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Fine mapping of Rf3 and Rf4 fertility restorer loci of WA-CMS of rice (Oryza sativa L.) and validation of the developed marker system for identification of restorer lines

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Abstract

The Wild Abortive (WA) system is the major cytoplasmic male sterility (CMS) source for hybrid rice production in indica rice and its fertility restoration is reported to be controlled by two major loci viz. Rf3 on chromosome 1 and Rf4 on chromosome 10. With the availability of the rice genome sequence, an attempt was made to fine map, develop candidate gene based markers for Rf3 and Rf4 and validate the developed marker system in a set of known restorer lines. Using polymorphic markers developed from microsatellite markers and candidate gene based markers from Rf3 and Rf4 loci, local linkage maps were constructed in two mapping populations of ~1,500 F2 progeny from KRH2 (IR58025A/KMR3R) and DRRH2 (IR68897A/DR714-1-2R) hybrids. QTLs and their interactions for fertility restoration in Rf3 and Rf4 loci were identified. The identified QTL in both mapping populations together explained 66–72 % of the phenotypic variance of the trait suggesting their utility in developing a marker system for identification of fertility restorers for WA-CMS. Sequence comparison of the two candidate genes from the Rf3 and Rf4 regions in male sterile (A) and restorer (R) lines showed 2–3 bp indels and a few substitutions in the Rf3 region and indels of 327 and 106 bp in the Rf4 region respectively. The marker system identified in the present study was validated in 212 restorers and 34 maintainers along with earlier reported markers for fertility restoration of WA-CMS. Together DRCG-RF4-14 and DRCG-RF4-8 for the Rf4 locus and DRRM-RF3-5/DRRM-RF3-10 for the Rf3 locus showed a maximum efficiency of 92 % for identification of restorers.

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Acknowledgments

The authors thank Department of Science and Technology, Government of India for the research grant and the two reviewers for suggestions and improvements.

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Authors and Affiliations

  1. Crop Improvement Section, Directorate of Rice Research, Rajendranagar, Hyderabad, 500030, India

    P. Balaji Suresh, B. Srikanth, V. Hemanth Kishore, I. Subhakara Rao, N. Dharika, R. M. Sundaram, M. S. Ramesha, B. C. Viraktamath & C. N. Neeraja

  2. Institute of Biotechnology, Acharya NG Ranga Agricultural University, Hyderabad, 500030, India

    L. R. Vemireddy

  3. Center for Biotechnology, Acharya Nagarjuna University, Guntur, AP, India

    K. R. S. Sambasiva Rao

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  1. P. Balaji Suresh
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  2. B. Srikanth
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  3. V. Hemanth Kishore
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  4. I. Subhakara Rao
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  10. B. C. Viraktamath
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Correspondence to C. N. Neeraja.

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Balaji Suresh, P., Srikanth, B., Hemanth Kishore, V. et al. Fine mapping of Rf3 and Rf4 fertility restorer loci of WA-CMS of rice (Oryza sativa L.) and validation of the developed marker system for identification of restorer lines. Euphytica 187, 421–435 (2012). https://doi.org/10.1007/s10681-012-0737-6

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