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

Jonghoon Lee, Nur Kholilatul Izzah, Murukarthick Jayakodi, Sampath Perumal, Ho Jun Joh, Hyeon Ju Lee, Sang Choon Lee, Jee Young Park, Ki Woung Yang, Il Sup Nou, Joodeok Seo, Jaeheung Yoo, Youngdeok Suh, Kyounggu Ahn, Ji Hyun Lee, Gyung Ja Choi, Yeisoo Yu, Heebal Kim, Tae Jin Yang

Research output: Contribution to journalArticlepeer-review

32 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article number32
JournalBMC Plant Biology
Volume15
Issue number1
DOIs
StatePublished - Feb 3 2015

Keywords

  • Black rot
  • Cabbage
  • Genetic linkage map
  • QTL
  • Whole-genome resequencing

ASJC Scopus subject areas

  • Plant Science

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