Molecular Genetics and Genomics

, Volume 293, Issue 3, pp 579–586 | Cite as

Mapping of a major quantitative trait locus for bakanae disease resistance in rice by genome resequencing

  • Hyeonso JiEmail author
  • Tae-Ho Kim
  • Gang-Seob Lee
  • Hyun-Ju Kang
  • Seung-Bum Lee
  • Seok Cheol Suh
  • Song Lim Kim
  • Inchan Choi
  • Jeongho Baek
  • Kyung-Hwan Kim
Original Article


Bakanae disease (BD) has emerged as a serious threat in almost all rice cultivation regions worldwide. Nampyeong is a Korean japonica rice variety known to be resistant to BD. In this study, quantitative trait locus (QTL) mapping was performed with F2 and F3 plants derived from a cross between the Nampyeong variety and a susceptible Korean japonica line, DongjinAD. First, resequencing of Nampyeong and DongjinAD was performed, which identified 171,035 single nucleotide polymorphisms (SNPs) between the two parental varieties. Using these SNPs, 161 cleaved amplified polymorphic sequence (CAPS) markers and six derived CAPS markers were developed; then, a genetic map was constructed from the genotypes of 180 plants from the DongjinAD/Nampyeong F2 plants. The total length of the constructed genetic map was 1386 cM, with an average interval of 8.9 cM between markers. The BD mortality rates of each F3 family were measured by testing 40 F3 progenies using in vitro seedling screening method. QTL analysis based on the genetic map and mortality rate data revealed a major QTL, qFfR1, on rice chromosome 1. qFfR1 was located at 89.8 cM with a logarithm of the odds (LOD) score of 22.7. Further, there were three markers at this point: JNS01033, JNS01037, and JNS01041. A total of 15 genes were identified with annotations related to defense against plant diseases among the 179 genes in the qFfR1 interval at 95% probability, thereby providing potential candidate genes for qFfR1. qFfR1 and its closely linked markers will be useful in breeding rice varieties resistant to BD.


Bakanae disease Resequencing Single nucleotide polymorphism Genetic map Quantitative trait locus 



This research was supported by grants from the National Institute of Agricultural Sciences (NIAS), project code PJ01008902, Republic of Korea.

Supplementary material

438_2017_1407_MOESM1_ESM.xls (130 kb)
Supplementary material 1 (XLS 130 KB)
438_2017_1407_MOESM2_ESM.docx (316 kb)
Supplementary material 2 (DOCX 316 KB)


