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）与罕见的缺陷等位基因（过早或废除的停止密码子，改变的开始密码子，基因中的替代剪接位点）相关联方面取得了巨大成功，但尚未对森林树木中的这种联系进行系统探索，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(木质素大大减少，例如)，因此在树木育种方面有很大的潜力来加速木材的改良。现在，通过下一代测序技术，我们可以在树基因组及其携带者中找到这种罕见的突变。* * NSERC DG计划下的拟议研究旨在将木材成分的增值和森林内基因组选择工具联系起来，并在这方面展示了可行性，并为未来在树木育种中使用基因功能发现和开发方法提供了路线图。这种综合方法通常将证明快速改进未驯化的近交种植物的概念。在这里，提议的目标是产生具有工业相关性状的大幅度改进的杨树（杨树），例如从自然基础种群中改进纤维特性。* *在本初步研究中，将对大量天然杨树材料（c.900）的全基因组序列数据中的基因空间（外显子组）进行研究，以寻找生物途径基因中罕见的功能缺陷变异，从而获得候选基因的预选择。那些在复杂性状、罕见变异关联遗传学中将被突出的变异将被进一步检测；但不是通过繁琐的育种的传统方式。这些罕见隐性等位基因的携带者及其后代更有可能是杂合的。因此，精确的位点特异性基因组修饰技术将用于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）可以处理不易处理的基因型，因此非常适合对源自当地基础种群的最佳精英品种进行靶向诱变（通过同源定向修复介导的敲入）。新种质在稳定、可控的整体表型方面的表现将进一步评估。引入的改良在纯种家族中的遗传，木材纤维特性的期望变化，应激反应和适应（物候学）将紧随其后。* *该项目将解决与数量性状选择和植物育种有关的进化背景下的许多研究问题，同时直接旨在为森林种植和林产品部门提供更有效的选择。* * * * *

**** * **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.* ****