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Identification of QTLs and candidate genes for days to heading in an upland New Rice for Africa (NERICA) variety

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Abstract

To produce rice varieties adaptable to unfavorable environments in Africa, New Rice for Africa (NERICA) varieties have been developed by inter-specific crossings. The basic idea of NERICA was to combine the useful characteristics of the African rice species Oryza glaberrima and an Asian rice species, Oryza sativa. However, the genetic basis of the agronomic characteristics of NERICA varieties is not fully understood. We performed a QTL analysis to examine the genetic basis of days to heading (DTH) in an upland variety, NERICA10. We found that NERICA10 had weaker photoperiod sensitivity (PS) and shorter DTH under long day-length conditions than its parental varieties. We then examined QTLs controlling DTH under natural long-day-length conditions by using segregating populations. We found three QTLs for DTH, on chromosomes 4, 6, and 8. Among them, qDTH8.1, located on chromosome 8, had the strongest effect. By comparing nucleotide sequences, we found that NERICA10 had a loss of the functional allele of DTH8, which was located in the candidate region of qDTH8.1. These results suggested that loss of function of DTH8 is the causal factor of weakened PS in NERICA10. The information on these QTLs will be useful for improving rice varieties for better adaption to African conditions.

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Acknowledgments

Y.K. thanks Drs. N. Kobayashi, D. Fujita, T. Abiko, K. Matsubara, K. Onishi, and N. Uwatoko for their invaluable suggestions and warm encouragement. This paper reports the results obtained in the JIRCAS projects “Development of rice production technologies in Africa” and “Rice innovation for environmentally sustainable production systems.” Financial support was also provided by a Research Fellowship of the Japan Society for the Promotion of Science for Young Scientists (22-6429 to Y.K.).

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Author notes

  1. Akiko Kawasaki-Tanaka

    Present address: Tottori University, 4-101 Koyama-Minami Tottori, Tottori, 680-8553, Japan

Authors and Affiliations

  1. Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi 1-1, Tsukuba, Ibaraki, 305-8686, Japan

    Yohei Koide, Akiko Kawasaki-Tanaka, Mitsuhiro Obara, Seiji Yanagihara & Yoshimichi Fukuta

  2. Hakubi Center for Advanced Research/Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan

    Yohei Koide

  3. Faculty of Agricultural Science, University of Abomey-Calavi, 01BP526, Cotonou, Benin

    Theophile Odjo

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  1. Yohei Koide
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Correspondence to Yoshimichi Fukuta.

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Fig. S1

Nucleotide sequences of CDS of Hd3a in NERICA10 and CG 14. The position of SNP was shown in a box (PDF 333 kb)

Fig. S2

Nucleotide sequences of exon1 of RFT1 in NERICA10, WAB56-104, and CG 14 (PDF 345 kb)

Supplementary material 3 (XLSX 17 kb)

Supplementary material 4 (XLSX 15 kb)

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Koide, Y., Kawasaki-Tanaka, A., Odjo, T. et al. Identification of QTLs and candidate genes for days to heading in an upland New Rice for Africa (NERICA) variety. Euphytica 203, 153–164 (2015). https://doi.org/10.1007/s10681-014-1289-8

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  • DOI: https://doi.org/10.1007/s10681-014-1289-8

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