal-white grains were detected on chromosomes 1, 3, and 8, and those for basal-white grains were detected on chromosomes 2, 3, and 12. QTLs on chromosome 8 for white-back grains were shared in the plants grown in both locations. Near-isogenic lines (NILs), which harbored a segment from ‘Chikushi 52’ on chromosome 8 with the genetic background of ‘Tsukushiroman’, showed relatively lower ratios of white-back grains than ‘Tsukushiroman’. Therefore, insertion of the ‘Chikushi 52’ genomic region of the QTL on chromosome 8 can improve the quality of rice when it is grown under heat stress conditions.

Validation of QTLs for Eating Quality of Japonica Rice 'Koshihikari' Using Backcross Inbred Lines

Abstract Using backcross inbred lines (BILs) derived from a cross between temperate japonica rice cultivars, Moritawase and Koshihikari, we validated the major quantitative trait loci (QTL) for eating quality and textural characteristics on chromosomes (Chr) 1, 2, 3, 6, 7, 10, and 12. Significant genetic differences in eating quality among BILs were detected at the QTL on Chr 3 and corresponded to the differences between the parents. Although differences in eating quality on the other chromosomes were not significant by t-test, cluster analysis and principal component analysis clearly showed that the genetic effects of the QTLs on Chr 6, 7, and 10 were similar to that on Chr 3, but the genetic effects of QTLs on Chr 1, 2, and 12 were entirely different from that on Chr 3. We previously identified that textural characteristics were highly correlated with eating quality. In this study, genetic differences in textural characteristics were similar to the genetic differences in eating quality among BILs. These results reveal major QTLs for eating quality of Koshihikari on Chr 3, 6, 7, and 10. The QTL on Chr 3 contributed most to the improvement of eating quality and textural characteristics.

Detection and validation of QTLs for milky-white grains caused by high temperature during the ripening period in Japonica rice

The occurrence of chalky rice (Oryza sativa L.) grains caused by high temperature is a serious problem in rice production. Of the several kinds of chalky grains, milky-white grains are not well analyzed. The milky-white rice grain phenomenon is caused by genetic factors as well as environmental and nutritional conditions. To analyze the genetic control system for rice grain quality, we raised recombinant inbred lines from progeny produced from ‘Tsukushiroman’ (high temperature sensitive) and ‘Chikushi 52’ (high temperature tolerant) cultivars. Quantitative trait locus (QTL) analysis revealed that the QTL on chromosome 4, linked to the simple sequence repeat marker RM16424, contributed substantially to the occurrence of milky-white grains, as it was detected over two experimental years. To validate the effect of the QTL, we developed near isogenic lines that have the ‘Chikushi 52’ segment on the short arm of chromosome 4 in the ‘Tsukushiroman’ genetic background, and that had a lower milky-white grain ratio than that of ‘Tsukushiroman’ when exposed to high temperatures during the ripening period. These results suggest that the ‘Chikushi 52’ allele on chromosome 4 suppresses the occurrence of milky-white grains and improves rice grain quality under heat stress during the grain ripening period.

Development and characterization of a new rice cultivar, ‘Chikushi-kona 85’, derived from a starch-branching enzyme IIb-deficient mutant line

A new super-hard rice cultivar, ‘Chikushi-kona 85’, which was derived from a cross between ‘Fukei 2032’ and ‘EM129’, was developed via bulk method breeding. ‘Chikushi-kona 85’ showed a higher content of resistant starch than the normal non-glutinous rice cultivar, ‘Nishihomare’, and a higher grain yield than the first super-hard rice cultivar, ‘EM10’. The amylopectin chain length of ‘Chikushi-kona 85’ and its progenitor line ‘EM129’ was longer than that of ‘Nishihomare’, and was similar to that of ‘EM10’. This suggests that the starch property of ‘Chikushi-kona 85’ was inherited from ‘EM129’, which is a mutant line deficient in a starch branching enzyme similar to ‘EM10’. Genetic analysis of ‘Chikushi-kona 85’ crossed with ‘Nishihomare’ also showed that the starch property of ‘Chikushi-kona 85’ was regulated by a single recessive gene. Consumption of processed cookies made from ‘Chikushi-kona 85’ flour showed a distinctive effect in controlling blood sugar levels in comparison to the normal non-glutinous rice cultivar ‘Hinohikari’. These results show that ‘Chikushi-kona 85’ is a novel genetic source to develop new products made of rice, which could reduce calorie intake and contribute to additional health benefits.

Development and characterization of a strawberry MAGIC population derived from crosses with six strawberry cultivars

A strawberry Multi-parent Advanced Generation Intercrosses (MAGIC) population, derived from crosses using six strawberry cultivars was successfully developed. The population was composed of 338 individuals; genome conformation was evaluated by expressed sequence tag-derived simple short repeat (EST-SSR) markers. Cluster analysis and principal component analysis (PCA) based on EST-SSR marker polymorphisms revealed that the MAGIC population was a mosaic of the six founder cultivars and covered the genomic regions of the six founders evenly. Fruit quality related traits, including days to flowering (DTF), fruit weight (FW), fruit firmness (FF), fruit color (FC), soluble solid content (SC), and titratable acidity (TA), of the MAGIC population were evaluated over two years. All traits showed normal transgressive segregation beyond the founder cultivars and most traits, except for DTF, distributed normally. FC exhibited the highest correlation coefficient overall and was distributed normally regardless of differences in DTF, FW, FF, SC, and TA. These facts were supported by PCA using fruit quality related values as explanatory variables, suggesting that major genetic factors, which are not influenced by fluctuations in other fruit traits, could control the distribution of FC. This MAGIC population is a promising resource for genome-wide association studies and genomic selection for efficient strawberry breeding.