Genetic region responsible for the differences of starch properties in two glutinous rice cultivars in Hokkaido, Japan

Starch properties are major determinants of grain quality and food characteristics in rice (Oryza sativa L.). Control of starch properties will lead to the development of rice cultivars with desirable characteristics. We performed quantitative trait locus analysis and detected a putative region on chromosome 2 associated with phenotypic variation of starch properties in two glutinous rice varieties developed in the Hokkaido region of Japan: ‘Kitayukimochi’, which has a low pasting temperature and creates soft rice cakes, and ‘Shirokumamochi’, which has a high pasting temperature and creates hard rice cakes. Starch branching enzyme IIb (SbeIIb) was identified as a candidate gene within the region. Sequence analysis of SbeIIb in parental lines identified two single-nucleotide polymorphisms (SNPs) with non-synonymous mutations in the coding region of the ‘Shirokumamochi’ genotype (SbeIIb(sr)). We genotyped over 100 rice cultivars, including 28 rice varieties in the Honshu region of Japan, using the CAPS marker, which was designed using one of the SNPs. However, SbeIIb(sr) was not found in rice cultivars in Honshu. Distribution analysis indicated that SbeIIb(sr) was introduced to the rice breeding population in Hokkaido from the American variety ‘Cody’ via the Hokkaido cultivar ‘Kitaake’. As a result, SbeIIb(sr) was distributed only in progenies of ‘Kitaake’.