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Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis

Chen, Zhiqiang and Zan, Yanjun and Milesi, Pascal and Zhou, Linghua and Chen, Jun and Milani, Lili and Cui, BinBin and Niu, Shihui and Westin, Johan and Karlsson, Bo and Garcia Gil, Rosario and Lascoux, Martin and Wu, Harry (2021). Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis. Genome Biology. 22 , 179
[Research article]

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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.

Authors/Creators:Chen, Zhiqiang and Zan, Yanjun and Milesi, Pascal and Zhou, Linghua and Chen, Jun and Milani, Lili and Cui, BinBin and Niu, Shihui and Westin, Johan and Karlsson, Bo and Garcia Gil, Rosario and Lascoux, Martin and Wu, Harry
Title:Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
Series Name/Journal:Genome Biology
Year of publishing :2021
Volume:22
Article number:179
Number of Pages:30
Publisher:BMC
ISSN:1474-760X
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Forest Science
Keywords:Norway spruce, Frost damage, Genome-wide association study, Wood quality, Budburst stage, MAP3K gene
URN:NBN:urn:nbn:se:slu:epsilon-p-112763
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-112763
Additional ID:
Type of IDID
DOI10.1186/s13059-021-02392-1
Web of Science (WoS)000664094600002
ID Code:24845
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Forest Genetics and Plant Physiology
(NL, NJ) > Dept. of Forest Mycology and Plant Pathology
(S) > Dept. of Forest Mycology and Plant Pathology

(S) > Unit for Field-based Forest Research
Deposited By: SLUpub Connector
Deposited On:12 Jul 2021 11:25
Metadata Last Modified:12 Jul 2021 11:31

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