title: QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods.
abstract: QTL mapping using NGS-assisted BSA was successfully applied to an F2population 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 F2population, 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 F2confirmed dm2.2 (R2= 10.8-24 %) and dm5.2 (R2= 14-27.2 %) as major QTLs and dm4.1 (R2= 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R2= 28.2 %) was detected by the conventional QTL method using an F3population. 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.
authors.affiliation: Plant Genomics Laboratory, Department of Plant Biotechnology, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 143-747, Republic of Korea.
authors.forename: Khin Thanda
authors.initials: KT
authors.lastname: Win
authors.affiliation: Plant Genomics Laboratory, Department of Plant Biotechnology, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 143-747, Republic of Korea.|SESVANDERHAVE Belgium, Industriepark 15, 3300, Tienen, Belgium.
authors.forename: Juan
authors.initials: J
authors.lastname: Vegas
authors.affiliation: Plant Genomics Laboratory, Department of Plant Biotechnology, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 143-747, Republic of Korea.
authors.forename: Chunying
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Plant Genomics Laboratory, Department of Plant Biotechnology, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 143-747, Republic of Korea.|Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 143-747, Republic of Korea.
authors.forename: Kihwan
authors.initials: K
authors.lastname: Song
authors.affiliation: Plant Genomics Laboratory, Department of Plant Biotechnology, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 143-747, Republic of Korea. sanglee@sejong.ac.kr.|Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 143-747, Republic of Korea. sanglee@sejong.ac.kr.
authors.forename: Sanghyeob
authors.identifier: http://orcid.org/0000-0001-7684-2325
authors.initials: S
authors.lastname: Lee
mesh_terms: D002874:Chromosome Mapping; D018553:Cucumis sativus / Q000235:genetics* / Q000382:microbiology; D018744:DNA, Plant / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics*; D008040:Genetic Linkage; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D044742:Peronospora; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant