Abstract
Blast and bacterial leaf blight are major diseases of rice that limit grain yield significantly. These two devastating biotic stresses have to be controlled to meet the demand for 23 % more rice production by 2035 to feed the increasing number of rice consumers. Incorporating appropriate disease resistance genes into elite varieties is considered as the best method to enhance crop resistance. Molecular markers play an important role in multiple gene pyramiding programs to select desirable genotypes with targeted genes. Two major resistance genes, Pita and xa5, for blast and bacterial leaf blight races, respectively, have been used in many gene pyramiding programs. However, simple PCR-based functional codominant markers have not been reported for these genes. Hence, in the present study, time- and cost-effective codominant markers for Pita and xa5 have been developed and validated in segregating populations. High-throughput screening has been demonstrated using parallel capillary electrophoresis to replace laborious gel-based electrophoresis. Additionally, the presence of Pita and xa5 alleles was evaluated with 260 diverse rice varieties that were collected from different parts of the world. Of the 260 cultivars tested, 55 were identified with the Pita resistance allele while all the tested cultivars had the susceptible Xa5 allele. The identified Pita allele-derived cultivars can be used as an alternative resistance source for blast disease. The newly developed Pita and xa5 functional markers will help toward tracking the two target genes for blast and bacterial leaf blight resistance in breeding programs.
Similar content being viewed by others
References
Bryan GT, Wu KS, Farrall L, Jia Y, Hershey HP, McAdams SA, Faulk KN, Donaldson GK, Tarchini R, Valent B (2000) A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12:2033–2045
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21
Garris AJ, McCouch SR, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165:759–769
Hayashi K, Yoshida H, Ashikawa I (2006) Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes. Theor Appl Genet 113:251–260
Hittalmani S, Parco A, Mew TV, Zeigler RS, Huang N (2000) Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice. Theor Appl Genet 100:1121–1128
IRRI (2006) Stress and disease tolerance. http://www.knowledgebank.irri.org/ricebreedingcourse/Breeding_for_disease_resistance_Blight.htm. Accessed 28 August 2014
Iyer AS, McCouch SR (2004) The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol Plant-Microbe Interact 17:1348–1354
Iyer AS, McCouch SR (2007) Functional markers for xa5-mediated resistance in rice (Oryza sativa L.). Mol Breed 19:291–296
Jena KK, Mackill DJ (2008) Molecular markers and their use in marker-assisted selection in rice. Crop Sci 48:1266–1276
Jia Y, Wang Z, Singh P (2002) Development of dominant rice blast Pi-ta resistance gene markers. Crop Sci 42:2145–2149
Jia Y, Bryan GT, Farrall L, Valent B (2003) Natural variation at the Pi-ta rice blast resistance locus. Phytopathology 93:1452–1459
Jia Y, Redus M, Wang Z, Rutger JN (2004) Development of a SNLP marker from the Pi-ta blast resistance gene by tri-primer PCR. Euphytica 138:97–105
Kauffman HE, Reddy APK, Hsieh SPY, Merca SD (1973) An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae. Plant Dis Rep 57:537–541
Khush G, Jena KK (2009) Current status and future prospects for research on blast resistance in rice (Oryza sativa L.). In: Wang GL, Valent B (eds) Advances in genetics, genomics and control of rice blast disease. Springer, New York, pp 1–10
Kottapalli KR, Narasu ML, Jena KK (2010) Effective strategy for pyramiding three bacterial blight resistance genes into fine grain rice cultivar, Samba Mahsuri, using sequence tagged site markers. Biotechnol Lett 32:989–996
