Harnessing the potential of natural loss-of-function allelic variants in wild poplar germplasm for accelerated forest tree domestication

虽然医学研究最近在将表型（例如疾病）与基因型相关联方面取得了巨大成功，对于罕见的缺陷等位基因（过早或被废除的终止密码子、改变的起始密码子、基因中的可变剪接位点），还没有系统地探索林木中的这种联系，然而，很少有已经检测到的天然功能丧失等位基因可以与有利的木材表型（例如，因此在树木育种的背景下具有加速木材改良的高潜力。现在，下一代测序技术促进了对树基因组及其携带者中这种罕见突变的获取。 NSERC DG计划下的拟议研究旨在将木材组分的价值评估和森林基因组选择工具联系起来，并在这方面证明了未来在树木育种中使用基因功能发现和开发方法的可行性和路线图。这种综合方法通常是用于快速改良未驯化的远系繁殖植物的概念验证。在此，提出的目标是从天然基础群体产生具有工业相关性状（例如改善的纤维特性）的显著改善的杨（杨树）。 在这里提出的试点研究中，基因空间（外显子组）从全基因组序列数据的大量天然白杨加入（c.900）将被调查的罕见功能缺陷的变异生物通路基因，以获得预选的候选人。那些将在复杂性状罕见变异关联遗传学中突出显示的变异将被进一步测试;但不是通过繁琐的育种回合以常规方式进行测试。这些罕见的隐性等位基因携带者及其后代更有可能是杂合子。因此，将使用精确的位点特异性基因组修饰技术来引入双等位基因修饰并绕过回交育种努力以获得携带所需突变的纯合个体。所提出的基因组编辑技术（CRISPR/Cas9）可以解决不太容易处理的基因型，因此非常适合对源自本地基础群体的最佳优良品种进行靶向诱变（通过同源定向修复介导的敲入），如本文所提出的。将进一步评估新菌种在稳定、受控的总体表型方面的表现。将遵循家系中引入的修改的遗传、木材纤维性质的期望变化、胁迫反应和适应（物候学）。 该项目将在进化的背景下解决许多研究问题，涉及对数量性状的选择和植物育种，同时直接旨在为森林种植和森林产品部门提供更多的生产选择。

While medical research has had great success recently in correlating phenotypes (disease, e.g.) with rare defective alleles (premature or abolished stop codons, altered start codons, alternative splice sites in genes), there has been no systematic exploration of such connection in forest trees, yet, few already detected natural loss-of-function alleles could be connected with advantageous wood phenotypes (substantially less lignin, e.g.) and have therefore high potential for accelerating wood improvement in the context of tree breeding. The access to such rare mutations in tree genomes and their carriers is now facilitated by next-generation sequencing. The proposed research under the NSERC DG program aims at linking wood components' valorization and in-forest genomic selection tools and in this respect demonstrate the feasibility and provision of a roadmap towards the future use of gene function discovery and exploitation approach in tree breeding. This integrative approach will generally be proof-of-concept for rapid improvement of undomesticated outbred plants. Here, the proposed aim is the generation of substantially improved Populus (poplars) for industrially relevant traits such as improved fibre characteristics from a natural base population. In the pilot study presented here, the gene space (exome) from whole genome sequence data of a large number of natural poplar accessions (c.900) will be investigated for rare functionally defective variants within bio-pathway genes to obtain a pre-selection of candidates. Those variants that will be highlighted in complex trait rare variant association genetics will be further tested; but not in the conventional way through cumbersome rounds of breeding. Carrier of these rare recessive alleles and their offspring are more likely to be heterozygous. Therefore, precise site-specific genome modification technology will be used to introduce biallelic modifications and bypass backcross breeding efforts to obtain homozygous individuals carrying the desired mutation. The proposed genome editing technology (CRISPR/Cas9) can tackle less tractable genotypes and is therefore well suited to perform targeted mutagenesis (via homology-directed repair mediated knock-in) on the best elite varieties originating from a local base population, as proposed here. The new germplasms' performance in terms of a stable, controlled overall phenotype will be further evaluated. Inheritance of the introduced modification in pedigreed families, the desired change in wood fibre properties, stress responses, and adaptation (phenology) will be followed. The project will address many research questions in the context of evolution that relates to selection acting on quantitative traits, and plant breeding, while directly aiming at delivering more productive options for the forest growing and forest product sectors.