全基因组关联研究(GWAS)确定了复杂性状变异的潜在基因座。GWAS的主要限制之一是可靠的表型数据的可用性,特别是对于长寿树种。尽管育种计划中已经存在大量的表型数据,对其高度异质性的核算是一个巨大的挑战。我们结合了空间和因子分析,以标准化来自挪威云杉483,424个后代的120个田间实验的异构数据,以使用来自5056个亲本树的外显子组测序的134605个SNP对树木实施最大的GWAS报告。
我们鉴定了55个与表型变异相关的新数量性状基因座(QTL)。最大数量的QTL与budburst阶段相关联,其次是胸高直径,木材质量,和霜冻损坏。两个效应最大的QTL对芽突阶段具有多效性效应,霜冻损坏,和直径,并与MAP3K基因相关。来自外显子组捕获的基因型数据,最近开发的SNP阵列和基因表达数据间接支持这一发现。
已经在几个南部和北部的后代种植园中验证了与生长和霜冻破坏相关的几个重要QTL,表明这些基因座可用于QTL辅助基因组选择。我们的研究还表明,来自育种计划的现有异质表型数据,收集了几十年,是GWAS的重要来源,并且这种集成到GWAS中应该是将来的主要研究领域。
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 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.