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'.

Keywords: Starch branching enzyme IIb; glutinous rice; local breeding population; pasting temperature; rice cake hardness.

Fig. 1.

Comparison of chain-length distribution profiles of amylopectin from ‘Kitayukimochi’ and ‘Shirokumamochi’. The difference in the profiles was calculated by subtracting the ratio of a chain of given length of ‘Kitayukimochi’ from that of the value of ‘Shirokumamochi’. Values are the means of two replicates in 2012 and 2013, respectively.

Fig. 2.

Genetic map around the QTL. A. Additional genetic mapping of F₃ recombinants and progeny testing. Recombinants between marker loci FA2431 and FA2438 were selected from 96 F₂ plants. White bars indicate homozygous ‘Kitayukimochi’ and black bars indicate homozygous ‘Shirokumamochi’. Each pairing of No. 25 & 24, 12 & 13, and 66 & 65 originated from the same F₂ recombinant individual. * and ** mean 1% and 0.1% sufficiency according to t-test, respectively. B. Schematic diagrams of SbeIIb gene. Open and black boxes indicate untranslated regions and exons, respectively. Letters indicate DNA sequences of exons and introns, respectively. Translated amino acids are shown under the DNA sequence. Substituted nucleotides and amino acids are shown by red letters.

Fig. 3.

Band patterns of digested DNA. Amplicon lengths are indicated on the right. M means size marker. KY: ‘Kitayukimochi’, SR: ‘Shirokumamochi’, H: Hetero.

Fig. 4.

The pedigree of ‘Kitayukimochi’ and ‘Shirokumamochi’. Gray boxes indicate glutinous rice, and white boxes indicate non-glutinous rice. Letters represent the results genotyped by CAPS marker SbeIIb Ex3-1. KY and SR represent the genotype of ‘Kitayukimochi’ and ‘Shirokumamochi’, respectively. ND means ‘not determined’. The thick black lines indicate the way SbeIIb^sr was inherited.