Low-temperature germination is one of the major determinants for stable stand establishment in the direct seeding method in temperate regions, and at high altitudes of tropical regions. Quantitative trait loci (QTLs) controlling low-temperature germinability in rice were identified using 122 backcross inbred lines (BILs) derived from a cross between temperate japonica varieties, Italica Livorno and Hayamasari. The germination rate at 15 degrees C was measured to represent low-temperature germination and used for QTL analysis. The germination rate at 15 degrees C for 7 days of Italica Livorno and Hayamasari was 98.7 and 26.8%, respectively, and that of BILs ranged from 0 to 83.3%. Using restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers, we constructed a linkage map which corresponded to about 90% of the rice genome. Three putative QTLs associated with low-temperature germination were detected. The most effective QTL, qLTG-3-1 on chromosome 3, accounted for 35.0% of the total phenotypic variation for low-temperature germinability. Two additional QTLs, qLTG-3-2 on chromosome 3 and qLTG-4 on chromosome 4, were detected and accounted for 17.4 and 5.5% of the total phenotypic variation, respectively. The Italica Livorno alleles in all detected QTLs increased the low-temperature germination rate.

Plant breeding programs in local regions may have genetic and phenotypic variations that are desirable and shape adaptability during the establishment of local populations. Despite the characterization of genetic population structures in various kinds of populations, the effects of variations in phenotype on agro-economical traits currently remain unclear. In the present study, we evaluated phenotypic changes in 26 agro-economical traits among the local population during rice breeding programs in Hokkaido. Wide variations were observed in all 26 agro-economical traits with continuous distributions. In order to elucidate improvements in these agro-economic traits during rice breeding programs in Hokkaido, values were compared between genetic population structures. Traits were classified into four patterns based on the timing of significant differences. Patterns A and B showed significant differences once and twice, respectively. Pattern C gradually showed significant differences. Pattern D showed no significant differences for the desired directions. Based on the changes in phenotype observed in the present study and the genetic population structure for the local population in Hokkaido, a model of the artificial selection for phenotypes in genetic diversity among the local population during plant breeding programs has been proposed.

Low-temperature is one of the most common environmental stresses that affect plant growth and development and places a major limit on plant productivity. Tolerance to low-temperature is an important objective of rice breeding programs in temperate areas and at high altitudes in tropical and sub-tropical areas. Vigorous rice growth during the seedling stage at low-temperature is an important characteristic for stable seedling establishment (SES) in direct seeding methods, in which rice is sown directly into a flooded field. The aim of this study was to identify QTLs controlling SES using 3 mapping populations of backcrossed inbred lines (BILs) with Arroz Da Terra and Italica Livorno as the donor parents. SES was evaluated by a field evaluation system in this study, which is used in current rice breeding programs because of the complexity of environmental conditions in SES in rice cultivation in a paddy field. A total of 9 chromosomal regions for SES were identified, which explained 10.9% to 25.6% of total phenotypic variation. For all of QTLs except for qSES5-2, alleles from the donor parents increased phenotypic values. These QTLs should be useful for the improvement of SES in rice breeding programs in low-temperature regions.

Improving the eating quality of cooked rice has been one of the most important objectives in rice breeding programs. Eating quality of cooked rice is a complex trait including several components, such as external appearance, taste, aroma, and texture. Therefore, dissection of these components followed by marker-assisted selection of detected QTL(s) may be a useful approach for achieving desirable eating quality in rice breeding. Whiteness of cooked rice (WCR) is an important factor related to the external appearance of cooked rice. WCR is known to be associated with the amylose and protein contents of the endosperm. However, the genetic basis of WCR remains unclear. In this study, we evaluated phenotypic variation in WCR among recently developed rice cultivars from Hokkaido, Japan. Then, we developed doubled haploid lines (DHLs) derived from a cross between two cultivars from Hokkaido, Joiku No. 462 (high WCR) and Jokei06214 (low WCR). Using the DHLs, we detected two QTLs for WCR, qWCR3 and qWCR11, on chromosomes 3 and 11, respectively. We also examined the dosage effect of the two QTLs based on both the categorized segregants in the DHLs and the relationship between the WCR phenotype and inheritance around the QTL regions in cultivars from Hokkaido.

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