Theoretical and Applied Genetics

, Volume 130, Issue 1, pp 199–211 | Cite as

QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods

  • Khin Thanda Win
  • Juan Vegas
  • Chunying Zhang
  • Kihwan Song
  • Sanghyeob LeeEmail author
Original Article


Key message

QTL mapping using NGS-assisted BSA was successfully applied to an F 2 population for downy mildew resistance in cucumber. QTLs detected by NGS-assisted BSA were confirmed by conventional QTL analysis.


Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive foliar diseases in cucumber. QTL mapping is a fundamental approach for understanding the genetic inheritance of DM resistance in cucumber. Recently, many studies have reported that a combination of bulked segregant analysis (BSA) and next-generation sequencing (NGS) can be a rapid and cost-effective way of mapping QTLs. In this study, we applied NGS-assisted BSA to QTL mapping of DM resistance in cucumber and confirmed the results by conventional QTL analysis. By sequencing two DNA pools each consisting of ten individuals showing high resistance and susceptibility to DM from a F2 population, we identified single nucleotide polymorphisms (SNPs) between the two pools. We employed a statistical method for QTL mapping based on these SNPs. Five QTLs, dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1, were detected and dm2.2 showed the largest effect on DM resistance. Conventional QTL analysis using the F2 confirmed dm2.2 (R 2 = 10.8–24 %) and dm5.2 (R 2 = 14–27.2 %) as major QTLs and dm4.1 (R 2 = 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R 2 = 28.2 %) was detected by the conventional QTL method using an F3 population. This study demonstrated the effectiveness of NGS-assisted BSA for mapping QTLs conferring DM resistance in cucumber and revealed the unique genetic inheritance of DM resistance in this population through two distinct major QTLs on chromosome 2 that mainly harbor DM resistance.


Downy Mildew Composite Interval Mapping Bulk Segregant Analysis InDel Marker Putative QTLs 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was supported by grants from the Bio-industry Technology Development Program (111057-5) of iPET (Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry).

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.


This work was supported by grants from the Bio-industry Technology Development Program (111057-5) of iPET (Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry).

Supplementary material

122_2016_2806_MOESM1_ESM.pdf (819 kb)
Supplementary material 1 (PDF 819 kb)
122_2016_2806_MOESM2_ESM.pdf (606 kb)
Supplementary material 2 (PDF 606 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Plant Genomics Laboratory, Department of Plant Biotechnology, College of Life SciencesSejong UniversitySeoulRepublic of Korea
  2. 2.SESVANDERHAVE BelgiumTienenBelgium
  3. 3.Plant Engineering Research InstituteSejong UniversitySeoulRepublic of Korea

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