Allelic effects on starch structure and properties of six starch biosynthetic genes in a rice recombinant inbred line population

Abstract

Background: The genetic diversity of six starch biosynthetic genes (Wx, SSI, SSIIa, SBEI, SBEIIa and SBEIIb) in indica and japonica rices opens an opportunity to produce a new variety with more favourable grain starch quality. However, there is limited information about the effects of these six gene allele combinations on starch structure and properties. A recombinant inbred line population from a cross between indica and japonica varieties offers opportunities to combine specific alleles of the six genes.

Results: The allelic (indica vs japonica) effects of six starch biosynthetic genes on starch structure, functional properties, and abundance of granule bound proteins in rice grains were investigated in a common genetic background using a recombinant inbred line population. The indica Wx (Wxi) allele played a major role while indica SSI (SSIi), japonica SSIIa (SSIIaj) and indica SBEI (SBEIi) alleles had minor roles on the increase of amylose content. SSIIaj and japonica SBEIIb (SBEIIbj) alleles had a major and a minor role on high ratio of ∑DP ≤ 10 to ∑DP ≤ 24 fractions (RCL10/24), respectively. Both major alleles (Wxi and SSIIaj) reduced peak viscosity (PV), onset, peak and end gelatinization temperatures (GTs) of amylopectin, and increased amylose-lipid complex dissociation enthalpy compared with their counterpart-alleles, respectively. SBEIIai and SBEIIbj decreased PV, whereas SSIi and SBEIIbj decreased FV. SBEIi reduced setback viscosity and gelatinization enthalpy. RCL10/24 of chain length distribution in amylopectin is negatively correlated with PV and BD of paste property and GTs of thermal properties. We also report RILs with superior starch properties combining Wxi, SSIj, SSIIaj, SBEIi and SBEIIbj alleles. Additionally, a clear relation is drawn to starch biosynthetic gene alleles, starch structure, properties, and abundance of granule bound starch biosynthetic enzymes inside starch granules.

Conclusions: Rice Wxi and SSIIaj alleles play major roles, while SSIi, SBEIi, SBEIIai and SBEIIbj alleles have minor roles in the determination of starch properties between indica and japonica rice through starch structural modification. The combination of these alleles is a key factor for starch quality improvement in rice breeding programs. RCL10/24 value is critical for starch structure and property determination.

Keywords: DSC; RVA; Rice; Starch; Starch branching enzymes; Starch property; Starch synthases.

Figure 1

Generation of RILs for each of two alleles of six starch synthetic genes. Six genes for genotyping of alleles are Wx, SSI, SSIIa, SBEI, SBEIIa, SBEIIb. Parental lines are IR64 and Nipponbare. The arrows indicate descendants of each line. The numbers with slash line indicate the name of each line. The numbers following ‘F’ imply the generation on the left of the figure. The italic letters followed by ‘i’ or ‘j’ (indicating indica and japonica, respectively) indicate alleles of the RILs.

Figure 2

Comparison of amylose content among 12 alleles of six starch synthetic genes using the SEC method. Starches from five plants of each allele were isolated and analysed seperately. Two replicates were set up for each sample. The columns indicate starch AC of RIL grains. Black columns indicate those allelles containing Wxi allele and grey columns indicate those allelles containing Wxj allele. The error bars show the standard error of the mean. The identity of each column is indicated underneath. Columns with different letters are significantly different at p < 0.05.

Figure 3

Comparison of chain length distribution of debranched starch of six allele groups for six starch synthetic genes. Starches from five plants of each allele were used for the analysis. Two replicates were set up for each sample. For each allele group, values of chain lengths for japonica allele lines were subtracted from values of chain length for the indica allele lines. A: Wx, B: SSI, C: SSIIa, D: SBEI, E: SBEIIa, F: SBEIIb. Each bar corresponds to the difference of a chain length in mole percentage. The error bars are the standard errors.

Figure 4

Analysis of starch GBPs in mature rice grain starch of RILs from six allele graoups of six starch synthetic genes by SDS-PAGE. Starches from five RIL lines of each allele were used. Section A: Wx allele group, B: SSI allele group, C: SSIIa allele group, D: SBEI allele group, E: SBEIIa allele group, F: SBEIIb allele group. The molecular sizes are labelled on the left of protein marker bands in kDa. The identity of each protein band in the samples is indicated on the right side of the pictures by an arrow head.

Figure 5

Immunodetection analysis of GBPs of purified starch from mature rice grains. A, parental lines; B and C, selected RIL lines. The names of alleles are labelled on top of each lane for Wxj (3-14-13), Wxi (3-14-12), SSIIaj (3-6-1) and SSIIai (3-6-9). The estimated molecular weight of protein bands are shown on the left. The protein bands detected by various antibodies are indicated by arrows on the right.’Nip’ is the abbreviation for Nipponbare.