Identification of Parent-of-Origin-Dependent QTLs Using Bulk-Segregant Sequencing (Bulk-Seq)

  • Nuno D. PiresEmail author
  • Ueli Grossniklaus
Part of the Methods in Molecular Biology book series (MIMB, volume 1675)


Parent-of-origin effects play important roles in plant reproduction and are often mediated by epigenetic modifications at the histone or DNA level. However, the genetic basis underlying these modifications can be challenging to identify. Here, we describe an approach (Bulk-Seq) that can be used to map loci mediating parent-of-origin-dependent effects using whole-genome sequencing of pools of DNA.

Key words

Bulk-segregant sequencing Parent-of-origin effects Seed development Quantitative trait mapping Segregation distortion Arabidopsis thaliana 


  1. 1.
    Raissig MT, Baroux C, Grossniklaus U (2011) Regulation and flexibility of genomic imprinting during seed development. Plant Cell 23:16–26. doi: 10.1105/tpc.110.081018 CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Pires N (2014) Seed evolution: parental conflicts in a multi-generational household. Biomol Concepts 5:71–86CrossRefPubMedGoogle Scholar
  3. 3.
    García-Aguilar M, Gillmor CS (2015) Zygotic genome activation and imprinting: Parent-of-origin gene regulation in plant embryogenesis. Curr Opin Plant Biol 27:29–35. doi: 10.1016/j.pbi.2015.05.020 CrossRefPubMedGoogle Scholar
  4. 4.
    Piskurewicz U, Iwasaki M, Susaki D et al (2016) Dormancy-specific imprinting underlies maternal inheritance of seed dormancy in Arabidopsis thaliana. Elife 5:e19573CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Pires ND, Bemer M, Müller LM et al (2016) Quantitative genetics identifies cryptic genetic variation involved in the paternal regulation of seed development. PLoS Genet 12:e1005806. doi: 10.1371/journal.pgen.1005806 CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Grossniklaus U, Vielle-Calzada J-P, Hoeppner MA, Gagliano WB (1998) Maternal control of embryogenesis by MEDEA, a Polycomb group gene in Arabidopsis. Science 280:446–450. doi: 10.1126/science.280.5362.446 CrossRefPubMedGoogle Scholar
  7. 7.
    Makarevich G, Leroy O, Akinci U et al (2006) Different polycomb group complexes regulate common target genes in Arabidopsis. EMBO Rep 7:947–952. doi: 10.1038/sj.embor.7400760 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Takagi H, Abe A, Yoshida K et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183. doi: 10.1111/tpj.12105 CrossRefPubMedGoogle Scholar
  9. 9.
    Yang Z, Huang D, Tang W et al (2013) Mapping of quantitative trait loci underlying cold tolerance in rice seedlings via high-throughput sequencing of pooled extremes. PLoS One 8:e68433. doi: 10.1371/journal.pone.0068433 CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal 17:1Google Scholar
  11. 11.
    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Alonso-Blanco C, Andrade J, Becker C et al (2016) 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166:481–491. doi: 10.1016/j.cell.2016.05.063 CrossRefGoogle Scholar
  14. 14.
    Magwene PM, Willis JH, Kelly JK (2011) The statistics of bulk segregant analysis using next generation sequencing. PLoS Comput Biol 7:e1002255. doi: 10.1371/journal.pcbi.1002255 CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. doi: 10.1093/bioinformatics/btq033 CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140. doi: 10.1093/bioinformatics/btp616 CrossRefPubMedGoogle Scholar
  18. 18.
    Schneeberger K, Ossowski S, Ott F et al (2011) Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci U S A 108:10249–10254. doi: 10.1073/pnas.1107739108 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.Department of Plant and Microbial Biology, Zürich-Basel Plant Science CenterUniversity of ZürichZürichSwitzerland

Personalised recommendations