Mapping and validation of markers linked to Rf gene in sweet pepper (Capsicum annuum var grossum)

  • Manoj Kumar Nalla Division of Vegetable Science, ICAR-IARI, New Delhi 110012. 2Division of Germplasm Evaluation, ICAR-NBPGR, New Delhi 110012.
  • Vinod Kumar Sharma Division of Vegetable Science, ICAR-IARI, New Delhi 110012. 2Division of Germplasm Evaluation, ICAR-NBPGR, New Delhi 110012.
  • Vinukonda Rakesh Sharma Division of Vegetable Science, ICAR-IARI, New Delhi 110012. 2Division of Germplasm Evaluation, ICAR-NBPGR, New Delhi 110012.


Cytoplasmic male sterility (CMS), is the most valuable system in commercial hybrid seed production in hot pepper. Whereas in sweet pepper (Capsicum annuum var grossum), the unavailability of a stable restorer’s line is one of the major constraints in commercial hybrid breeding. Identifying the markers linked to CMS and nuclear restorer-of-fertility (Rf) genes will help in the production of CMS hybrids in sweet pepper. In the present study, we identified seven markers co-segregating with Rf genes using bulk segregating analysis (BSA) on the F2 Rf-segregating mapping population. Among these, the CRF-SCAR marker proved to be linked to the fertility restorer gene and it could be used for screening of genotypes to identify restorers and non-restorer lines in future Capsicum breeding programs and help in the establishment of CMS system for commercial hybrid seed production.


Alsebaeai, M., A.K. Chauhan, Arvind and P. Yadav. 2020. Consumption of Green Chilli and Its Nutritious Effect on Human Health. In: Mishra P., Mishra R.R., Adetunji C.O. (eds) Innovations in Food Technology. Springer, Singapore. 373-384.
Bueckmann, H., K. Thiele, A. Huesken and J. Schiemann. 2014. Influence of Air Temperature on the Stability of Cytoplasmic Male Sterility (CMS) in Maize (Zea mays L.). Ag. Bio. Forum. 17: 205-212.
Chang, C. T., C.G. Wang, C.B. Chen, F. Wu and D.L. Sun. 2005. Identification of molecular markers linked to the fertility restoring gene for the CMS (Capsicum annuum L.)Shi Yan Sheng Wu Xue Bao. 38(3): 227-232.
Chaudhari, S., A.N. Tikle, Uttamchand, K.B. Saxena and A. Rathore. 2015. Stability of Cytoplasmic Genetic Male Sterility and Fertility Restoration in Pigeonpea. J. Crop. Impr. 29(3): 269-280.
Chen, L. and Y.G. Liu. 2014. Male sterility and fertility restoration in crops. Annu. Rev. Plant. Biol. 65: 579–606.
Dhaliwal, M.S. and S.K. Jindal. 2014. Induction and exploitation of nuclear and cytoplasmic male sterility in pepper (Capsicum spp.): A review. J. Hortic. Sci. Biotechnol. 89(5): 471-479.
Govindaraj, K. and S. S. Virmani. 1988. Genetics of fertility restoration of ‘WA’ type cytoplasmic genic male sterility in rice. Crop Sci. 28: 787-792.
Gulyas, G., K. Pakodzi, J. S. Lee and Y. Hirata. 2006. Analysis of fertility restoration by using cytoplasmic red pepper (Capsicum annuum L.) lines. Breeding Sci. 56: 331-334. DOI:10.1270/JSBBS.56.331
Jessy, M.K.K., D. C. L. Reddy, Y.B. Manoj and K. M. Reddy. 2020. Validation of Molecular Markers Genetically Linked to S-Cytoplasm and Restoration-of-fertility (Rf) loci in Hot Pepper (Capsicum annuum L.). J. Horti. Sci. 15(1): 52-61. DOI:
Jo, Y. D., Y. Ha, J. H. Lee, M. Park, A. C. Bergsma, S. Goritschnig, B. Kloosterman, V. P. J. Dijk, D. Choi and B. C. Kang. 2016. Fine mapping of Restorer‑of‑fertility in pepper (Capsicum annuum L.) identified a candidate gene encoding a pentatricopeptide repeat (PPR) containing protein. Theo. Appl. Genet. 129(10): 2003-2017. DOI: 10.1007/s00122-016-2755-6
Jo, Y. D., Y. M. Kim, M.N. Park, J. H. Yoo, M. Park, B.D. Kim and B.C. Kang. 2010. Development and evaluation of broadly applicable markers for Restorer-of-fertility in pepper. Mol. Breed. 25: 187-201.
