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Molecular Biology Reports

, Volume 45, Issue 5, pp 773–785 | Cite as

Identification of NBS-encoding genes linked to black rot resistance in cabbage (Brassica oleracea var. capitata)

  • Khandker Shazia Afrin
  • Md Abdur Rahim
  • Jong-In Park
  • Sathishkumar Natarajan
  • Hoy-Taek Kim
  • Ill-Sup NouEmail author
Original Article

Abstract

Heading cabbage is a nutritionally rich and economically important cruciferous vegetable. Black rot disease, caused by the bacterium Xanthomonas campestris pv. campestris, reduces both the yield and quality of the cabbage head. Nucleotide binding site (NBS)-encoding resistance (R) genes play a vital role in the plant immune response to various pathogens. In this study, we analyzed the expression and DNA sequence variation of 31 NBS-encoding genes in cabbage (Brassica oleracea var. capitata). These genes encoded TIR, NBS, LRR and RPW8 protein domains, all of which are known to be involved in disease resistance. RNA-seq revealed that these 31 genes were differentially expressed in leaf, root, silique, and stem tissues. Furthermore, qPCR analyses revealed that several of these genes were more highly expressed in resistant compared to susceptible cabbage lines, including Bol003711, Bol010135, Bol010559, Bol022784, Bol029866, Bol042121, Bol031422, Bol040045 and Bol042095. Further analysis of these genes promises to yield both practical benefits, such as molecular markers for marker-assisted breeding, and fundamental insights to the mechanisms of resistance to black rot in cabbage.

Keywords

Black rot Cabbage Resistance NBS-encoding genes Expression 

Abbreviations

ANOVA

Analysis of variance

R gene

Resistance gene

CC

Coiled-coil

CDD

Conserved domain database

FPKM

Fragments per kilobase of transcript per million mapped reads

GEO

Gene expression omnibus

InDel

Insertion/deletion

LRR

Leucine-rich repeats

NBS

Nucleotide binding site

qPCR

Quantitative real time polymerase chain reaction

SNP

Single nucleotide polymorphism

TIR

Toll interleukin-1 receptor

Notes

Acknowledgements

This research work was financially supported by the Golden Seed Project (Center for Horticultural Seed Development, Grant No. 213007-05-2-CG100) of the Ministry of Agriculture, Food and Rural affairs in the Republic of Korea (MAFRA).

Author contributions

I-SN, J-IP and H-TK designed the research. KSA conducted the experiments. KSA and MAR analyzed the data and created figures and tables. SN contributed to the in silco identification of genetic variants. KSA and MAR wrote the manuscript. All the authors contributed to, read and approved the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that there are no competing interests.

Ethical approval

This article does not contain any studies with human participants and/or animals performed by any of the authors.

Supplementary material

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Supplementary material Figure S1 (DOCX 460 KB)
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Supplementary material Table S1 (DOCX 20 KB)
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Supplementary material Table S2 (XLSX 16 KB)
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Supplementary material Table S3 (XLSX 14 KB)
11033_2018_4217_MOESM5_ESM.xlsx (19 kb)
Supplementary material Table S4 (XLSX 18 KB)
11033_2018_4217_MOESM6_ESM.xlsx (10 kb)
Supplementary material Table S5 (XLSX 9 KB)

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Khandker Shazia Afrin
    • 1
  • Md Abdur Rahim
    • 1
    • 2
  • Jong-In Park
    • 1
  • Sathishkumar Natarajan
    • 1
  • Hoy-Taek Kim
    • 1
  • Ill-Sup Nou
    • 1
    Email author
  1. 1.Department of HorticultureSunchon National UniversitySuncheonRepublic of Korea
  2. 2.Department of Genetics and Plant BreedingSher-e-Bangla Agricultural UniversityDhakaBangladesh

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