Theoretical and Applied Genetics

, Volume 131, Issue 5, pp 1017–1030 | Cite as

Identification of a molecular marker tightly linked to bacterial wilt resistance in tomato by genome-wide SNP analysis

  • Boyoung Kim
  • In Sun Hwang
  • Hyung Jin Lee
  • Je Min Lee
  • Eunyoung Seo
  • Doil Choi
  • Chang-Sik Oh
Original Article


Key message

Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis


Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar ‘Hawaii7996’. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease. In total, 5259 non-synonymous SNPs were found between the two groups. Among them, only 265 SNPs were located in the coding DNA sequences, and the majority of these SNPs were located on chromosomes 6 and 12. The genes that both carry SNP(s) and are near Bwr-6 and Bwr-12 were selected. In particular, four genes in chromosome 12 encode putative leucine-rich repeat (LRR) receptor-like proteins. SNPs within these four genes were used to develop SNP markers, and each SNP marker was validated by a high-resolution melting method. Consequently, one SNP marker, including a functional SNP in a gene, Solyc12g009690.1, could efficiently distinguish tomato varieties resistant to bacterial wilt from susceptible varieties. These results indicate that Solyc12g009690.1, the gene encoding a putative LRR receptor-like protein, might be tightly linked to Bwr-12, and the SNP marker developed in this study will be useful for selection of tomato cultivars resistant to bacterial wilt.



We are grateful to Dr. Young Hoon Park and RDA-Gene Bank for providing tomato seeds. This work was supported by the Golden Seed Project (Center for Horticultural Seed Development No. 213003-04-4-SBG20 and No. 213007-05-1-SBF20), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA), and Korea Forest Service (KFS) and also by the National Research Foundation of Korea (NRF) Grant funded by the Korean government (MSIP) (No. 2016R1A2B4011566).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

122_2018_3054_MOESM1_ESM.pdf (368 kb)
Supplementary material 1 (PDF 368 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Boyoung Kim
    • 1
  • In Sun Hwang
    • 1
  • Hyung Jin Lee
    • 1
  • Je Min Lee
    • 2
  • Eunyoung Seo
    • 3
  • Doil Choi
    • 3
  • Chang-Sik Oh
    • 1
  1. 1.Department of Horticultural Biotechnology, College of Life ScienceKyung Hee UniversityYonginSouth Korea
  2. 2.Department of Horticultural ScienceKyungpook National UniversityDaeguSouth Korea
  3. 3.Department of Plant ScienceSeoul National UniversitySeoulSouth Korea

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