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Genetic and epistatic effects for grain quality and yield of three grain-size QTLs identified in brewing rice (Oryza sativa L.).

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Abstract

Rice (Oryza sativa L.) in Japan is not only a food staple but also an important material for the Japanese alcoholic beverage, sake. The grain used in sake brewing has different characters from the cooking rice grain, including a large grain size and high white-core expression rate (WCE). Because large-sized grains often have a heavy grain weight and higher yield, this trait is also important for cooking rice. Chalky grains, such as white-core or white-belly grains, are not ideal as cooking rice. Here, we report that three grain-size quantitative trait loci (QTLs; qGL4-2, qGWh5, qGWh10), derived from the brewing cultivar, Yamadanishiki, affect grain shape, chalky grain rate, and yield, using near isogenic and pyramiding lines in the genetic background of the cooking cultivar, Koshihikari. First, these QTLs influenced multiple components of grain shape, where epistatic effects were detected between qGL4-2 and qGWh5, for grain width and thickness, and between qGL4-2 and qGWh10, for grain length. Therefore, these QTLs may coordinate to control grain shape. Second, lines harboring qGWh5 or qGWh10 at the Yamadanishiki allele exhibited increased WCE, whereas lines with qGL4-2 and qGWh10 exhibited decreased white-belly grain rate (WBR). Thus, grain shape is associated with the occurrence of chalky grain, where the chalky type depends on the QTL. Finally, we used total panicle weight of plants as a simplified rice yield index, and a promising line pyramiding qGL4-2 and qGWh5 emerged. In conclusion, qGL4-2 would be useful for the breeding of cooking rice, to decrease WBR, while qGWh5 and qGWh10 were definitely more beneficial for that of brewing rice, to increase grain weight and WCE.

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Abbreviations

ANOVA:

Analyses of variance

BWR:

Basal-white grain rate

DTH:

Days to heading

GL:

Grain length

GT:

Grain thickness

GWh:

Grain width

MWR:

Milky white grain rate

NIL:

Near isogenic line

PN:

Panicle number

PYL:

Pyramiding line

QTL:

Quantitative trait locus

SN:

Spikelet number per panicle

TGW:

1000-grain weight

TPW:

Total panicle weight per plant

WCE:

White-core expression rate

WBR:

White-belly grain rate

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Acknowledgments

We would like to thank Miki Suehiro and Wakana Yokoyama for their help with sampling.

Funding

This work was supported by JSPS KAKENHI Grant Number 17J01082 and the Japan Science and Technology Agency (JST) CREST Grant Number JPMJCR17O3.

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Contributions

SO and MY designed experiments; SO, KI, and KH performed genotyping; SO conducted phenotyping and data analysis; and SO and MY wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Masanori Yamasaki.

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Okada, S., Iijima, K., Hori, K. et al. Genetic and epistatic effects for grain quality and yield of three grain-size QTLs identified in brewing rice (Oryza sativa L.).. Mol Breeding 40, 88 (2020). https://doi.org/10.1007/s11032-020-01166-0

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