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qAC2, a novel QTL that interacts with Wx and controls the low amylose content in rice (Oryza sativa L.)

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This manuscript reports the fine mapping of a novel QTL, qAC2 controlling the low amylose in rice. The action mechanism of the qAC2 is also investigated by the analysis of genetic interactions to Wx a, Wx b, du1, du2 and du3.


Amylose content of the rice (Oryza sativa L.) endosperm greatly affects starch properties and eating quality of cooked rice. Seeds of japonica rice cultivar Kuiku162 have low amylose content (AC) and good eating quality. Our analysis revealed a novel QTL, designated as qAC2 that contributed to the low AC of Kuiku162. qAC2 was fine mapped within a 74.9-kb region between two insertion and deletion markers, KID3001 and KID5101, on the long arm of chromosome 2. Seven genes are predicted in this region, but none of them is known to be related to the regulation of AC. The AC of a near-isogenic line (NIL110) carrying qAC2 Kuiku, the Kuiku162 allele of qAC2, in the genetic background of japonica cultivar Itadaki was lower by 1.1 % points than that of Itadaki. The chain length distributions of amylopectin were similar in NIL110 and Itadaki; therefore, the low AC of NIL110 was caused by a decrease in the actual AC, but not by a difference in the amylopectin structure. The interaction analyses revealed that qAC2 Kuiku has epistatic interaction with Wx a. The qAC2 Kuiku has epistatic interactions with two loci, du1 and du2, on Wx b, whereas the genetic effect of qAC2 Kuiku has additive to that of du3 on Wx b. Thus, similar to du1 and du2, qAC2 may have a function related to Wx b mRNA splicing.

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We thank Dr. T. Kumamaru (Kyushu University), for providing EM2, EM12 and EM23 seeds, and the local independent administrative agency Hokkaido Research Organization for providing Kuiku162 seeds. We thank Y. Yabuki, R. Mikami, and S. Kinoshita for their technical assistance. This work was supported by a Grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Integrated research project for plant, insect and animal using genome technology, QT2011, DM1001 and DM1002, Genomics for Agricultural Innovation, QTL4010, and Genomics-based Technology for Agricultural Improvement, RBS2011).

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Correspondence to Yoshinobu Takeuchi.

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Communicated by Yunbi Xu.

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Figure S1 Breeding scheme for the development of materials for QTL mapping, high-resolution mapping, NIL evaluation and genetic interaction analysis (DOCX 168 kb)


Figure S2 Frequency distribution of amylose content in 125 BC3F2 plants. White arrow indicates the mean value for Itadaki. Horizontal line under the arrow indicates SD (DOCX 466 kb)

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Takemoto-Kuno, Y., Mitsueda, H., Suzuki, K. et al. qAC2, a novel QTL that interacts with Wx and controls the low amylose content in rice (Oryza sativa L.). Theor Appl Genet 128, 563–573 (2015).

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