Abstract
The major wide-compatibility gene locus S5 in rice (Oryza sativa L.) located on chromosome 6 has been recently cloned and a 136-bp deletion in the candidate gene encoding aspartyl protease has been characterized to be specific for wide-compatible varieties, while many single nucleotide polymorphisms have been identified at S5 between indica and japonica rice types. In the present study, we designed a PCR-based multiplex functional marker system targeting the deletion and the SNPs for precise determination of the allelic status at S5. By deploying the marker system, the allelic status at the S5 locus in 584 rice genotypes has been assayed. A total of 116 genotypes, including 11 cultivars, two known wide-compatible varieties, 48 IRRI germplasm lines, 12 Indian aromatic rice genotypes, 37 restorer lines and six breeding lines, have been identified to possess the 136-bp deletion specific for the neutral allele at S5. The marker system was able to clearly distinguish indica and japonica alleles from the neutral allele and has been validated in a mapping population derived from the three-way cross IR36/Dular//Akihikari, which segregated for spikelet sterility/fertility. The functional marker system targeting S5 developed in the present study will be very useful in rapid identification of wide-compatible genotypes, in predicting the success of inter-subspecific crosses and in targeted introgression of the wide-compatible allele of S5 into elite indica and japonica rice varieties.
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References
Bundock PC, Cross MJ, Shapter FM, Henry RJ (2006) Robust allele-specific polymerase chain reaction markers developed for single nucleotide polymorphisms in expressed barley sequences. Theor Appl Genet 112:358–365
Chen J, Ding J, Ouyang Y, Du H, Yang J, Cheng K, Zhao J, Qiu S, Zhang X, Yao J, Liu K, Wang L, Xu C, Li X, Xue Y, Xia M, Ji Q, Lu J, Xu M, Zhang Q (2008) A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice. Proc Natl Acad Sci USA 105:11436–11441
Collard BCY, Vera Cruz CM, McNally KL, Virk PS, Mackill DJ (2008) Rice molecular breeding laboratories in the genomics era: current status and future considerations. Int J Plant Genomics. doi:10.1155/2008/524847
Dellaporta SL, Wood J, Hick JB (1983) A plant DNA mini-preparation: version II. Plant Mol Biol Rep 1:19–21
Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS (1991) ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19:4008
Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108:1212–1220
Ikehashi H, Araki H (1984) Variety screening of compatibility types revealed in F1 fertility of distant cross in rice. Jpn J Breed 34:304–313
Ikehashi H, Araki H (1986) Genetics of F1 sterility in remote crosses of rice. In: IRRI (ed) Rice genetics. IRRI, Manila, pp 119–130
Kato S, Kosaka H, Hara S (1928) On the affinity of rice varieties as shown by fertility of hybrid plants. Bull Sci Fac Agric Kyushu Univ 3:132–147
Singh SP, Sundaram RM, Biradar SK, Ahmed MI, Viraktamath BC, Siddiq EA (2006) Identification of simple sequence repeat markers for utilizing wide-compatibility genes in inter-subspecific hybrids in rice (Oryza sativa L.). Theor Appl Genet 113:509–517
Soleimani VD, Baum BR, Johnson DA (2003) Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR, with an example from barley. Plant Mol Biol Rep 21:281–288
Tang S, Kishore VK, Knapp SJ (2003) PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower. Theor Appl Genet 107:6–19
Acknowledgments
The authors thank the Department of Biotechnology (DBT), Government of India and the Indian Council of Agricultural Research (ICAR) for providing funds for carrying out the research work. We also thank IRRI, Philippines, for providing rice germplasm accessions used in the study.
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R. M. Sundaram, K. Sakthivel, and A. S. Hariprasad have contributed equally.
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Sundaram, R.M., Sakthivel, K., Hariprasad, A.S. et al. Development and validation of a PCR-based functional marker system for the major wide-compatible gene locus S5 in rice. Mol Breeding 26, 719–727 (2010). https://doi.org/10.1007/s11032-010-9482-5
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DOI: https://doi.org/10.1007/s11032-010-9482-5