Genomic Breeding and Comparative Genomics in Plant

NAISS 2023/5-513


NAISS Medium Compute

Principal Investigator:

Harry Wu


Sveriges lantbruksuniversitet

Start Date:


End Date:


Primary Classification:

10203: Bioinformatics (Computational Biology) (applications to be 10610)



Since the publication of the large and complex (conifer) Norway spruce genome in 2013, we have initiated genome re-sequencing, genome-wide association studies (GWAS) using exome sequencing, development of 50K SNP array from genome re-sequencing, and exploration of pilot genomic selection for Norway spruce. These genomic science projects were funded by one large Swedish Foundation for Strategic Research (SSF) project (RBP14-0040) and two Formas projects (2014-00171, 2014-427) and with the support of several SNIC medium (2016/1-122; 2016/1-385, b2017108) and several SNIC small projects, which have facilitated our delivery of the projects with more than 30 publications so far. With the success of these initial, genome re-sequencing, GWAS and genomic selection, we are now scaling up the GWAS and genomic selection in partnership with the Swedish national tree breeding organization Skogforsk to implement genome re-sequencing, the GWAS and genomic selection for Swedish national breeding programs of Norway spruce and Scot pine. The scaling-up project to the breeding program include: (1) re-sequencing 1104 Norway spruce trees (Genome size 20Gb) and 300 Scots pine trees (Genome size 25 Gb) at 10X coverage to study genome structure variation, (2) developing an extra-high density 800K SNP array for Norway spruce, and a high density 50K SNP array for Scots pine using genome re-sequencing SNP calling; (3) Genotyping 18,000 Norway spruce trees and 10,000 Scots pine trees using high density SNP arrays; (4) Conducting GWAS to discover major genes for 15-18 quantitative traits for population size from 300 to 18,000 individuals; (5) Conducting SNP calling and genomic selection for 20 Norway spruce and 10 Scots pine breeding populations; (6) study genomic selection across generations using 50,000 genomic markers. These researches are supported by one Formas project (2019-00874) and the Knut and Alice Wallenberg Foundation (KAW) project (2018-0272). In 2022, we are granted new funding from SSF (2022-2026) to re-sequencing 600 additional Norway spruce trees for GWAS and from Kempe foundation (2023-2024) to resequencing 180 pines trees from 5 species to study comparative genomics and genomic signatures of adaptive evolution in gymnosperm. In 2024, we will map and SNP calling for these 780 trees with a total of 78,000 Gb sequencing data. Besides scaling up genomic based breeding and comparative genomics for conifers, our group also secured two projects for climate adaptation study of Norway spruce (EU Horizon2020-773383) and gene by gene and gene by environment interaction (Formas mobility 2019-01600). For the former, adaptation of 1100 Norway spruce populations collected from species-wide and planted at 20 locations in 12 European countries will be phenotyped and genotyped, and genomic base of adaptation of different populations will be analyzed. For the mobility project, 6000 maize lines phenotyped across 5 locations along a climate gradient will be analyzed using whole genome re-sequence, transcriptomic and metabolomics data. Results from these projects will offer unprecedented resources to help breeders improve the way we produce fiber, wood, food in plants that will have superb and stable performance for mitigation to climate change.