Kumar PN, Sujatha K, Laha GS, Rao KS, Mishra B, Viraktamath BC, Hari Y, Reddy CS, Balachandran SM, Ram T, Madhav MS, Rani NS, Neeraja CN, Reddy GA, Shaik H, Sundaram RM (2012) Identification and fine-mapping of Xa33, a novel gene for resistance to Xanthomonas oryzae pv. oryzae. Phytopathology 102:222–228
Lee S, Jia Y, Jia M, Gealy DR, Olsen KM, Caicedo AL (2011) Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA. PLoS One 6:e26260
Li C, Wei J, Lin Y, Chen H (2012) Gene silencing using the recessive rice bacterial blight resistance gene xa13 as a new paradigm in plant breeding. Plant Cell Rep 31:851–862
Lin F, Chen S, Que ZQ, Wang L, Liu XQ, Pan QH (2007) The blast resistance gene Pi37 encodes a nucleotide binding site-leucine-rich repeat protein and is a member of a resistance gene cluster on rice chromosome 1. Genetics 177:1871–1880
Mew T, Alvarez A, Leach J, Swings J (1993) Focus on bacterial blight of rice. Plant Dis 77:5–12
Ou SH (1985) Rice diseases, 2nd edn. Surrey Commonwealth Mycological Institute, Kew, p 380
Ramkumar G, Sakthivel K, Sundaram RM, Neeraja CN, Balachandran SM, Rani NS, Viraktamath BC, Madhav MS (2010a) Allele mining in crops: prospects and potentials. Biotechnol Adv 28:451–461
Ramkumar G, Sivaranjani AKP, Pandey MK, Sakthivel K, Rani NS, Sudarshan I, Prasad GSV, Neeraja CN, Sundaram RM, Viraktamath BC, Madhav MS (2010b) Development of a PCR-based SNP marker system for effective selection of kernel length and kernel elongation in rice. Mol Breed 26:735–740
Ramkumar G, Srinivasarao K, Mohan KM, Sudarshan I, Sivaranjani AKP, Gopalakrishna K, Neeraja CN, Balachandran SM, Sundaram RM, Prasad MS, Rani NS, Prasad AMR, Viraktamath BC, Madhav MS (2011) Development and validation of functional marker targeting an InDel in the major rice blast disease resistance gene Pi54 (Pik h). Mol Breed 27:129–135
Ramkumar G, Madhav MS, Devi SJSR, Manimaran P, Mohan KM, Prasad MS, Balachandran SM, Neeraja CN, Sundaram RM, Viraktamath BC (2014) Nucleotide diversity of Pita, a major blast resistance gene and identification of its minimal promoter. Gene 546:250–256. doi:10.1016/j.gene.2014.06.001
Suh JP, Jeung JU, Noh TH, Cho YC, Park SH, Park HS, Shin MS, Kim CK, Jena KK (2013) Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice. Rice 6:5. doi:10.1186/1939-8433-6-5
Sundaram RM, Vishnupriya MR, Biradar SK, Laha GS, Reddy GA, Rani NS, Sarma NP, Sonti RV (2008) Marker assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite indica rice variety. Euphytica 160:411–422
Sundaram RM, Vishnupriya MR, Laha GS, Rani NS, Rao PS, Balachandran SM, Reddy GA, Sarma NP, Sonti RV (2009) Introduction of bacterial blight resistance into Triguna, a high yielding, mid-early duration rice variety. Biotechnol J 4:400–407
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Wang Y, Li J (2005) The plant architecture of rice (Oryza sativa). Plant Mol Biol 59:75–84
Wang Z, Jia Y, Rutger JN, Xia Y (2007) Rapid survey for presence of a blast resistance gene Pi-ta in rice cultivars using the dominant DNA markers derived from portions of the Pi-ta gene. Plant Breed 126:36–42
Wang X, Jia Y, Shu QY, Wu D (2008) Haplotype diversity at the Pi-ta locus in cultivated rice and its wild relatives. Phytopathology 98:1305–1311
Acknowledgments
We are grateful to the Global Rice Science Partnership (GRiSP) program of IRRI for financially supporting this project. We thank Bill Hardy for editing the manuscript.
Conflict of interest
The authors declare no conflict of interest.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Ramkumar, G., Prahalada, G.D., Hechanova, S.L. et al. Development and validation of SNP-based functional codominant markers for two major disease resistance genes in rice (O. sativa L.). Mol Breeding 35, 129 (2015). https://doi.org/10.1007/s11032-015-0323-4
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11032-015-0323-4