Kim, D. H. and B. D. Kim. 2006. The organization of mitochondrial atp6 gene region in male fertile and CMS lines of pepper (Capsicum annuum L.). Curr. Genet. 49: 59-67.
Kim, D. S. 2005. Development of RAPD and AFLP markers linked to fertility restorer (Rf) gene in chili pepper (Capsicum annuum L.). (Doctoral dissertation), Seoul National University
Kim, Y. M., Y. D. Jo, J. K. Kwon, I. T. Kim and B. C. Kang. 2013. Characterization and inheritance of a novel thermo-sensitive restoration of cytoplasmic male sterility in Capsicum annuum. Sci. Hortic. 164: 512-520.
Kosambi, D. D. 1944. The estimation of map distance. Ann. Eugenics. 12: 505-525.
Kumar, S., V. Singh, M. Singh, S. Rai, S. Kumar, S. K. Rai and M. Rai. 2007. Genetics and distribution of fertility restoration associated RAPD markers in inbreds of pepper (Capsicum annuum L.). Sci. Horti. 111: 197-202. DOI:10.1016/j.scienta.2006.10.021
Lander, E. S., P. Green, J. Abrahamson, A. Barlow, M. J. Daly, S. E. Lincoln and L. Newburg. 1987. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. 1(2):174-181.
Lee, H. R., H. J. An, D. C. Yang, S. H. Choi, H. J. Kim, H. G. Rhee and Harn, C. H. 2012. Development of a high resolution melting (HRM) marker linked to genic male sterility in Capsicum annuum L. Plant. Breed. 131: 444-448.
Lee, J., J. B. Yoon, and H. G. Park. 2008a. A CAPS marker associated with the partial restoration of cytoplasmic male sterility in chili pepper (Capsicum annuum L.). Mol. Breed. 21: 95-104. doi:10.1007/s11032-007-9111-0
Lee, J., J. B. Yoon, and H. G Park. 2008b. Linkage analysis between the partial restoration (pr) and the restorer-of-fertility (Rf) loci in pepper cytoplasmic male sterility. Theo. Appl. Genet. 117: 383-389.
Lin, S.W., H.C. Shieh, Y.W. Wang, C.W. Tan, R. Schafleitner, W.J. Yang and S. Kumar. 2015. Restorer breeding in sweet pepper: Introgressing Rf allele from hot pepper through marker–assisted backcrossing. Sci. Hortic. 197: 170-175.
Lin, S.W., S. C. Shieh, Y.W. Wang, C. W. Tan, R. Schafleitner, J. W. Yang and K. Sanjeet. 2015. Restorer breeding in sweet pepper: Introgressing Rf allele from hot pepper through marker assisted backcrossing. Sci. Hort. 197: 170-175.
Luo, D., H. Xu, Z. Liu, J. Guo, H. Li and L. Chen, et al. 2013. A detrimental mitochondrial-nuclear interaction causes cytoplasmic male sterility in rice. Nat. Genet. 45: 573–577.
Ma, Y., W. Huang, J. J. Ji, Z. H. Gong, C. C. Yin, S. S. Ahmed and Z. L. Zhao. 2013. Maintaining and restoration cytoplasmic male sterility systems in pepper (Capsicum annuum L.). Genet. Mol. Res. 12(3): 2320-2331. doi: 10.4238/2013.January.4.8
Min, W. K., S. Kim, S. K. Sung, B. D. Kim and S. Lee. 2009. Allelic discrimination of the restorer-of-fertility gene and its inheritance in peppers (Capsicum annuum L.). Theor. Appl. Genet. 119:1289-1299.
