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

Genome Biology
Zhi-Qiang ChenHarry X Wu

Abstract

Genome-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. We 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. Several important QTLs associated with growth and frost damage have been verified in several southern a...Continue Reading

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Citations

Nov 21, 2021·The Plant Journal : for Cell and Molecular Biology·Amanda R De La TorreThomas N Buckley

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Software Mentioned

synbreed package
BLINK
Genome Variant Call
ASReml
CMLM
Rus
R package “ sleuth
missForest
SAMTools
BLINK R

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