Abstract：
Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. (A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae.
摘要：
linariae（Neerg。）Simmons是一种经济上重要的叶面病原体，会导致西红柿的早期疫病。了解遗传多样性，种群遗传结构，进化潜力对于考虑有效的疾病管理策略至关重要。我们利用测序基因分型（GBS）技术比较了124种链格孢菌分离株的全基因组变异。(A.Alternata,A.linariae,和A.solani）进行比较基因组分析，并测试从北卡罗来纳州西部的番茄中收集的A.linariae的遗传分化和连锁不平衡（LD）的假设。我们使用GBSapp进行了pangenome感知变体调用和过滤，并确定了在三个链格孢菌属的参考基因组中保守的53,238个变体。在1号染色体（7Mb）上观察到最高的标记密度。主要成分的判别分析（DAPC）和基于贝叶斯模型的结构分析均显示出三个亚群的混合最少。银杏亚种群内的遗传分化系数(FST)相似且较高(0.86),表明亚群中的等位基因是固定的，遗传结构可能是由于限制性重组。分子方差分析表明，种群之间的差异（89％）高于种群内部（11％）。我们在linariae的一对基因座之间发现了远程LD，支持无性繁殖有限的真菌病原体预期的低重组假说。我们的发现提供了一个高水平的群体遗传分化的证据。这加强了开发具有广谱抗性的番茄品种的重要性。
