Hisatoshi Ohta

Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars

BackgroundHigh-yielding cultivars of rice (Oryza sativa L.) have been developed in Japan from crosses between overseas indica and domestic japonica cultivars. Recently, next-generation sequencing technology and high-throughput genotyping systems have shown many single-nucleotide polymorphisms (SNPs) that are proving useful for detailed analysis of genome composition. These SNPs can be used in genome-wide association studies to detect candidate genome regions associated with economically important traits. In this study, we used a custom SNP set to identify introgressed chromosomal regions in a set of high-yielding Japanese rice cultivars, and we performed an association study to identify genome regions associated with yield.ResultsAn informative set of 1152 SNPs was established by screening 14 high-yielding or primary ancestral cultivars for 5760 validated SNPs. Analysis of the population structure of high-yielding cultivars showed three genome types: japonica-type, indica-type and a mixture of the two. SNP allele frequencies showed several regions derived predominantly from one of the two parental genome types. Distinct regions skewed for the presence of parental alleles were observed on chromosomes 1, 2, 7, 8, 11 and 12 (indica) and on chromosomes 1, 2 and 6 (japonica). A possible relationship between these introgressed regions and six yield traits (blast susceptibility, heading date, length of unhusked seeds, number of panicles, surface area of unhusked seeds and 1000-grain weight) was detected in eight genome regions dominated by alleles of one parental origin. Two of these regions were near Ghd7, a heading date locus, and Pi-ta, a blast resistance locus. The allele types (i.e., japonica or indica) of significant SNPs coincided with those previously reported for candidate genes Ghd7 and Pi-ta.ConclusionsIntrogression breeding is an established strategy for the accumulation of QTLs and genes controlling high yield. Our custom SNP set is an effective tool for the identification of introgressed genome regions from a particular genetic background. This study demonstrates that changes in genome structure occurred during artificial selection for high yield, and provides information on several genomic regions associated with yield performance.

Effects of the number of pollen grains on cold tolerance at the booting stage in rice lines with QTLs for cold tolerance

Abstract This study was conducted to clarify the relationship between the number of pollen grains per anther and spikelet fertility under low temperature conditions in the rice cultivars and lines including lines with quantitative trait loci (QTL) for cold tolerance, adapted to the Tohoku region of northern Japan. Cold-water treatment decreased anther length, the number of pollen grains per anther, and spikelet fertility in all cultivars and lines. The number of pollen grains was proportional to anther length in all cultivars and lines and under all temperatures. Spikelet fertility decreased with decreasing the number of pollen grains in cold-water treatments at 18.5 and 19.3u2009°C. ‘Ouu 415’, with the qLTB3 QTL for cold tolerance, had 28% more pollen grains and 9% higher spikelet fertility than the recurrent parent, ‘Hitomebore’, in the 18.5u2009°C cold-water treatment, suggesting that qLTB3 increased both parameters. Lines with the qCTB8 QTL for cold tolerance had significantly more pollen grains in two of the three years and significantly higher spikelet fertility in all three years in the 19.3u2009°C cold-water treatment, suggesting that qCTB8 reinforced cold tolerance. Ctb1, a proposed cold-tolerance QTL, had no effect on the number of pollen grains or spikelet fertility. In conclusion, the cultivars and lines with more pollen grains had a higher cold tolerance. Some of QTLs were inferred to increase the number of pollen grains and reinforce cold tolerance.