GBS and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.)
GBS and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.)
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GBS 和新开发的 mRNA-GBS 方法将群体遗传和转录组分析联系起来，揭示了红三叶草（Trifolium pratense L）位点和处理之间的模式差异
DOI：
10.1101/2021.11.30.470612
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发表时间：
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影响因子：
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通讯作者：
Müller C-M
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文献类型：
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作者：
Gemeinholzer B;Rupp O;Becker A;Strickert M;Müller C-M
红三叶草（Trifolium pratenseL.）被广泛种植作为牛饲料和土壤改良。野生种群和地方品种具有丰富的自然多样性，可用于改良栽培红三叶草。然而，迄今为止，对该物种的自然遗传和表型多样性的了解仍然不足。在这里，我们开发了一种低成本的转录组分析（mRNA-GBS），降低了复杂性，并将结果与群体遗传（GBS）和先前发表的mRNA-Seq数据进行了比较，以评估是否可以同时分析群体内和群体间的种内变异和转录组反应。mRNA-GBS方法是成功的。来自mRNA-GBS方法的SNP分析揭示了与GBS结果相当的模式，但不可能将具有降低的复杂性和测序深度的转录组分析与先前发表的温室和田间表达研究联系起来。使用短序列上游的多聚（A）尾的mRNA，以减少复杂性是有前途的方法，联合收割机结合群体遗传学和表达谱分析，以分析许多个人的性状差异，同时和成本效益，即使在非模式物种。我们的mRNA-GBS方法揭示了太多额外的短mRNA序列，阻碍了序列比对深度和SNP恢复。正在讨论优化。然而，我们在德国不同地区的研究设计也具有挑战性，因为使用复杂性降低的差异表达分析，其中mRNA在特定位点而不是随机片段化，在自然条件下最有可能被低测序深度的高度复杂的植物反应抵消。
The important worldwide forage crop red clover (Trifolium pratenseL.) is widely cultivated as cattle feed and for soil improvement. Wild populations and landraces have great natural diversity that could be used to improve cultivated red clover. However, to date, there is still insufficient knowledge about the natural genetic and phenotypic diversity of the species. Here, we developed a low-cost transcriptome analysis (mRNA-GBS) with reduced complexity and compared the results with population genetic (GBS) and previously published mRNA-Seq data, to assess whether analysis of intraspecific variation within and between populations and transcriptome responses is possible simultaneously. The mRNA-GBS approach was successful. SNP analyses from the mRNA-GBS approach revealed comparable patterns to the GBS results, but it was not possible to link transcriptome analyses with reduced complexity and sequencing depth to previously published greenhouse and field expression studies. The use of short sequences upstream of the poly(A) tail of mRNA to reduce complexity are promising approaches that combine population genetics and expression profiling to analyze many individuals with trait differences simultaneously and cost-effectively, even in non-model species. Our mRNA-GBS approach revealed too many additional short mRNA sequences, hampering sequence alignment depth and SNP recovery. Optimizations are being discussed. Nevertheless, our study design across different regions in Germany was also challenging as the use of differential expression analyses with reduced complexity, in which mRNA is fragmented at specific sites rather than randomly, is most likely counteracted under natural conditions by highly complex plant reactions at low sequencing depth.
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3.3
作者：
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影响因子：
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DOI：
--
发表时间：
2016
期刊：
影响因子：
--
作者：
Imane Medoukali;I. Bellil;D. Khelifi
通讯作者：
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