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Genetic dissection of grain traits in Yamadanishiki, an excellent sake-brewing rice cultivar

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Abstract

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The grain traits of Yamadanishiki, an excellent sake-brewing rice cultivar in Japan, are governed by multiple QTLs, namely, a total of 42 QTLs including six major QTLs.

Abstract

Japanese rice wine (sake) is produced using brewing rice (Oryza sativa L.) that carries traits desirable for sake-brewing, such as a larger grain size and higher white-core expression rate (WCE) compared to cooking rice cultivars. However, the genetic basis for these traits in brewing rice cultivars is still unclear. We performed analyses of quantitative trait locus (QTL) of grain and days to heading over 3 years on populations derived from crosses between Koshihikari, a cooking rice, and Yamadanishiki, an excellent sake-brewing rice. A total of 42 QTLs were detected for the grain traits, and the Yamadanishiki alleles at 16 QTLs contributed to larger grain size. Two major QTLs essential for regulating both 100-grain weight (GWt) and grain width (GWh) were harbored in the same regions on chromosomes 5 and 10. An interaction was noted between the environment and the QTL associated with WCE on chromosome 6, which was detected in two of 3 years. In addition, two QTLs for WCE on chromosomes 3 and 10 overlapped with the QTLs for GWt and GWh, suggesting that QTLs associated with grain size also play an important role in the formation of white-core. Despite differences in the rate of grain growth in both Koshihikari and Yamadanishiki across 2 years, the WCE in Yamadanishiki remained consistent, thus demonstrating that the formation of white-core does not depend on grain filling speed. These data can be informative for programs involved in breeding better cooking and brewing rice cultivars.

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Authors and Affiliations

  1. Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, 1348 Uzurano, Kasai, Hyogo, 675-2103, Japan

    Satoshi Okada, Miki Suehiro & Masanori Yamasaki

  2. Genetic Resources Center, National Agriculture and Food Research Organization, Ibaraki, Japan

    Kaworu Ebana

  3. Institute of Crop Science, National Agriculture and Food Research Organization, Ibaraki, Japan

    Kiyosumi Hori

  4. Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan

    Akio Onogi & Hiroyoshi Iwata

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  1. Satoshi Okada
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  2. Miki Suehiro
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  3. Kaworu Ebana
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  4. Kiyosumi Hori
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  5. Akio Onogi
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  6. Hiroyoshi Iwata
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  7. Masanori Yamasaki
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Correspondence to Masanori Yamasaki.

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Communicated by Dr. Michael Thomson.

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122_2017_2977_MOESM1_ESM.pptx

Supplementary Fig. 1 Classification of chalky grains (a)-(f), with reference to Yoshioka et al. (2007). Upper row shows grayscale images of rice grains, lower row shows the corresponding binary images. (a) Perfect grain, (b) white-back grain, (c) basal-white grain, (d) white-belly, (e) white-core grain, (f) milky-white grain. (g) Brown grains of Koshihikari (upper) and Yamadanishiki (lower). (PPTX 27391 kb)

122_2017_2977_MOESM2_ESM.pptx

Supplementary Fig. 2 Histograms of each trait for 2010, 2013, and 2014. White and black arrows indicate the average trait values of Koshihikari and Yamadanishiki respectively. DTH: days to heading, GWt: 100-grains weight, GWh: grain width, GL: grain length, LWR: grain length to width ratio, WCE: white-core expression rate. (PPTX 4531 kb)

122_2017_2977_MOESM3_ESM.pptx

Supplementary Fig. 3 Transition of daily mean air temperatures in 2010, 2013, and 2014, represented by black, blue, and red lines, respectively. The black double-headed arrow around August 19 indicates the period around the average heading date of Yamadanishiki. (PPTX 469 kb)

122_2017_2977_MOESM4_ESM.pptx

Supplementary Fig. 4 Linkage maps showing the positions of QTLs that were detected by QTL analysis with the effects of Hd6 and Hd16 on DTH taken into consideration. The left and right linkage maps were generated from the F2 generation and the RIL populations respectively. Bars beside the QTLs indicate 1-LOD support CI. QTLs are named according to the following convention: “(trait name) reg(year)-(number)”, e.g. the second QTL detected in GWt from 2013 data is named “GWt reg13-2”. GWt reg: residual value of 100-grains weight, GWh reg: residual value of grain width, LWR reg: residual value of grain length to width ratio, WCE reg: residual value of white-core expression rate. (PPTX 1725 kb)

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Okada, S., Suehiro, M., Ebana, K. et al. Genetic dissection of grain traits in Yamadanishiki, an excellent sake-brewing rice cultivar. Theor Appl Genet 130, 2567–2585 (2017). https://doi.org/10.1007/s00122-017-2977-2

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