A Picea Abies Linkage Map Based on SNP Markers Identifies QTLs for Four Aspects of Resistance to Heterobasidion Parviporum Infection

PLoS One. 2014 Jul 18;9(7):e101049. doi: 10.1371/journal.pone.0101049. eCollection 2014.

Abstract

A consensus linkage map of Picea abies, an economically important conifer, was constructed based on the segregation of 686 SNP markers in a F1 progeny population consisting of 247 individuals. The total length of 1889.2 cM covered 96.5% of the estimated genome length and comprised 12 large linkage groups, corresponding to the number of haploid P. abies chromosomes. The sizes of the groups (from 5.9 to 9.9% of the total map length) correlated well with previous estimates of chromosome sizes (from 5.8 to 10.8% of total genome size). Any locus in the genome has a 97% probability to be within 10 cM from a mapped marker, which makes the map suited for QTL mapping. Infecting the progeny trees with the root rot pathogen Heterobasidion parviporum allowed for mapping of four different resistance traits: lesion length at the inoculation site, fungal spread within the sapwood, exclusion of the pathogen from the host after initial infection, and ability to prevent the infection from establishing at all. These four traits were associated with two, four, four and three QTL regions respectively of which none overlapped between the traits. Each QTL explained between 4.6 and 10.1% of the respective traits phenotypic variation. Although the QTL regions contain many more genes than the ones represented by the SNP markers, at least four markers within the confidence intervals originated from genes with known function in conifer defence; a leucoanthocyanidine reductase, which has previously been shown to upregulate during H. parviporum infection, and three intermediates of the lignification process; a hydroxycinnamoyl CoA shikimate/quinate hydroxycinnamoyltransferase, a 4-coumarate CoA ligase, and a R2R3-MYB transcription factor.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Basidiomycota / physiology*
  • Chromosome Mapping / methods*
  • Disease Resistance / genetics*
  • Genes, Plant / genetics
  • Genetic Markers / genetics
  • Picea / genetics
  • Picea / microbiology*
  • Picea / physiology
  • Plant Diseases / microbiology*
  • Polymorphism, Single Nucleotide / genetics*
  • Quantitative Trait Loci / genetics*

Substances

  • Genetic Markers

Grant support

Financial support was received from the European Community's Sixth Framework Programme, under the Network of Excellence Evoltree (www.evoltree.eu/), by the Seventh Framework Programme (FP7/2007-2013) under the grant agreement n° 211868 (Project Noveltree, www.noveltree.eu/), and by the Swedish Research Council FORMAS grant dnr 217-2007-433 (www.formas.se/en). Support also came from the Biodiversa projects Linktree (www.igv.fi.cnr.it/linktree/) and TipTree, grant ANR-12-EBID-0003 (www.agence-nationale-recherche.fr/en/anr-funded-project/?tx_lwmsuivibilan_pi2[CODE] = ANR-12-EBID-0003), and from the Swedish Foundation for Strategic Research (SSF), grant number R8b08-0011 (www.stratresearch.se). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.