Detection of a Gravitropism Phenotype in glutamate receptor-like 3.3 Mutants of Arabidopsis thaliana Using Machine Vision and Computation
Detection of a Gravitropism Phenotype in glutamate receptor-like 3.3 Mutants of Arabidopsis thaliana Using Machine Vision and Computation
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DOI：
10.1534/genetics.110.118711
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发表时间：
2010-10-01
期刊：
影响因子：
3.3
通讯作者：
Spalding, Edgar P.
中科院分区：
文献类型：
--
作者：
Miller, Nathan D.;Brooks, Tessa L. Durham;Spalding, Edgar P.
在模式植物拟南芥中，基因中断经常不产生表型，使基因功能的研究复杂化。基因家族成员之间的功能冗余是一种常见的解释，但检测方法不足也可能是原因之一。在这里，新开发的方法自动捕获和处理的时间序列的图像，然后通过计算分析，采用改进的线性判别分析（LDA）和基于小波的分化，在缺乏谷氨酸受体样3.3基因的突变体的研究。根向重力性被选为高时空分辨率研究的过程，因为GLR3.3编码的配体门控Ca2+渗透通道可能有助于根中与重力信号转导相关的离子通量。从野生型和两个不同的glr3.3突变体收集根尖角度的时间序列，跨越网格的种子大小和苗龄条件，以前发现是重要的向地性。平均反应的统计检验没有发现人口之间的显着差异，但LDA分离的野生型的突变等位基因。将数据投影到LDA溶液载体上后，glr3.3突变体在所有四种条件下均显示出比野生型更大的群体方差。在三种条件下，突变体和野生型之间的投影平均值也存在显着差异。原始响应曲线的小波分析表明，LDA检测到的表型与glr3.3突变体的早期减速和随后的缓慢弯曲阶段有关。这些统计学显著的、可遗传的、基于计算的表型产生了对GLR 3.3在向地性中的功能的深入了解。该方法可普遍适用于表型的研究，因此基因功能。
Gene disruption frequently produces no phenotype in the model plant Arabidopsis thaliana, complicating studies of gene function. Functional redundancy between gene family members is one common explanation but inadequate detection methods could also be responsible. Here, newly developed methods for automated capture and processing of time series of images, followed by computational analysis employing modified linear discriminant analysis (LDA) and wavelet-based differentiation, were employed in a study of mutants lacking the Glutamate Receptor-Like 3.3 gene. Root gravitropism was selected as the process to study with high spatiotemporal resolution because the ligand-gated Ca2+-permeable channel encoded by GLR3.3 may contribute to the ion fluxes associated with gravity signal transduction in roots. Time series of root tip angles were collected from wild type and two different glr3.3 mutants across a grid of seed-size and seedling-age conditions previously found to be important to gravitropism. Statistical tests of average responses detected no significant difference between populations, but LDA separated both mutant alleles from the wild type. After projecting the data onto LDA solution vectors, glr3.3 mutants displayed greater population variance than the wild type in all four conditions. In three conditions the projection means also differed significantly between mutant and wild type. Wavelet analysis of the raw response curves showed that the LDA-detected phenotypes related to an early deceleration and subsequent slower-bending phase in glr3.3 mutants. These statistically significant, heritable, computation-based phenotypes generated insight into functions of GLR3.3 in gravitropism. The methods could be generally applicable to the study of phenotypes and therefore gene function.