The multi-scale structures of rice starches from 16 recombinant inbred lines and their parents with different combinations of Wx, SSIIa and FLO2 alleles were investigated. Results indicated that the starch multi-scale structures were significantly affected by genotype, environment and genotype × environment interaction. Wx, SSIIa and FLO2 alleles and their interactions significantly affected the starch fine structure. Starches with Wxa allele had higher amylose content (AC) in different amylose chain regions (hAm,i~iii), degree of polymerization (DP) of amylose peak (XAm), Bragg long period distance (dac), but lower relative crystallinity (RC) compared with Wxb. The starches with SSIIaGC allele had higher XAm, more amylopectin B1 chains (fb1) and RC, but less A chains (fa) and dac than those of SSIIaTT. The floury2 (flo2) mutant starch displayed increased ratio of the peak heights of amylopectin (hAP2/hAP1), fb2 and dac, but decreased RC compared to the wildtype. The Wx × SSIIa interaction had a significant impact on AC, XAP1, βAm,iii, average chain length of amylopectin molecules (X¯) and RC. The interaction effects of FLO2 × Wx were significant for AC, hAm/hAp1, hAm,ii, βAm,iii, hAm,iii, RC, D and dac. Significant FLO2 × SSIIa interaction was detected for XAM, hAP2/hAP1, βAm,ii, fb1, fb3 and RC. FLO2 × Wx×SSIIa effect was significant for XAP1, hAP2/hAP1, βAm,ii, fa, fb3 and X¯. This study will help us to further understand the individual and interaction effects of the Wx, SSIIa and FLO2 and the effect of environments on the starch fine structure, but also promote high-quality rice breeding through structural modification of starch.
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