Academic Bibliography

 Search 200 years of publications by Ghent University researchers.
Advanced search
1 file | 2.01 MB
Add to list
  1. Search results
  2. SNP detection in Pinus pinaster trans...

SNP detection in Pinus pinaster transcriptome and association with resistance to pinewood nematode

Inês Sofia Barrios Modesto (UGent) , Vera Inácio, Polina Novikova, Isabel Carrasquinho, Yves Van de Peer (UGent) and Célia M. Miguel
(2022) FORESTS. 13(6).
Author
Organization
Abstract
Pinewood nematode (PWN, Bursaphelenchus xylophilus) is the causal agent of pine wilt disease (PWD), which severely affects Pinus pinaster stands in southwestern Europe. Despite the high susceptibility of P. pinaster, individuals of selected half-sib families have shown genetic variability in survival after PWN inoculation, indicating that breeding for resistance can be a valuable strategy to control PWD. In this work, RNA-seq data from susceptible and resistant plants inoculated with PWN were used for SNP discovery and analysis. A total of 186,506 SNPs were identified, of which 31 were highly differentiated between resistant and susceptible plants, including SNPs in genes involved in cell wall lignification, a process previously linked to PWN resistance. Fifteen of these SNPs were selected for validation through Sanger sequencing and 14 were validated. To evaluate SNP-phenotype associations, 40 half-sib plants were genotyped for six validated SNPs. Associations with phenotype after PWN inoculation were found for two SNPs in two different genes (MEE12 and PCMP-E91), as well as two haplotypes of HIPP41, although significance was not maintained following Bonferroni correction. SNPs here detected may be useful for the development of molecular markers for PWD resistance and should be further investigated in future association studies.
Keywords
maritime pine, pine wilt disease, RNA-seq, single nucleotide polymorphism, molecular markers, PENTATRICOPEPTIDE REPEAT PROTEINS, BURSAPHELENCHUS-XYLOPHILUS, STATISTICAL-METHOD, GENE, EXPRESSION, DEFENSE, GENOME, TOLERANCE, FORMAT

Downloads

  • Download
    Modesto et al. 2022 Forests 13 946.pdf
    • full text (Published version)
    • |
    • open access
    • |
    • PDF
    • |
    • 2.01 MB

Citation

Please use this url to cite or link to this publication:

MLA
Barrios Modesto, Inês Sofia, et al. “SNP Detection in Pinus Pinaster Transcriptome and Association with Resistance to Pinewood Nematode.” FORESTS, vol. 13, no. 6, 2022, doi:10.3390/f13060946.
APA
Barrios Modesto, I. S., Inácio, V., Novikova, P., Carrasquinho, I., Van de Peer, Y., & Miguel, C. M. (2022). SNP detection in Pinus pinaster transcriptome and association with resistance to pinewood nematode. FORESTS, 13(6). https://doi.org/10.3390/f13060946
Chicago author-date
Barrios Modesto, Inês Sofia, Vera Inácio, Polina Novikova, Isabel Carrasquinho, Yves Van de Peer, and Célia M. Miguel. 2022. “SNP Detection in Pinus Pinaster Transcriptome and Association with Resistance to Pinewood Nematode.” FORESTS 13 (6). https://doi.org/10.3390/f13060946.
Chicago author-date (all authors)
Barrios Modesto, Inês Sofia, Vera Inácio, Polina Novikova, Isabel Carrasquinho, Yves Van de Peer, and Célia M. Miguel. 2022. “SNP Detection in Pinus Pinaster Transcriptome and Association with Resistance to Pinewood Nematode.” FORESTS 13 (6). doi:10.3390/f13060946.
Vancouver
1.
Barrios Modesto IS, Inácio V, Novikova P, Carrasquinho I, Van de Peer Y, Miguel CM. SNP detection in Pinus pinaster transcriptome and association with resistance to pinewood nematode. FORESTS. 2022;13(6).
IEEE
[1]
I. S. Barrios Modesto, V. Inácio, P. Novikova, I. Carrasquinho, Y. Van de Peer, and C. M. Miguel, “SNP detection in Pinus pinaster transcriptome and association with resistance to pinewood nematode,” FORESTS, vol. 13, no. 6, 2022.
@article{8757276,
  abstract     = {{Pinewood nematode (PWN, Bursaphelenchus xylophilus) is the causal agent of pine wilt disease (PWD), which severely affects Pinus pinaster stands in southwestern Europe. Despite the high susceptibility of P. pinaster, individuals of selected half-sib families have shown genetic variability in survival after PWN inoculation, indicating that breeding for resistance can be a valuable strategy to control PWD. In this work, RNA-seq data from susceptible and resistant plants inoculated with PWN were used for SNP discovery and analysis. A total of 186,506 SNPs were identified, of which 31 were highly differentiated between resistant and susceptible plants, including SNPs in genes involved in cell wall lignification, a process previously linked to PWN resistance. Fifteen of these SNPs were selected for validation through Sanger sequencing and 14 were validated. To evaluate SNP-phenotype associations, 40 half-sib plants were genotyped for six validated SNPs. Associations with phenotype after PWN inoculation were found for two SNPs in two different genes (MEE12 and PCMP-E91), as well as two haplotypes of HIPP41, although significance was not maintained following Bonferroni correction. SNPs here detected may be useful for the development of molecular markers for PWD resistance and should be further investigated in future association studies.}},
  articleno    = {{946}},
  author       = {{Barrios Modesto, Inês Sofia and Inácio, Vera and Novikova, Polina and Carrasquinho, Isabel and Van de Peer, Yves and Miguel, Célia M.}},
  issn         = {{1999-4907}},
  journal      = {{FORESTS}},
  keywords     = {{maritime pine,pine wilt disease,RNA-seq,single nucleotide polymorphism,molecular markers,PENTATRICOPEPTIDE REPEAT PROTEINS,BURSAPHELENCHUS-XYLOPHILUS,STATISTICAL-METHOD,GENE,EXPRESSION,DEFENSE,GENOME,TOLERANCE,FORMAT}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{16}},
  title        = {{SNP detection in Pinus pinaster transcriptome and association with resistance to pinewood nematode}},
  url          = {{http://doi.org/10.3390/f13060946}},
  volume       = {{13}},
  year         = {{2022}},
}
Altmetric
View in Altmetric
Web of Science
Times cited: