Abstract
Two major nuclear genes, Rf3 and Rf4, are known to be associated with fertility restoration of wild-abortive cytoplasmic male sterility (WA-CMS) in rice. In the present study, through a comparative sequence analysis of the reported putative candidate genes, viz. PPR9-782-(M,I) and PPR762 (for Rf4) and SF21 (for Rf3), among restorer and maintainer lines of rice, we identified significant polymorphism between the two lines and developed a set of PCR-based codominant markers, which could distinguish maintainers from restorers. Among the five markers developed targeting the polymorphisms in PPR9-782-(M,I), the marker RMS-PPR9-1 was observed to show clear polymorphism between the restorer (n = 120) and maintainer lines (n = 44) analyzed. Another codominant marker, named RMS-PPR762 targeting PPR762, displayed a lower efficiency in identification of restorers and maintainers, indicating that PPR9-782-(M,I) is indeed the candidate gene for Rf4. With respect to Rf3, a codominant marker, named RMS-SF21-5 developed targeting SF21, displayed significantly lower efficiency in identification of restorers and non-restorers as compared to the Rf4-specific markers. Validation of these markers in a F2 mapping population segregating for fertility restoration indicated that Rf4 has a major influence on fertility restoration and Rf3 is a minor gene. Further, the functional marker RMS-PPR9-1 was observed to be very useful in identification of impurities in a seed lot of the popular hybrid, DRRH3. Interestingly, when RMS-PPR9-1 and RMS-SF21-5 were considered in conjunction with analysis, near-complete, marker–trait co-segregation was observed, indicating that deployment of the candidate gene-specific markers both Rf4 and Rf3, together, can be helpful in accurate identification of fertility restorer lines and can facilitate targeted transfer of the two restorer genes into elite varieties through marker-assisted breeding.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Ahmadikhah A, Karlov GI (2006) Molecular mapping of the fertility-restoration gene Rf4 for WA-cytoplasmic male sterility in rice. Plant Breed 125:363–367
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Balaji S, Vemireddy LR, Srikanth B, Dharika N, Sambasiva Rao KRS, Hemanth Kishore V, Sundaram RM, Viraktamath BC, Subhakara Rao I, Ramesha MS, Neeraja CN (2012) Fine mapping of Rf3 and Rf4 fertility restorer loci of WACMS of rice (Oryza sativa L.) and validation of the developed marker system for identification of restorer lines. Euphytica 187:421–435
Bharaj TS, Bains SS, Sidhu GS, Gagneja MR (1991) Genetics of fertility restoration of ‘Wild Abortive’ cytoplasmic male sterility in rice (Oryza sativa L.). Euphytica 56:199–203
Bharaj TS, Virmani SS, Khush GS (1995) Chromosomal location of fertility restoring genes for wild abortive cytoplasmic male sterility using primary trisomics in rice. Euphytica 83:169–173
Cai J, Liao QP, Dai ZJ, Zhu HT, Zeng RZ, Zhang ZM, Zhang ZM (2013) Allelic differentiations and effects of the Rf3 and Rf4 genes on fertility restoration in rice with wild abortive cytoplasmic male sterility. Biol Plant 57:274–280
Cai J, Dai ZJ, Zhu HT, Zeng RZ, Zhang ZM, Ma TF, Zhang GQ (2014) Comparitive analysis of fertility restoaration genes for WA, Y, and DA cytoplasmic male sterility in rice. Biol Plant 58:241–246
Dellaporta RP, Wood J, Hicks JD (1983) A plant DNA mini preparation: version II. Plant Mol Biol Rep 1:19–21
Gomez KA, Gomez AA (1984) Statistical procedures for agricultural research, 2nd edn. Wiley, New York
Govinda Raj K, Virmani SS (1988) Genetics of fertility restoration of WA type cytoplasmic male sterility in rice. Crop Sci 28:787–792
Hall T (2007) BioEdit version 7.0.9. Carlsbad: Computer Program and documentation, Ibis Biosciences. http://www.mbio.ncsu.edu/BioEdit/bioedit.html
Higgins D, Thompson J, Gibson Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Kazama T, Toriyama K (2014) A fertility restorer gene, Rf4, widely used for hybrid rice breeding encodes a pentatricopeptide repeat protein. Rice 7:28
Li YC, Yuan LP (1986) Genetic analysis of fertility restoration in male sterile lines of rice. In: IRRI (ed) Rice genetics. Hybrid rice/proceedings of the IRG symposium. IRRI, Manila, pp 617–632
Lin SC, Yuan LP (1980) Hybrid rice breeding in China. In: IRRI (ed) Innovative approaches to rice breeding. International Rice Research Institute, Manila, pp 35–51
Nandakumar N, Singh AK, Sharma RK, Mohapatra T, Prabhu KV, Zaman FU (2004) Molecular fingerprinting of hybrids and assessment of genetic purity of hybrid seeds in rice using microsatellite markers. Euphytica 136:257–264
Nas TMS, Casal CL, Li Z, Virmani SS (2003) Application of molecular markers for identification of restorers. Rice Genet Newsl 20:69–71
Ngangkham U, Parida SK, De S, Anand Raj Kumar K, Singh AK, Singh SK, Mohapatra T (2010) Genic markers for wild abortive (WA) cytoplasm based male sterility and its fertility restoration in rice. Mol Breeding 26(2):275–292
Pranathi K, Viraktamath BC, Neeraja CN, Balachandran SM, Hariprasad AS, Koteswara Rao P, Kulkarni SR, Senguttuvel P, Hajira SK, Balachiranjeevi CH, Bhaskar Naik S, Abhilash V, Anila M, Mahadevaswamy HK, Rekha G, Madhav MS, Revathi P, Harika G, Dilip T, Kemparaju B, Sundaram RM (2016) Comparative analysis of sequences of mitochondrial genomes of wild abortive male sterile (WA-CMS) and male fertile lines of rice, development of functional markers for WA-CMS trait and their use in assessment of genetic purity of seeds of WA-CMS lines. Mol Breeding 36:21
Rajendrakumar P, Biswal AK, Balachandran SM, Ramesha MS, Viraktamath BC, Sundaram RM (2007) A mitochondrial repeat specific marker for distinguishing wild abortive type cytoplasmic male sterile rice lines from their cognate isogenic maintainer lines. Crop Sci 47:207–211
Sattari M, Kathiresan A, Gregorio GB, Hernandez JE, Nas TM, Virman SS (2007) Development and use of a two-gene markeraided selection system for fertility restorer genes in rice. Euphytica 153:35–42
Sattari M, Kathiresan A, Glenn B, GregorioS Virmani S (2008) Comparative genetic analysis and molecular mapping of fertility restoration genes for WA, Dissi, and Gambiaca cytoplasmic male sterility systems in rice. Euphytica 160:305–315
Sheeba NK, Viraktamath BC, Sivaramakrishnan S, Gangashetti MG, Khera P, Sundaram RM (2009) Validation of molecular markers linked to fertility restorer gene(s) for WA-CMS lines of rice. Euphytica 167:217–227
Singh AK, Mahapatra T, Prabhu KV, Singh VP, Zaman FU, Mishra GP, Nandakumar N, Joseph M, Gopalakrishnan S, Aparajita G, Tyagi NK, Prakash P, Sharma RK, Shab US, Singh SK (2005) Application of molecular markers in rice breeding: progress at IARI. In: Advances in marker assisted selection workshop. Trainee’s manual, Handouts and references
Sundaram RM, Naveenkumar B, Biradar SK et al (2008) Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment. Euphytica 63:215–224
Tang H, Luo D, Zhou D, Zhang Q, Tian D, Zheng X, Chen L, Liu YG (2014) The rice restorer Rf4 for wild-abortive cytoplasmic male sterility encodes a PPR protein that functions in reduction of WA352 transcripts. Mol Plant 7:1497–1500
Teng LS, Shen ZT (1994) Inheritance of fertility restoration for cytoplasmic male sterility in rice. Rice Genet Newsl 11:95–97
Virmani SS (1996) Hybrid rice. Adv Agron 57:377–462
Virmani SS, Wan BH (1988) Development of CMS lines in hybrid rice breeding. In: IRRI (ed) Hybrid rice. International Rice Research Institute, Manila, pp 103–114
Virmani SS, Raj KG, Casal C, Dalmacio RD and Aurin PA (1986) Current knowledge of and outlook on cytoplasmic-genetic male sterility and fertility restoration in rice. In: IRRI (ed) Rice genetics proceedings of the international rice genetic symposium IRRI, Manila, pp 633–648
Yao FY, Xu CG, Yu SB, Li JX, Gao YJ, Li XH, Zhang Q (1997) Mapping and genetic analysis of two fertility restorer loci in the wild-abortive cytoplasmic male sterility system of rice (Oryza sativa L). Euphytica 98:183–187
Yashitola J, Thirumurugan T, Sundaram RM, Naseerullah MK, Ramesha MS, Sarma NP, Sonti RV (2002) Hybrids using microsatellite and STS markers. Crop Sci 42:1369–1373
Young JB, Virmani SS (1984) Inheritance of fertility restoration in a rice cross. Rice Genet Newsl 1:102–103
Zhang Q, Bharaj TS, Virmani SS, Huang H (1997) Mapping of the Rf3 nuclear fertility restoring gene for WA cytoplasmic male sterility in rice using RAPD and RFLP markers. Theor Appl Genet 94:27–33
Zheng KL, Subudhi PK, Dmingo J, Magpantag G, Huang N (1995) Rapid DNA isolation for marker assisted selection in rice breeding. Rice Genet Newsl 12:255–257
Acknowledgments
K. Pranathi would like to thank Department of Science and Technology (DST), Government of India, for the INSPIRE fellowship awarded for Ph.D. studies. The authors would also like to thank the Indian Council of Agricultural Research and Department of Biotechnology, Government of India, for the generous funding support for the research work presented in the study.
Author information
Authors and Affiliations
Corresponding author
Additional information
K. Pranathi and R. M. Sundaram have contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Pranathi, K., Viraktamath, B.C., Neeraja, C.N. et al. Development and validation of candidate gene-specific markers for the major fertility restorer genes, Rf4 and Rf3 in rice. Mol Breeding 36, 145 (2016). https://doi.org/10.1007/s11032-016-0566-8
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11032-016-0566-8