Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce 

First author: Ilga Porth; Affiliations: Université Laval (拉瓦尔大学): Québec, Canada

Corresponding author: Ilga Porth

In plants, there can be a trade-off between resource allocations (资源分配) to growth vs defense. Here, we use partial correlation analysis (偏相关分析) of gene expression to make inferences about the nature of this interaction. We studied segregating progenies of Interior spruce subject to weevil (象鼻虫) attack. In a controlled experiment, we measured pre-attack plant growth and post-attack damage with several morphological measures, and profiled transcriptomes of 188 progeny. We used partial correlations of individual transcripts (expressed sequence tags, ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, for example, those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs. A terpenoid (类萜) ABC transporter gene showed strongest correlations (P = 0.019); its transcript represented a hub (中心) within the compact 166-member gene–gene interaction network (P = 0.004) of the negative genetic correlations between growth and subsequent pest attack. A small 21-member interaction network (P = 0.004) represented the uncovered positive correlations. Our study demonstrates partial correlation analysis identifies important gene networks underlying growth and susceptibility to the weevil in spruce. In particular, we found transcripts that strongly modify the trade-off between growth and defense, and allow identification of networks more central to the trade-off.

植物中在生长和抗性之间的资源分配存在一个权衡的过程。本文利用基因表达的偏相关分析来推断该过程的特性。作者研究了室内云杉的分离子代遭受象鼻虫侵害。在实验室的环境下，作者对188个子代通过几个形态学的测量来衡量攻击前的生长和攻击后的伤害，同时还测了攻击前后的转录谱。作者通过对单个转录本（即表达序列标签EST）和生长/抗性性状之间的偏相关分析来鉴定在推断的潜在基因网络中重要的节点和边，比如和单个EST转录本具有高互相关的生长/抗性性状对。作者给出来鉴定这类EST的方法。一个类萜ABC转运体基因具有最强的相关，其转录本在一个完整的具有166个成员的基因-基因互作网络中处于中心位置，该网络属于生长和随后虫害的负遗传相关。一个小的具有21个成员的基因-基因互作网络是一个不曾发现的正相关。本文的研究表明偏相关分析能够鉴定云杉生长和对于象鼻虫的易感性潜在的基因网络。尤其是，作者发现了能够强烈调节生长与抗性之间平衡的转录本，并鉴定到了该平衡中心范围的基因网络。

通讯：Ilga Porth (https://www.sbf.ulaval.ca/professeurs/ilga-porth)

个人简介：1999年，维也纳大学，生物化学硕士；2004年，维也纳大学，遗传学博士；2009年，哥伦比亚大学，林业生物技术博士后。

doi: 10.1111/nph.15075

Journal: New Phytologist

First Published date: 05 March, 2018

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