Genetic architecture of disease resistance and tolerance in Douglas-fir trees

Understanding the genetic architecture of tolerance and resistance to pathogens is important to monitor and maintain resilient tree populations. Here we investigate the genetic basis of tolerance and resistance to needle cast disease in Douglas-fir (Pseudotsuga menziesii) caused by two fungal pathogens: Swiss needle cast (SNC) caused by Nothophaeocryptopus gaeumannii, and Rhabdocline needle cast (RNC) caused by Rhabdocline pseudotsugae). We performed a case-control genome-wide association analysis (GWA) and found these traits to be polygenic and under selection. We showed that stomatal regulation as well as ethylene and jasmonic acid pathways are important for resisting SNC infection and secondary metabolite pathways play a role in tolerating SNC once the plant is infected. We identified a key upstream transcription factor of plant defence, ERF1, as the main candidate for RNC resistance. Our findings contribute to the understanding of the highly polygenic architectures underlying diseas..., We used a pool-sequencing approach that targeted exon regions. For probe design details, see Lind et al. (2022). Briefly, the sequence capture probes were designed using genes identified in Douglas-fir RNA-seq data from (1) daily and cyclic-induced experiments (Cronn et al., 2017) and (2) needle samples infected by the fungal pathogen causing SNC Nothophaeocryptopus gaeumannii and wasp (unpublished). Exon sequences with a length of at least 100bp were submitted to Roche NimbleGen for Custom SeqCap EZ probe design. DNA was extracted from Douglas-fir diploid needle tissue. DNA samples were normalised at 10ng/μl and 10 to 20 individuals were pooled per site (See File S2) by combining equimolar amounts of individual DNA samples prior to library preparation. Barcoded (Kapa, Dual-Indexed Adapter Kit) libraries were made using 100-150ng of DNA from each pooled DNA sample with an approximately 450-bp mean insert size. SeqCap library preparation was performed using custom Nimblegen SeqCap probe..., , # Genetic architecture of disease resistance and tolerance in Douglas-fir trees [https://doi.org/10.5061/dryad.jdfn2z3dp](https://doi.org/10.5061/dryad.jdfn2z3dp) ·      Understanding the genetic basis of how plants defend against pathogens is important to monitor and maintain resilient tree populations. Swiss needle cast (SNC) and Rhabdocline needle cast (RNC) epidemics are responsible for major damage of forest ecosystems in North America. ·      Here we investigate the genetic architecture of tolerance and resistance to needle cast diseases in Douglas-fir (*Pseudotsuga menziesii*) caused by two fungal pathogens: SNC caused by *Nothophaeocryptopus gaeumannii*, and RNC caused by *Rhabdocline pseudotsugae*. ·      We performed case-control genome-wide association analyses and found disease resistance and tolerance in Douglas-fir to be polygenic and under strong selection. We show that stomatal regulation as well as ethylene and jasmonic acid pathways are important for resisting S...# 花旗松林木病害抗性与耐受性的遗传架构 https://doi.org/10.5061/dryad.jdfn2z3dp 解析植物对病原菌的耐受性与抗性的遗传架构，对于监测并维持具有恢复力的林木种群至关重要。本研究针对由两种真菌病原菌引发的针枯病，解析花旗松（Douglas-fir, *Pseudotsuga menziesii*）对该病害的耐受性与抗性的遗传基础：其中瑞士针枯病（Swiss needle cast, SNC）由*Nothophaeocryptopus gaeumannii*引起，而雷氏针枯病（Rhabdocline needle cast, RNC）由*Rhabdocline pseudotsugae*引起。 本研究开展了病例对照全基因组关联分析（Genome-Wide Association Analysis, GWA），发现上述性状属于多基因调控性状，并处于选择压力之下。研究表明，气孔调控以及乙烯、茉莉酸信号通路在花旗松抵御SNC侵染过程中发挥关键作用；而当植株已被侵染时，次生代谢通路则参与调控其对SNC的耐受性。本研究鉴定得到植物防御通路的关键上游转录因子ERF1，将其作为RNC抗性的核心候选基因。本研究结果有助于深入解析病害背后高度复杂的多基因调控架构…… 本研究采用靶向外显子区域的混池测序（pool-sequencing）策略，探针设计细节详见Lind等人2022年的研究。简言之，本研究的序列捕获探针基于花旗松的RNA测序数据设计而来，这些数据来源于两类实验：其一为昼夜及周期性诱导实验（Cronn等人，2017）；其二为感染SNC病原菌*Nothophaeocryptopus gaeumannii*的针叶样本与寄生蜂样本的测序数据（未发表）。本研究将长度不低于100bp的外显子序列提交至罗氏NimbleGen公司，以定制SeqCap EZ探针。 本研究从花旗松二倍体针叶组织中提取基因组DNA，将DNA样品浓度归一化至10ng/μl，并在文库制备前，通过按等摩尔比混合单个DNA样品的方式，对每个采样点的10至20个个体进行混池（详见补充文件S2）。使用Kapa双端索引接头试剂盒（Kapa Dual-Indexed Adapter Kit）构建带条形码的文库，每个混池DNA样品使用100-150ng DNA，插入片段平均长度约为450bp。本研究使用定制NimbleGen SeqCap探针完成SeqCap文库制备…… · 解析植物抵御病原菌的遗传基础，对于监测并维持具有恢复力的林木种群至关重要。瑞士针枯病（SNC）与雷氏针枯病（RNC）的流行已对北美森林生态系统造成严重破坏。 · 本研究针对由两种真菌病原菌引发的针枯病，解析花旗松（*Pseudotsuga menziesii*）对该病害的耐受性与抗性的遗传架构：其中SNC由*Nothophaeocryptopus gaeumannii*引起，RNC由*Rhabdocline pseudotsugae*引起。 · 本研究开展病例对照全基因组关联分析，发现花旗松的病害抗性与耐受性属于多基因调控性状，并处于强烈的选择压力之下。研究表明，气孔调控以及乙烯、茉莉酸信号通路在抵御SNC侵染中发挥关键作用……