Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
Plant Biotechnol J. 2019 Jan;17(1):302-315. doi: 10.1111/pbi.12978. Epub 2018 Jul 16.
Lignin provides structural support in perennial woody plants and is a complex phenolic polymer derived from phenylpropanoid pathway. Lignin biosynthesis is regulated by coordinated networks involving transcription factors (TFs), microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). However, the genetic networks underlying the lignin biosynthesis pathway for tree growth and wood properties remain unknown. Here, we used association genetics (additive, dominant and epistasis) and expression quantitative trait nucleotide (eQTN) mapping to decipher the genetic networks for tree growth and wood properties in 435 unrelated individuals of Populus tomentosa. We detected 124 significant associations (P ≤ 6.89E-05) for 10 growth and wood property traits using 30 265 single nucleotide polymorphisms from 203 lignin biosynthetic genes, 81 TF genes, 36 miRNA genes and 71 lncRNA loci, implying their common roles in wood formation. Epistasis analysis uncovered 745 significant pairwise interactions, which helped to construct proposed genetic networks of lignin biosynthesis pathway and found that these regulators might affect phenotypes by linking two lignin biosynthetic genes. eQTNs were used to interpret how causal genes contributed to phenotypes. Lastly, we investigated the possible functions of the genes encoding 4-coumarate: CoA ligase and cinnamate-4-hydroxylase in wood traits using epistasis, eQTN mapping and enzymatic activity assays. Our study provides new insights into the lignin biosynthesis pathway in poplar and enables the novel genetic factors as biomarkers for facilitating genetic improvement of trees.
木质素为多年生木本植物提供结构支撑，是一种源自苯丙烷途径的复杂酚类聚合物。木质素生物合成受涉及转录因子（TFs）、microRNAs（miRNAs）和长非编码 RNA（lncRNAs）的协调网络调控。然而，树木生长和木材特性的木质素生物合成途径的遗传网络仍然未知。在这里，我们使用关联遗传学（加性、显性和上位性）和表达数量性状核苷酸（eQTN）图谱来解析毛白杨 435 个无关个体的树木生长和木材特性的遗传网络。我们使用来自 203 个木质素生物合成基因、81 个 TF 基因、36 个 miRNA 基因和 71 个 lncRNA 基因座的 30356 个单核苷酸多态性，检测到 10 个生长和木材特性的 124 个显著关联（P ≤ 6.89E-05），表明它们在木材形成中具有共同作用。上位性分析发现了 745 个显著的成对相互作用，有助于构建木质素生物合成途径的遗传网络，并发现这些调节剂可能通过连接两个木质素生物合成基因来影响表型。eQTN 用于解释因果基因如何导致表型。最后，我们使用上位性、eQTN 图谱和酶活性测定研究了编码 4-香豆酸：CoA 连接酶和肉桂酸-4-羟化酶的基因在木材特性中的可能功能。我们的研究为杨树木质素生物合成途径提供了新的见解，并为促进树木遗传改良的新遗传因素作为生物标志物提供了依据。