Mishra, G. P., R. K. Singh, T. Mohapatra, A. K. Singh, K.V. Prabhu, F.U. Zaman and R.K. Sharma. 2003. Molecular mapping of gene for fertility restoration of wild abortive (WA) cytoplasmic male sterility using a basmati rice restorer line. J. Plant Biochem. Biotech. 12: 37-42.
Mulyantoro, S. Y., A. Chen, Wahyono and H.M. Ku. 2009. Modified complementation test of male sterility mutants in pepper (Capsicum annuum L.): Preliminary study to convert male sterility system from GMS to CMS. Euphytica. 169: 353-361. DOI:10.1007/s10681-009-9968-6
Murray, M. G. and W. F. Thompson. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic acids res. 8(19): 4321-4326. doi: 10.1093/nar/8.19.4321
Novak, F., J. Betlach and J. Dubovsky. 1971. Cytoplasmic male sterility in sweet pepper (Capsicum annuum L.). Phenotype and inheritance of male sterile character Z. Pflanzenzücht. 65: 129-140.
Ortega, F.A., D.W. Barchenger and B. Wei, et al. 2020. Development of a genotype-specific molecular marker associated with restoration-of-fertility (Rf) in chile pepper (Capsicum annuum L.). Euphytica. 216: 43.
Pakozdi, K., J. Taller, Z. Alfoldi and Y. Hirata. 2002. Pepper (Capsicum annuum L.) cytoplasmic male sterilty. J. Central. Euro. Agri. 3: 149-158.
Panse, V. G. and P. V. Sukhatme. 1985. Statistical Methods for Agricultural Workers. New Delhi, ICAR. 70-72.
Peterson, P. A. 1958. Cytoplasmic inheritance of male sterility in Capsicum annuum. Am. Nat., 92: 111-119.
Quarrie, S., V. Lazi-Jani, D. Kovaevi, A. Steed and S. Peki. 1999. Bulk segregant analysis with molecular markers and its use for improving drought resistance in maize. J. Exp. Bot. 50 (337): 1299-1306.
Sandeep, A.M. and L.K. Sanjay. 2017. Inheritance of restorer gene in chilli (Capsicum annuum L.) J. Glob. Biosci. 6(8): 5201-5204.
Wang, L. H., B. X. Zhang, V. Lefebvre, S. W. Huang, A. M. Daubèze and A. Palloix. 2004. QTL analysis of fertility restoration in cytoplasmic male sterile pepper. Theor. Appl. Genet. 109: 1058-1063.
Wei., B. Q., L. L. Wang, R. Zhang and J. N. Zhang. 2017. Identification of two major quantitative trait loci restoring the fertility of cytoplasmic male sterility in Capsicum annuum. J. Agri. Biotechnol. 25(1): 43-49.
Yang, C. J., B. J. Chen, J. G. Liu and S. Li. 2008. Study on the superiority of hybrid breeding by male sterility in hot pepper. J. China Capsicum. 1: 36-38.
Yu, I. W. 1990. The inheritance of male sterility and its utilization for breeding in pepper (Capsicum spp.). (Doctoral dissertation), Kyung Hee University, Seoul.
Zhang, B. X., S. W. Huang, G.M. Yang and J. Z. Guo. 2000. Two RAPD markers linked to a major fertility restorer gene in pepper. Euphytica. 113: 155-161.
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How to Cite
Nalla, M. K., V. K. Sharma, and V. R. Sharma. “Mapping and Validation of Markers Linked to Rf Gene in Sweet Pepper (Capsicum Annuum Var Grossum)”. Emirates Journal of Food and Agriculture, Vol. 33, no. 6, Aug. 2021, pp. 443-9, doi: Accessed 2 Dec. 2022.
Research Article