Allele Frequency Changes Provide Evidence for Selection and Identification of Candidate Loci for Survival in Red Clover (Trifolium pratense L.)
Allele Frequency Changes Provide Evidence for Selection and Identification of Candidate Loci for Survival in Red Clover (Trifolium pratense L.)
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DOI：
10.3389/fpls.2019.00718
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发表时间：
2019-06-11
影响因子：
5.6
通讯作者：
Rognli, Odd Arne
中科院分区：
文献类型：
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作者：
Ergon, Ashild;Skot, Leif;Rognli, Odd Arne
通过测序进行基因分型，对挪威南部田间实验中的红三叶草（Trifolium pratense L.）幸存者种群进行了遗传特征分析，并与原始种群和彼此之间进行了比较。使用主成分分析，根据单核苷酸多态性 (SNP) 的等位基因频率来表征群体之间的遗传分化。已选择的 SNP，即幸存者群体中相对于原始群体或接受不同治疗的幸存者群体之间等位基因频率显着不同的 SNP，通过使用 BayeScan 和利用现场实验的复制群体的简单且严格的基于 F-ST 的测试分析 F-ST 值来识别。此外，我们还测试了在测序之前合并 DNA 样本以及在 DNA 提取和测序之前合并叶子样本的可能性，然后根据变异读数的数量进行等位基因频率估计。总体而言，幸存者种群之间的差异比原始种群更大，这表明等位基因频率的随机变化、针对田间实验中地块之间条件的局部变化的选择或抽样误差。然而，在纯林或物种混合物播种的地块、以不同密度播种的地块以及采用不同收获制度的地块之间观察到了一些差异。可以从合并的 DNA 中准确估计等位基因频率，并且在提取 DNA 之前合并叶子样本时可以识别选择的 SNP。然而，巨大的抽样误差需要重复群体和/或大量抽样个体。我们鉴定了一些在纯林地块中相对于原始播种群体进行选择的染色体基因座，以及在红三叶草纯林与在物种混合物中生长的红三叶草中进行差异选择的基因座。这些都是红三叶草建立成功或持久的候选基因座。
Survivor populations of red clover (Trifolium pratense L.) from plots in a field experiment in southern Norway were genetically characterized using genotyping by sequencing, and compared with the original population and each other. Genetic differentiation between populations was characterized on the basis of allele frequencies of single nucleotide polymorphisms (SNPs), using principal component analysis. SNPs that had been under selection, i.e., SNPs with significantly different allele frequencies in survivor populations relative to the original population, or between survivor populations that had received different treatments, were identified by analysis of F-ST values, using BayeScan and a simple and stringent F-ST-based test utilizing replicate populations from the field experiment. In addition, we tested the possibility of pooling DNA samples prior to sequencing, and pooling leaf samples prior to DNA extraction and sequencing, followed by allele frequency estimation on the basis of number of variant reads. Overall, survivor populations were more different from each other than from the original population, indicating random changes in allele frequency, selection in response to local variation in conditions between plots in the field experiment, or sampling error. However, some differentiation was observed between plots sown as pure stands or species mixtures, plots sown at different densities, and plots subjected to different harvesting regimes. Allele frequencies could be accurately estimated from pooled DNA, and SNPs under selection could be identified when leaf samples were pooled prior to DNA extraction. However, substantial sampling error required replicate populations and/or a high number of sampled individuals. We identified a number of chromosomal loci that had been under selection in pure stand plots relative to the original sown population, and loci that had been under differential selection in pure stands of red clover vs. red clover grown in species mixtures. These are all candidate loci for establishment success or persistence in red clover.