Table_3_Select and Sequence of a Segregating Sugar Beet Population Provides Genomic Perspective of Host Resistance to Seedling Rhizoctonia solani Infection.xlsx

Understanding the genetic basis of polygenic traits is a major challenge in agricultural species, especially in non-model systems. Select and sequence (SnS) experiments carried out within existing breeding programs provide a means to simultaneously identify the genomic background of a trait while improving the mean phenotype for a population. Using pooled whole genome sequencing (WGS) of selected and unselected bulks derived from a synthetic outcrossing sugar beet population EL57 (PI 663212), which segregates for seedling rhizoctonia resistance, we identified a putative genomic background involved in conditioning a resistance phenotype. Population genomic parameters were estimated to measure fixation (He), genome divergence (FST), and allele frequency changes between bulks (DeltaAF). We report on the genome wide patterns of variation resulting from selection and highlight specific genomic features associated with resistance. Expected heterozygosity (He) showed an increased level of fixation in the resistant bulk, indicating a greater selection pressure was applied. In total, 1,311 biallelic loci were detected as significant FST outliers (p < 0.01) in comparisons between the resistant and susceptible bulks. These loci were detected in 206 regions along the chromosomes and contained 275 genes. We estimated changes in allele frequency between bulks resulting from selection for resistance by leveraging the allele frequencies of an unselected bulk. DeltaAF was a more stringent test of selection and recovered 186 significant loci, representing 32 genes, all of which were also detected using FST. Estimates of population genetic parameters and statistical significance were visualized with respect to the EL10.2 physical map and produced a candidate gene list that was enriched for function in cell wall metabolism and plant disease resistance, including pathogen perception, signal transduction, and pathogen response. Specific variation associated with these genes was also reported and represents genetic markers for validation and prediction of resistance to Rhizoctonia. Select and sequence experiments offer a means to characterize the genetic base of sugar beet, inform selection within breeding programs, and prioritize candidate variation for functional studies.

解析多基因性状的遗传基础是农业物种，尤其是非模式生物体系中的核心研究难题之一。在现有育种项目中开展的选择测序（Select and sequence, SnS）实验，可在改良群体平均表型的同时，同步鉴定目标性状的基因组背景。本研究以存在幼苗立枯丝核菌抗性性状分离的合成异交甜菜群体EL57（PI 663212）为材料，对其选择混合组与未选择混合组开展混合全基因组测序（pooled whole genome sequencing, WGS），由此鉴定出调控抗性表型的推定基因组背景。我们估算了群体基因组参数，以量化固定水平（以期望杂合度He表征）、基因组分化水平（FST）以及混合组间的等位基因频率变化（DeltaAF）。本研究报道了选择作用下的全基因组变异模式，并明确了与抗性相关的特异性基因组特征。期望杂合度（He）分析结果显示，抗病混合组的固定水平更高，表明实验施加了更强的选择压力。在抗病与感病混合组的比较中，共检测到1311个双等位基因位点为显著FST离群位点（p < 0.01），这些位点分布于染色体上的206个区域，共包含275个功能基因。我们借助未选择混合组的等位基因频率，估算了由抗性选择导致的混合组间等位基因频率变化；DeltaAF作为更为严格的选择检测方法，共筛选出186个显著位点，对应32个功能基因，且所有这些位点均通过FST分析被检出。我们以EL10.2物理图谱为参照，对群体遗传参数估算结果与统计显著性进行可视化分析，最终得到候选基因列表；该列表显著富集了细胞壁代谢、植物抗病相关功能，包括病原体识别、信号转导及病原体响应通路。本研究同时报道了与这些基因相关的特异性变异，这些变异可作为用于立枯丝核菌抗性验证与预测的遗传标记。选择测序（SnS）实验可为甜菜遗传基础的解析、育种项目中的选择优化提供方法支撑，并为功能研究筛选出优先开展研究的候选变异位点。