title: Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.).
abstract: Clubroot is a devastating disease caused by Plasmodiophora brassicae and results in severe losses of yield and quality in Brassica crops. Many clubroot resistance genes and markers are available in Brassica rapa but less is known in Brassica oleracea. Here, we applied the genotyping-by-sequencing (GBS) technique to construct a high-resolution genetic map and identify clubroot resistance (CR) genes. A total of 43,821 SNPs were identified using GBS data for two parental lines, one resistant and one susceptible lines to clubroot, and 18,187 of them showed >5× coverage in the GBS data. Among those, 4,103 were credibly genotyped for all 78 F2 individual plants. These markers were clustered into nine linkage groups spanning 879.9 cM with an average interval of 1.15 cM. Quantitative trait loci (QTLs) survey based on three rounds of clubroot resistance tests using F2 : 3 progenies revealed two and single major QTLs for Race 2 and Race 9 of P. brassicae, respectively. The QTLs show similar locations to the previously reported CR loci for Race 4 in B. oleracea but are in different positions from any of the CR loci found in B. rapa. We utilized two reference genome sequences in this study. The high-resolution genetic map developed herein allowed us to reposition 37 and 2 misanchored scaffolds in the 02-12 and TO1000DH genome sequences, respectively. Our data also support additional positioning of two unanchored 3.3 Mb scaffolds into the 02-12 genome sequence.
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Jonghoon
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea Indonesian Research Institute for Industrial and Beverage Crops (IRIIBC), Pakuwon, Sukabumi, Indonesia.
authors.forename: Nur Kholilatul
authors.initials: NK
authors.lastname: Izzah
authors.affiliation: Phyzen Genomics Institute, Seoul 151-836, Republic of Korea.
authors.forename: Beom-Soon
authors.initials: BS
authors.lastname: Choi
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Ho Jun
authors.initials: HJ
authors.lastname: Joh
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Sang-Choon
authors.initials: SC
authors.lastname: Lee
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Sampath
authors.initials: S
authors.lastname: Perumal
authors.affiliation: Joeun Seed, Goesan-Gun, Chungcheongbuk-Do 367-833, Republic of Korea.
authors.forename: Joodeok
authors.initials: J
authors.lastname: Seo
authors.affiliation: Joeun Seed, Goesan-Gun, Chungcheongbuk-Do 367-833, Republic of Korea.
authors.forename: Kyounggu
authors.initials: K
authors.lastname: Ahn
authors.affiliation: Research Center for Biobased Chemistry, Korea Research Institute of Chemical Technology, Daejeon 305-600, Republic of Korea.
authors.forename: Eun Ju
authors.initials: EJ
authors.lastname: Jo
authors.affiliation: Research Center for Biobased Chemistry, Korea Research Institute of Chemical Technology, Daejeon 305-600, Republic of Korea.
authors.forename: Gyung Ja
authors.initials: GJ
authors.lastname: Choi
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon 540-950, Republic of Korea.
authors.forename: Ill-Sup
authors.initials: IS
authors.lastname: Nou
authors.affiliation: Phyzen Genomics Institute, Seoul 151-836, Republic of Korea.
authors.forename: Yeisoo
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 232-916, Republic of Korea tjyang@snu.ac.kr.
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
mesh_terms: D001937:Brassica / Q000235:genetics*; D029741:Brassica rapa / Q000235:genetics; D002874:Chromosome Mapping; D008040:Genetic Linkage; D018745:Genome, Plant; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D056909:Plasmodiophorida; D040641:Quantitative Trait Loci
keywords: QTL; cabbage; clubroot; genetic linkage map; genotyping-by-sequencing