Theoretical and Applied Genetics

, Volume 130, Issue 1, pp 41–52 | Cite as

Rapid identification of QTLs underlying resistance to Cucumber mosaic virus in pepper (Capsicum frutescens)

  • Guangjun Guo
  • Shubin WangEmail author
  • Jinbing Liu
  • Baogui Pan
  • Weiping Diao
  • Wei Ge
  • Changzhou Gao
  • John C. Snyder
Original Article


Key message

Next-generation sequencing enabled a fast discovery of QTLs controlling CMV resistant in pepper. The gene CA02g19570 as a possible candidate gene of qCmr2.1 was identified for resistance to CMV in pepper.


Cucumber mosaic virus (CMV) is one of the most important viruses infecting pepper, but the genetic basis of CMV resistance in pepper is elusive. In this study, we identified a candidate gene for CMV resistance QTL, qCmr2.1 through SLAF-seq. Segregation analysis in F2, BC1 and F2:3 populations derived from a cross between two inbred lines ‘PBC688’ (CMV-resistant) and ‘G29’ (CMV-susceptible) suggested quantitative inheritance of resistance to CMV in pepper. Genome-wide comparison of SNP profiles between the CMV-resistant and CMV-susceptible bulks constructed from an F2 population identified two QTLs, designated as qCmr2.1 on chromosome 2 and qCmr11.1 on chromosome 11 for resistance to CMV in PBC688, which were confirmed by InDel marker-based classical QTL mapping in the F2 population. As a major QTL, joint SLAF-seq and traditional QTL analysis delimited qCmr2.1 to a 330 kb genomic region. Two pepper genes, CA02g19570 and CA02g19600, were identified in this region, which are homologous with the genes LOC104113703, LOC104248995, LOC102603934 and LOC101248357, which were predicted to encode N-like protein associated with TMV-resistant in Solanum crops. Quantitative RT-PCR revealed higher expression levels of CA02g19570 in CMV resistance genotypes. The CA02g19600 did not exhibit obvious regularity in expression patterns. Higher relative expression levels of CA02g19570 in PBC688 and F1 were compared with those in G29 during days after inoculation. These results provide support for CA02g19570 as a possible candidate gene of qCmr2.1 for resistance to CMV in pepper.


Tobacco Mosaic Virus Cucumber Mosaic Virus Disease Index Bulk Segregant Analysis InDel Marker 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was supported by the National Natural Science Foundation of China (NSFC 31401866), Natural Science Foundation of Jiangsu Province (CN) (4111415), Jiangsu Provincial Fund for Independent Innovation of Agricultural Sciences [CX (14)5013], and Jiangsu Agriculture Science and Technology Innovation Fund [CX (12)1004].

Compliance with ethical standards

Conflict of interest

The authors have declared that no competing interests exist.

Ethical standard

The experiments in this study comply with the current laws of China.

Supplementary material

122_2016_2790_MOESM1_ESM.pdf (507 kb)
Supplementary material 1 (PDF 507 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Guangjun Guo
    • 1
  • Shubin Wang
    • 1
    Email author
  • Jinbing Liu
    • 1
  • Baogui Pan
    • 1
  • Weiping Diao
    • 1
  • Wei Ge
    • 1
  • Changzhou Gao
    • 1
  • John C. Snyder
    • 2
  1. 1.Institute of Vegetable CropsJiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjingChina
  2. 2.Department of HorticultureUniversity of KentuckyLexingtonUSA

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