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Analysis of variation patterns in rice milled quality in the offspring of indicajaponica hybridization

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Asian cultivated rice (Oryza sativa L.) is divided into two subspecies, indica (O. sativa L. subsp. indica) and japonica (O. sativa L. subsp. japonica). Variation patterns in rice quality become more complex in the offspring produced from indica–japonica hybridization owing to interactions between inter-subspecies components. No QTLs underlying rice milled quality have been successfully cloned; hence, improving rice milled quality is a key dilemma, especially in the offspring of inter-subspecies hybridization. In this study, we analyzed variation patterns in rice milled quality caused by components introduced from indica, including both regulatory genes controlling influence factors (milled grain width and chalkiness) and the frequency of random introductions from the indica genetic backgrounds. Two populations (RILs and BILs) derived from indicajaponica hybridization were used. Both the frequency distribution value of indica components introduced (Di value) and grain-width regulatory genes (GS5 and GW5) had a significant impacted on variation in milled rice width (MRW), and their interaction accounted for the major MRW variance in RILs and BILs. The Di value had a significant impact on variation in chalkiness degree (C) in RILs and BILs; the regulatory gene Chalk5 also participated in the regulation of C in BILs. The Di value further influenced head rice rate (HR), with the average HR gradually decreasing as the Di value increased. Taken together, our results suggest that we should utilize backcrossing or multiple crosses to reduce the Di value in offspring produced by indicajaponica hybridization and promote the use of favorable genes during individual selections.

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Recombinant inbred lines


Backcross recombinant inbred lines

Di value:

Frequency distribution value of indica components introduced


Milled rice width


Chalkiness degree


Head rice rate










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This research was funded by Science Foundation of Liaoning Academy of Agricultural Sciences (2019-QN-08), Science Foundation of Liaoning Academy of Agricultural Sciences (2020-QN-2416), Science Foundation of Liaoning Province (2019-ZD-0397), and PhD research startup foundation of Liaoning Province (2020-BS-300).

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All authors have read and approved the final version of the manuscript. TM and ZZ performed most of the experiments, S-JN and Y-ZZ performed the DNA isolation and field planting, XL and L-LZ performed part of the quality analysis. YL provided the rice materials used in this study. XL designed the experiments.

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Correspondence to Xu Li.

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Mao, T., Zhan Zhang, Ni, SJ. et al. Analysis of variation patterns in rice milled quality in the offspring of indicajaponica hybridization. Genet Resour Crop Evol 68, 1785–1797 (2021).

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