Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.)

Jonghoon Lee, Nur Kholilatul Izzah, Beom Soon Choi, Ho Jun Joh, Sang Choon Lee, Sampath Perumal, Joodeok Seo, Kyounggu Ahn, Eun Ju Jo, Gyung Ja Choi, Ill Sup Nou, Yeisoo Yu, Tae Jin Yang

Research output: Contribution to journalArticle

35 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)29-41
Number of pages13
JournalDNA Research
Volume23
Issue number1
DOIs
StatePublished - Aug 2 2015
Externally publishedYes

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Quantitative Trait Loci
Brassica
Brassica rapa
Genome
Genotyping Techniques
Plasmodiophorida
Genes
Single Nucleotide Polymorphism

Keywords

  • cabbage
  • clubroot
  • genetic linkage map
  • genotyping-by-sequencing
  • QTL

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

Cite this

Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.). / Lee, Jonghoon; Izzah, Nur Kholilatul; Choi, Beom Soon; Joh, Ho Jun; Lee, Sang Choon; Perumal, Sampath; Seo, Joodeok; Ahn, Kyounggu; Jo, Eun Ju; Choi, Gyung Ja; Nou, Ill Sup; Yu, Yeisoo; Yang, Tae Jin.

In: DNA Research, Vol. 23, No. 1, 02.08.2015, p. 29-41.

Research output: Contribution to journalArticle

Lee, J, Izzah, NK, Choi, BS, Joh, HJ, Lee, SC, Perumal, S, Seo, J, Ahn, K, Jo, EJ, Choi, GJ, Nou, IS, Yu, Y & Yang, TJ 2015, 'Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.)', DNA Research, vol. 23, no. 1, pp. 29-41. https://doi.org/10.1093/dnares/dsv034
Lee, Jonghoon ; Izzah, Nur Kholilatul ; Choi, Beom Soon ; Joh, Ho Jun ; Lee, Sang Choon ; Perumal, Sampath ; Seo, Joodeok ; Ahn, Kyounggu ; Jo, Eun Ju ; Choi, Gyung Ja ; Nou, Ill Sup ; Yu, Yeisoo ; Yang, Tae Jin. / Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.). In: DNA Research. 2015 ; Vol. 23, No. 1. pp. 29-41.
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AU - Lee, Jonghoon

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AU - Choi, Beom Soon

AU - Joh, Ho Jun

AU - Lee, Sang Choon

AU - Perumal, Sampath

AU - Seo, Joodeok

AU - Ahn, Kyounggu

AU - Jo, Eun Ju

AU - Choi, Gyung Ja

AU - Nou, Ill Sup

AU - Yu, Yeisoo

AU - Yang, Tae Jin

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N2 - 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.

AB - 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.

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