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

Abstract

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'.

Physical mapping of qDTH3 for heading date reveals the evolutionary history of cultivated rice

“…Once genes associated with desirable traits are introduced, they can spread to the entire population (Fujino et al 2019b). Previously, we demonstrated that major genes associated with desirable traits in elite varieties were introduced into the local gene pool, such as rice blast disease resistance Pi-cd, plant type Hd1, and eating quality SbeIIb (Fujino et al 2019b, d;Ikegaya and Ashida 2021). Understanding genetic diversity involved in local varieties may be of use in crop breeding programs for rice and other crops.…”

Three Starch Synthase IIa (SSIIa) Alleles Reveal the Effect of SSIIa on the Thermal and Rheological Properties, Viscoelasticity, and Eating Quality of Glutinous Rice

“…By contrast, the loss of BEIIb in wx ae , derived from EM16 (selected from the MNU-mutagenized population of Kinmaze), decreased the number of short amylopectin chains (DP < 15) and increased the number of long amylopectin chains (DP > 15), which in turn increased the gelatinization temperature (to 83 °C) as well as the pasting temperature [ 48 ]. Similarly, Shirokumamochi, possessing BEIIb derived from Kitaake, contains Leu94Val and His196Arg substitutions and produced harder rice cakes compared to Kitayukimochi [ 49 ], likely because of a slight reduction in BEIIb activity. Although the genetic factors affecting amylopectin branch structures in the vast majority of other glutinous rice cultivars remain unknown, the results of the present study support the idea that rice lines containing starch with fewer short amylopectin chains and more long amylopectin chains exhibit higher gelatinization and pasting temperatures and produce harder rice cakes, whereas those with starch containing more short amylopectin chains and fewer long amylopectin chains exhibit lower gelatinization and pasting temperatures and produce softer rice cakes [ 50 , 51 ].…”

Interaction between genetic regions responsible for the starch properties in non-glutinous rice varieties in Hokkaido, Japan

“…Cultivation management followed the standard procedures used at the Hokkaido Agricultural Research Center as described by Ikegaya and Ashida (2021). Sowing and transplanting were performed on 20 April and 20 May 2020, respectively.…”

“…Mutant BEI, BEIIa, and BEIIb lines have been isolated from rice (Nakamura 2002, Nishi et al 2001, Satoh et al 2003a, 2003b. Previously, starch branching enzyme IIb (SbeIIb) was identified on chromosome 2 as a candidate gene for the differences in starch properties between glutinous rice varieties in Hokkaido (Ikegaya and Ashida 2021). SbeIIb is known as an amylose extender (AE) gene.…”

“…The sbeIIb mutant showed a decreased proportion of the amylopectin short chain (degree of polymerisation [DP] < 17) and an increased proportion of the mid-length chain (DP 18-35) (Nishi et al 2001), resulting in a higher gelatinisation temperature (Jane et al 1999). The glutinous variety/line with SbeIIb sr , the genotype originating from the American variety 'Cody', showed a higher pasting temperature (PT) and higher hardness of rice flour paste under the condition of storage at 4°C for 24 h (Ikegaya and Ashida 2021). The chromosomal region, including the SbeIIb sr genotype, causes changes in the chain-length distribution of amylopectin; the proportions of short (DP 6-24) and long chains (DP 25-60) decreased and increased, respectively.…”