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Population structure, landscape genomics, and genetic signatures of adaptation to exotic disease pressure in Cornus florida L. – insights from GWAS and GBS data
Journal of Systematics and Evolution ( IF 3.7 ) Pub Date : 2020-05-30 , DOI: 10.1111/jse.12592
Andrew L. Pais 1 , Ross W. Whetten 2 , Qiu‐Yun (Jenny) Xiang 1
Affiliation  

Understanding the consequences of exotic diseases on native forests is important to evolutionary ecology and conservation biology because exotic pathogens have drastically altered US eastern deciduous forests. Cornus florida L. (flowering dogwood tree) is one such species facing heavy mortality. Characterizing the genetic structure of C. florida populations and identifying the genetic signature of adaptation to dogwood anthracnose (an exotic pathogen responsible for high mortality) remain vital for conservation efforts. By integrating genetic data from genotype by sequencing (GBS) of 289 trees across the host species range and distribution of disease, we evaluated the spatial patterns of genetic variation and population genetic structure of C. florida and compared the pattern to the distribution of dogwood anthracnose. Using genome‐wide association study and gradient forest analysis, we identified genetic loci under selection and associated with ecological and diseased regions. The results revealed signals of weak genetic differentiation of three or more subgroups nested within two clusters—explaining up to 2%–6% of genetic variation. The groups largely corresponded to the regions within and outside the eastern Hot‐Continental ecoregion, which also overlapped with areas within and outside the main distribution of dogwood anthracnose. The fungal sequences contained in the GBS data of sampled trees bolstered visual records of disease at sampled locations and were congruent with the reported range of Discula destructiva, suggesting that fungal sequences within‐host genomic data were informative for detecting or predicting disease. The genetic diversity between populations at diseased vs. disease‐free sites across the range of C. florida showed no significant difference. We identified 72 single‐nucleotide polymorphisms (SNPs) from 68 loci putatively under selection, some of which exhibited abrupt turnover in allele frequencies along the borders of the Hot‐Continental ecoregion and the range of dogwood anthracnose. One such candidate SNP was independently identified in two prior studies as a possible L‐type lectin‐domain containing receptor kinase. Although diseased and disease‐free areas do not significantly differ in genetic diversity, overall there are slight trends to indicate marginally smaller amounts of genetic diversity in disease‐affected areas. Our results were congruent with previous studies that were based on a limited number of genetic markers in revealing high genetic variation and weak population structure in C. florida.

中文翻译:

佛罗里达州山茱萸的种群结构、景观基因组学和适应外来疾病压力的遗传特征——来自 GWAS 和 GBS 数据的见解

了解外来疾病对原生森林的影响对于进化生态学和保护生物学很重要,因为外来病原体已经彻底改变了美国东部落叶林。Cornus florida L.(开花山茱萸树)就是这样一种面临严重死亡的物种。表征佛罗里达州 C. 种群的遗传结构并确定适应山茱萸炭疽病(一种导致高死亡率的外来病原体)的遗传特征对于保护工作仍然至关重要。通过整合来自宿主物种范围和疾病分布的 289 棵树的基因型测序 (GBS) 遗传数据,我们评估了佛罗里达州的遗传变异和种群遗传结构的空间模式,并将该模式​​与山茱萸炭疽病的分布进行了比较. 使用全基因组关联研究和梯度森林分析,我们确定了与生态和患病区域相关的选择基因位点。结果揭示了嵌套在两个簇内的三个或更多亚组的弱遗传分化信号——解释了高达 2%–6% 的遗传变异。这些群体主要对应于东部热大陆生态区内外的区域,也与山茱萸炭疽病主要分布的内外区域重叠。采样树木的 GBS 数据中包含的真菌序列支持了采样位置的疾病视觉记录,并且与报道的 Discula destructiva 范围一致,表明宿主基因组数据中的真菌序列可为检测或预测疾病提供信息。C. florida 范围内患病和无病位点种群之间的遗传多样性没有显着差异。我们从假定选择的 68 个基因座中鉴定了 72 个单核苷酸多态性 (SNP),其中一些在热大陆生态区的边界和山茱萸炭疽病的范围内表现出等位基因频率的突变。在之前的两项研究中,一个这样的候选 SNP 被独立鉴定为可能含有 L 型凝集素结构域的受体激酶。虽然患病区和无病区在遗传多样性上没有显着差异,但总体上有轻微趋势表明受病区遗传多样性略小。
更新日期:2020-05-30
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