Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage

Persistent Link:
http://hdl.handle.net/10150/610296
Title:
Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage
Author:
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
Affiliation:
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
Issue Date:
2015
Publisher:
BioMed Central Ltd
Citation:
Lee et al. BMC Plant Biology (2015) 15:32 DOI 10.1186/s12870-015-0424-6
Journal:
BMC Plant Biology
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)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
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. 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.
EISSN:
1471-2229
DOI:
10.1186/s12870-015-0424-6
Keywords:
Cabbage; Whole-genome resequencing; Genetic linkage map; Black rot; QTL
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2229/15/32

Full metadata record

DC FieldValue Language
dc.contributor.authorLee, Jonghoonen
dc.contributor.authorIzzah, Nur K.en
dc.contributor.authorJayakodi, Murukarthicken
dc.contributor.authorPerumal, Sampathen
dc.contributor.authorJoh, Ho J.en
dc.contributor.authorLee, Hyeon J.en
dc.contributor.authorLee, Sang-Choonen
dc.contributor.authorPark, Jee Y.en
dc.contributor.authorYang, Ki-Woungen
dc.contributor.authorNou, Il-Supen
dc.contributor.authorSeo, Joodeoken
dc.contributor.authorYoo, Jaeheungen
dc.contributor.authorSuh, Youngdeoken
dc.contributor.authorAhn, Kyoungguen
dc.contributor.authorLee, Ji Hyunen
dc.contributor.authorChoi, Gyung Jaen
dc.contributor.authorYu, Yeisooen
dc.contributor.authorKim, Heebalen
dc.contributor.authorYang, Tae-Jinen
dc.date.accessioned2016-05-20T09:03:31Z-
dc.date.available2016-05-20T09:03:31Z-
dc.date.issued2015en
dc.identifier.citationLee et al. BMC Plant Biology (2015) 15:32 DOI 10.1186/s12870-015-0424-6en
dc.identifier.doi10.1186/s12870-015-0424-6en
dc.identifier.urihttp://hdl.handle.net/10150/610296-
dc.description.abstractBACKGROUND: 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.en
dc.language.isoenen
dc.publisherBioMed Central Ltden
dc.relation.urlhttp://www.biomedcentral.com/1471-2229/15/32en
dc.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)en
dc.subjectCabbageen
dc.subjectWhole-genome resequencingen
dc.subjectGenetic linkage mapen
dc.subjectBlack roten
dc.subjectQTLen
dc.titleGenome-wide SNP identification and QTL mapping for black rot resistance in cabbageen
dc.typeArticleen
dc.identifier.eissn1471-2229en
dc.contributor.departmentDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National Universityen
dc.contributor.departmentIndonesian Researcg Institute for Industrial and Beverage Crops (IRIIBC), Pakuwonen
dc.contributor.departmentDepartment of Horticulture, Sunchon National Universityen
dc.contributor.departmentJoeun Seeden
dc.contributor.departmentResearch Center for Biobased Chemistry, Korea Research Institute of Chemical Technologyen
dc.contributor.departmentArizona Genomics Institute, School of Plant Sciences, University of Arizonaen
dc.contributor.departmentDepartment of Agricultural Biotechnology, Seoul National Universityen
dc.contributor.departmentCHO & KIM genomics, Seoul National University Mt.4-2en
dc.identifier.journalBMC Plant Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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