Abstract

BackgroundGenome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.ResultsWe identify 55 novel quantitative trait loci (QTLs) that are associated with phenotypic variation. The largest number of QTLs is associated with the budburst stage, followed by diameter at breast height, wood quality, and frost damage. Two QTLs with the largest effect have a pleiotropic effect for budburst stage, frost damage, and diameter and are associated with MAP3K genes. Genotype data called from exome capture, recently developed SNP array and gene expression data indirectly support this discovery.ConclusionSeveral important QTLs associated with growth and frost damage have been verified in several southern and northern progeny plantations, indicating that these loci can be used in QTL-assisted genomic selection. Our study also demonstrates that existing heterogeneous phenotypic data from breeding programs, collected over several decades, is an important source for GWAS and that such integration into GWAS should be a major area of inquiry in the future.

Keywords

Norway spruce; Frost damage; Genome-wide association study; Wood quality; Budburst stage; MAP3K gene

Published in

Genome Biology
2021, Volume: 22, number: 1, article number: 179
Publisher: BMC

SLU Authors

• Chen, Zhiqiang

  • Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
    

• Wu, Harry

  • Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
    
  • Beijing Forestry University
  • Commonwealth Scientific and Industrial Research Organisation (CSIRO)

• Zan, Yanjun

  • Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
    

• Zhou, Linghua

  • Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
    

• Chen, Jun

  • Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences
    

• Westin, Johan

  • Unit for Field-based Forest Research, Swedish University of Agricultural Sciences
    
  • Forestry Research Institute of Sweden, Skogforsk

• Garcia Gil, Rosario

  • Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Forest Science


Publication identifier

DOI: https://doi.org/10.1186/s13059-021-02392-1

Permanent link to this page (URI)

https://res.slu.se/id/publ/112763