Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce
Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce
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DOI：
10.1111/tpj.14429
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发表时间：
2019-07-28
期刊：
影响因子：
7.2
通讯作者：
Garcia-Gil, M. Rosario
中科院分区：
文献类型：
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作者：
Baison, John;Vidalis, Amaryllis;Garcia-Gil, M. Rosario
挪威云杉是一种具有重要生态和经济价值的北方森林树种。因此，有一个强烈的必要性，剖析遗传学的重要木材质量性状的物种。我们进行了功能全基因组关联研究（GWAS）的17个木材性状在挪威云杉使用178 101单核苷酸多态性（SNP）产生的外显子组基因分型的517母树。木材性状的定义使用功能建模的木材性能跨年轮。我们应用了最小绝对收缩和选择算子（LASSO为基础）关联映射方法，使用功能多位点映射方法，利用潜在性状，与稳定性选择概率方法作为假设检验方法，以确定一个显着的数量性状位点。该分析提供了来自39个候选基因的52个显著SNP，包括先前在云杉和其他物种中涉及木材形成和树木生长的基因。我们的研究代表了挪威云杉复杂木材性状的多位点GWAS。这些结果促进了我们对影响木材性状的遗传学的理解，并为未来的功能研究确定了候选基因。
Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome-wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO-based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.