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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

Abstract

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.

Keywords

Bakanae disease Resequencing Single nucleotide polymorphism Genetic map Quantitative trait locus 

Notes

Acknowledgements

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)

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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

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