title: Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage.
abstract: BACKGROUND
  Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference.
  
  
  RESULTS
  Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F2:3 progenies and identified one major QTL and three minor QTLs.
  
  
  CONCLUSIONS
  We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.
authors: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. jonghoonlee@snu.ac.kr.
authors: Jonghoon
authors: J
authors: Lee
authors: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. lila_ref@yahoo.co.id.|Indonesian Research Institute for Industrial and Beverage Crops (IRIIBC), Pakuwon, Sukabumi, Indonesia. lila_ref@yahoo.co.id.
authors: Nur Kholilatul
authors: NK
authors: Izzah
authors: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. murukarthick@snu.ac.kr.
authors: Murukarthick
authors: M
authors: Jayakodi
authors: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. bioteksampath@gmail.com.
authors: Sampath
authors: S
authors: Perumal
authors: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. jun841011@hotmail.com.
authors: Ho Jun
authors: HJ
authors: Joh
authors: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. godpen1126@naver.com.
authors: Hyeon Ju
authors: HJ
authors: Lee
authors: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. sclee0923@snu.ac.kr.
authors: Sang-Choon
authors: SC
authors: Lee
authors: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. jypark74@snu.ac.kr.
authors: Jee Young
authors: JY
authors: Park
authors: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. s95yang@hotmail.com.|Department of Horticulture, Sunchon National University, Suncheon, 540-950, Republic of Korea. s95yang@hotmail.com.
authors: Ki-Woung
authors: KW
authors: Yang
authors: Department of Horticulture, Sunchon National University, Suncheon, 540-950, Republic of Korea. nis@sunchon.ac.kr.
authors: Il-Sup
authors: IS
authors: Nou
authors: Joeun Seed, #174, Munbang-Ri, Cheonhan-Myun, 367-833, Goesan-Gu, Chungcheongbuk-Do, Korea. joodeok.seo@joeunseeds.com.
authors: Joodeok
authors: J
authors: Seo
authors: Joeun Seed, #174, Munbang-Ri, Cheonhan-Myun, 367-833, Goesan-Gu, Chungcheongbuk-Do, Korea. andy.yoo@joeunseeds.com.
authors: Jaeheung
authors: J
authors: Yoo
authors: Joeun Seed, #174, Munbang-Ri, Cheonhan-Myun, 367-833, Goesan-Gu, Chungcheongbuk-Do, Korea. youngdeok.suh@joeunseeds.com.
authors: Youngdeok
authors: Y
authors: Suh
authors: Joeun Seed, #174, Munbang-Ri, Cheonhan-Myun, 367-833, Goesan-Gu, Chungcheongbuk-Do, Korea. kyounggu.ahn@joeunseeds.com.
authors: Kyounggu
authors: K
authors: Ahn
authors: Research Center for Biobased Chemistry, Korea Research Institute of Chemical Technology, Daejeon, 305-600, Yusong-Gu, Republic of Korea. jihyun@krick.re.kr.
authors: Ji Hyun
authors: JH
authors: Lee
authors: Research Center for Biobased Chemistry, Korea Research Institute of Chemical Technology, Daejeon, 305-600, Yusong-Gu, Republic of Korea. kjchoi@krict.re.kr.
authors: Gyung Ja
authors: GJ
authors: Choi
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA. yeisooyu@ag.arizona.edu.
authors: Yeisoo
authors: Y
authors: Yu
authors: Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea. heebal@snu.ac.kr.|CHO & KIM genomics, Seoul National University Mt.4-2, Main Bldg. #514, SNU Research Park, NakSeoungDae, Seoul, 151-919, Gwanakgu, Republic of Korea. heebal@snu.ac.kr.
authors: Heebal
authors: H
authors: Kim
authors: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. tjyang@snu.ac.kr.
authors: Tae-Jin
authors: TJ
authors: Yang
mesh_terms: D001937:Brassica / Q000235:genetics* / Q000382:microbiology; D018745:Genome, Plant; D009181:Mycoses / Q000276:immunology*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
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