  1. Basten CJ, Weir BS, Zeng Z-B (1996) QTL cartographer: a reference manual and tutorial for QTL mapping. Department of Statistics, North Carolina State University, RaleighGoogle Scholar
  2. Carter LL, Leslie JF, Webster RK (2008) Population structure of Fusarium fujikuroi from California rice and water grass. Phytopathology 98:992–998CrossRefPubMedGoogle Scholar
  3. Chen Z, Gao T, Liang S, Liu K, Zhou M, Chen C (2014) Molecular mechanism of resistance of Fusarium fujikuroi to benzimidazole fungicides. FEMS Microbiol Lett 357:77–84CrossRefPubMedGoogle Scholar
  4. Desjardins AE, Manandhar HK, Plattner RD, Manandhar GG, Poling SM, Maragos CM (2000) Fusarium species from nepalese rice and production of mycotoxins and gibberellic acid by selected species. Appl Environ Microbiol 66:1020–1025CrossRefPubMedPubMedCentralGoogle Scholar
  5. Fiyaz RA, Krishnan SG, Rajashekara H, Yadav AK, Bashyal BM, Bhowmick PK, Singh NK, Prabhu KV, Singh AK (2014) Development of high throughput screening protocol and identification of novel sources of resistance against bakanae disease in rice (Oryza sativa L.). Indian Journal of Genetics Plant Breeding 74:414–422CrossRefGoogle Scholar
  6. Fiyaz RA, Yadav AK, Krishnan SG, Ellur RK, Bashyal BM, Grover N, Bhowmick PK, Nagarajan M, Vinod KK, Singh NK, Prabhu KV, Singh AK (2016) Mapping quantitative trait loci responsible for resistance to Bakanae disease in rice. Rice (N Y) 9:45CrossRefGoogle Scholar
  7. Gupta AK, Solanki IS, Bashyal BM, Singh Y, Srivastava K (2015) Bakanae of rice—an emerging disease in Asia. The Journal of Animal Plant Sciences 25:1499–1514Google Scholar
  8. Hur YJ, Lee SB, Kim TH, Kwon T, Lee JH, Shin DJ, Park SK, Hwang UH, Cho JH, Yoon YN, Yeo US, Song YC, Kwak DY, Nam MH, Park DS (2015) Mapping of qBK1, a major QTL for bakanae disease resistance in rice. Mol Breeding 35:78CrossRefGoogle Scholar
  9. Hur YJ, Lee SB, Shin DJ, Kim TH, Cho JH, Han SI, Oh SH, Lee JY, Son YB, Lee JH, Kwon T, Park NB, Kim SY, Song YC, Nam MH, Kwon YU, Park DS (2016) Screening of rice germplasm for Bakanae disease resistance in rice. Korean J Breed Sci 48:22–28CrossRefGoogle Scholar
  10. Jeong I-S, Kim T-H, Lee S-B, Suh S-C, Ji H (2015) Genome-wide detection of DNA Polymorphisms between two Korean japonica rice varieties. Plant Breed Biotechnol 3:208–215CrossRefGoogle Scholar
  11. Kim SH, Park MR, Kim YC, Lee SW, Choi BR, Lee SW, Kim IS (2010) Degradation of prochloraz by rice Bakanae disease pathogen Fusarium fujikuroi with differing sensitivity: a possible explanation for resistance mechanism. J Korean Soc Appl Biol Chem 53:433–439CrossRefGoogle Scholar
  12. Kim MH, Hur YJ, Lee SB, Kwon T, Hwang UH, Park SK, Yoon YN, Lee JH, Cho JH, Shin D, Kim TH, Han SI, Yeo US, Song YC, Nam MH, Park DS (2014) Large-scale screening of rice accessions to evaluate resistance to bakanae disease. J Gen Plant Pathol 80:408–414CrossRefGoogle Scholar
  13. Lee YH, Lee MJ, Choi HW, Kim ST, Park JW, Myung IS, Park K, Lee SW (2011) Development of in vitro seedling screening method for selection of resistant rice against Bakanae disease. Res Plant Dis 17:288–294CrossRefGoogle Scholar
  14. Lorieux M (2012) MapDisto: fast and efficient computation of genetic linkage maps. Mol Breeding 30:1231–1235CrossRefGoogle Scholar
  15. Matic S, Bagnaresi P, Biselli C, Orru L, Amaral Carneiro G, Siciliano I, Vale G, Gullino ML, Spadaro D (2016) Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi. BMC Genom 17:608CrossRefGoogle Scholar
  16. Matic S, Gullino ML, Spadaro D (2017) The puzzle of bakanae disease through interactions between Fusarium fujikuroi and rice. Front Biosci (Elite Ed) 9:333–344Google Scholar
  17. Navarro L, Bari R, Achard P, Lison P, Nemri A, Harberd NP, Jones JD (2008) DELLAs control plant immune responses by modulating the balance of jasmonic acid and salicylic acid signaling. Curr Biol 18:650–655CrossRefPubMedGoogle Scholar
  18. Rosler SM, Sieber CMK, Humpf HU, Tudzynski B (2016) Interplay between pathway-specific and global regulation of the fumonisin gene cluster in the rice pathogen Fusarium fujikuroi. Appl Microbiol Biotechnol 100:5869–5882CrossRefPubMedGoogle Scholar
  19. Sang WG, Kim JH, Shin P, Cho HS, Seo MC, Park HK, Lee GH, Jeong NJ (2015) Physio-biochemical characterization of Bakanae disease-tolerant rice. Korean J Int Agric 27:460–468CrossRefGoogle Scholar
  20. Siciliano I, Carneiro GA, Spadaro D, Garibaldi A, Gullino ML (2015) Jasmonic acid, abscisic acid, and salicylic acid are involved in the phytoalexin responses of rice to Fusarium fujikuroi, a high gibberellin producer pathogen. J Agric Food Chem 63:8134–8142CrossRefPubMedGoogle Scholar
  21. Sun TP (2011) The molecular mechanism and evolution of the GA-GID1-DELLA signaling module in plants. Curr Biol 21:R338–R345CrossRefPubMedGoogle Scholar
  22. Volante A, Tondelli A, Aragona M, Valente MT, Biselli C, Desiderio F, Bagnaresi P, Matic S, Gullino ML, Infantino A, Spadaro D, Vale G (2017) Identification of bakanae disease resistance loci in japonica rice through genome wide association study. Rice (N Y) 10:29CrossRefGoogle Scholar
  23. Wiemann P, Sieber CM, von Bargen KW, Studt L, Niehaus EM, Espino JJ, Huss K, Michielse CB, Albermann S, Wagner D, Bergner SV, Connolly LR, Fischer A, Reuter G, Kleigrewe K, Bald T, Wingfield BD, Ophir R, Freeman S, Hippler M, Smith KM, Brown DW, Proctor RH, Munsterkotter M, Freitag M, Humpf HU, Guldener U, Tudzynski B (2013) Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog 9:e1003475CrossRefPubMedPubMedCentralGoogle Scholar
  24. Yang C-D, Guo L-B, Qian Q, Li X-M, Ji Z-J, Ma L-Y (2006) Analysis of QTLs for resistance to rice bakanae disease. Chin J Rice Sci 20:657–659Google Scholar
  25. Yang Y-R, Lee S-W, Lee S-W, Kim I-S (2012) Morphological changes of fungal cell wall and ABC transporter as resistance responses of rice Bakanae disease pathogen Fusarium fujikuroi CF337 to prochloraz. Korean J Environ Agric 31:20–36CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Department of Agricultural BiotechnologyNational Institute of Agricultural Sciences (NIAS)JeonjuRepublic of Korea

Personalised recommendations