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. CONCLUSION: 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.
| Identifer | oai:union.ndltd.org:arizona.edu/oai:arizona.openrepository.com:10150/610296 |
| Date | January 2015 |
| Creators | Lee, Jonghoon, Izzah, Nur K., Jayakodi, Murukarthick, Perumal, Sampath, Joh, Ho J., Lee, Hyeon J., Lee, Sang-Choon, Park, Jee Y., Yang, Ki-Woung, Nou, Il-Sup, Seo, Joodeok, Yoo, Jaeheung, Suh, Youngdeok, Ahn, Kyounggu, Lee, Ji Hyun, Choi, Gyung Ja, Yu, Yeisoo, Kim, Heebal, Yang, Tae-Jin |
| Contributors | 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, Indonesian Researcg Institute for Industrial and Beverage Crops (IRIIBC), Pakuwon, Department of Horticulture, Sunchon National University, Joeun Seed, Research Center for Biobased Chemistry, Korea Research Institute of Chemical Technology, Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Department of Agricultural Biotechnology, Seoul National University, CHO & KIM genomics, Seoul National University Mt.4-2 |
| Publisher | BioMed Central Ltd |
| Source Sets | University of Arizona |
| Language | English |
| Detected Language | English |
| Type | Article |
| Rights | © 2015 Lee et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0) |
| Relation | http://www.biomedcentral.com/1471-2229/15/32 |
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