Development and validation of SNP-based functional codominant markers for two major disease resistance genes in rice (O. sativa L.)

Molecular Breeding

Volumn 35, Issue 6, 2015, Pages

  Ramkumar, G ^a   Prahalada, G D ^a   Hechanova, Sherry Lou ^a   Vinarao, Ricky ^a   Jena, Kshirod K ^a  

^a INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

Bacterial leaf blight; Codominant marker; Pita; Rice blast; xa5

Indexed keywords

CAPILLARY ELECTROPHORESIS; COST EFFECTIVENESS; DIAGNOSIS; DNA SEQUENCES;

BACTERIAL LEAF BLIGHT; BIOTIC STRESS; CODOMINANT MARKERS; DISEASE-RESISTANCE GENES; GRAIN YIELD; LEAF BLIGHTS; O. SATIVA; PITA; RICE BLASTS; XA5;

GENES;

BACTERIA (MICROORGANISMS); ORYZA SATIVA;

EID: 84929459949     PISSN: 13803743     EISSN: 15729788     Source Type: Journal    
DOI: 10.1007/s11032-015-0323-4     Document Type: Article

References (32)

1. 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
2. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21
3. 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
4. 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
5. 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
6. IRRI (2006) Stress and disease tolerance. http://www.knowledgebank.irri.org/ricebreedingcourse/Breeding_for_disease_resistance_Blight.htm. Accessed 28 August 2014
7. 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
8. Iyer AS, McCouch SR (2007) Functional markers for xa5-mediated resistance in rice (Oryza sativa L.). Mol Breed 19:291–296
9. Jena KK, Mackill DJ (2008) Molecular markers and their use in marker-assisted selection in rice. Crop Sci 48:1266–1276
10. Jia Y, Wang Z, Singh P (2002) Development of dominant rice blast Pi-ta resistance gene markers. Crop Sci 42:2145–2149
11. Jia Y, Bryan GT, Farrall L, Valent B (2003) Natural variation at the Pi-ta rice blast resistance locus. Phytopathology 93:1452–1459
12. 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
13. 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
14. 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
15. 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
16. 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
17. 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
18. 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
19. 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
20. Mew T, Alvarez A, Leach J, Swings J (1993) Focus on bacterial blight of rice. Plant Dis 77:5–12
21. Ou SH (1985) Rice diseases, 2nd edn. Surrey Commonwealth Mycological Institute, Kew, p 380
22. 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
23. 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
24. h). Mol Breed 27:129–135
25. 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
26. 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
27. 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
28. 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
29. 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
30. Wang Y, Li J (2005) The plant architecture of rice (Oryza sativa). Plant Mol Biol 59:75–84
31. 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
32. 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