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Genetic factors determining varietal differences in characters affecting yield between two rice (Oryza sativa L.) varieties, Koshihikari and IR64

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Abstract

The yield of Koshihikari, a Japanese premium rice variety, is relatively lower than that of modern high yielding varieties. IR64 carries several well-known genes such as GS3, an important gene for grain size, sd-1, a semi-dwarf gene, and NARROW LEAF1 (NAL1), a gene for small, narrow flag leaves. In this study, we used two sets of chromosome segment substitution lines (CSSLs), from Koshihikari and IR64, and attempted to evaluate the genetic factors that cause differences between parents by analyzing the function of chromosome regions affecting a trait (CRATs). For 28 traits, we identified 312 CRATs in the Koshihikari background and 275 in the IR64 background. In these, donor alleles had positive effects in 84 and 103 CRATs, respectively. Among these, the CRAT related to GS3 and those for grain number expanded the potential sink size in Koshihikari, although this did not affect final yield. The combination of CRATs that enhances source ability may increase grain yield. Although the sd-1 gene might improve resistance to lodging, the yield of CSSLs with sd-1 decreased by 28.7 %. These results suggest that the smaller biomass conferred by sd-1 might reduce canopy photosynthesis. In the Koshihikari background, the CRAT related to NAL1 and those located on chr. 6 increased SPAD value but had the opposite effect on leaf size. Two CRATs that were detected on chr. 6 and 7 increased leaf area without any effect on the SPAD value. The combination of these CRATs for area and SPAD value might improve source ability.

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Abbreviations

CRAT:

Chromosome region affecting a trait

CSSL:

Chromosome segment substitution line

QTL:

Quantitative trait locus

SLA:

Specific leaf area

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Acknowledgments

This study was supported by a grants from the Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics for Agricultural Innovation, RBS2004). The seeds of Koshihikari were distributed from Rice Genome Resource Center in National Institute of Agrobiological Sciences. Yamamoto and Yano received the seeds of IR64 (IRGC66970) from International Rice Research Institute on the basis of standard material transfer agreement.

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Authors and Affiliations

  1. National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan

    Kazuhiro Ujiie, Toshio Yamamoto, Masahiro Yano & Ken Ishimaru

  2. Institute of Crop Sciences, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba, Ibaraki, 305-8518, Japan

    Masahiro Yano

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  1. Kazuhiro Ujiie
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  4. Ken Ishimaru
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Correspondence to Ken Ishimaru.

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Ujiie, K., Yamamoto, T., Yano, M. et al. Genetic factors determining varietal differences in characters affecting yield between two rice (Oryza sativa L.) varieties, Koshihikari and IR64. Genet Resour Crop Evol 63, 97–123 (2016). https://doi.org/10.1007/s10722-015-0237-3

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