SNIC
SUPR
SNIC SUPR
Resequencing the Norway spruce (Picea abies) genome
Dnr:

SNIC 2017/1-438

Type:

SNAC Medium

Principal Investigator:

Pär Ingvarsson

Affiliation:

Sveriges lantbruksuniversitet

Start Date:

2017-11-01

End Date:

2018-11-01

Primary Classification:

10609: Genetics (medical to be 30107 and agricultural to be 40402)

Secondary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)

Tertiary Classification:

10615: Evolutionary Biology

Allocation

Abstract

The availability of the Norway spruce genome sequence opens up possibilities for re-sequencing of additional Norway spruce individuals to study the extent of genomic variation for both single nucleotide polymorphisms (SNPs) as well as small and large-scale structural variation. By doing population re-sequencing we aim is to investigate: 1. How different evolutionary forces has shaped patterns of nucleotide polymorphism across the Noway spruce genome. Areas of interest includes identifying genomic regions that have been the target of recent positive selection (selective sweeps) and genomic regions of high population differentiation which could signify regions which are targets of diversifying selection across species range. 2. Study the extent if structural variation, such as copy number variation (CNV) and presence/absence variation (PAV), across the Norway spruce genome. Recent data suggest that the genome of a species can be subdivided into a core part (present in all individuals) and a dispensable part (absent in at least one individual) (Marroni et al. 2014). Of particular interest for Norway spruce, which has a genome characterized massive amplification of repetitive DNA (mainly transposable elements, TEs, Nystedt et al 2013), is to what extent the there is evidence for recent TE activity and particularly if there is evidence for polymorphic TE-insertions across the Norway spruce genome. 3. The available resources developed (SNPs and copy number variants) will be available for downstream applications such as genomics-based breeding efforts that are currently being developed in Norway spruce