The Persistent Homology Mathematical Framework Provides Enhanced Genotype-to-Phenotype Associations for Plant Morphology
The Persistent Homology Mathematical Framework Provides Enhanced Genotype-to-Phenotype Associations for Plant Morphology
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DOI：
10.1104/pp.18.00104
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发表时间：
2018-08-01
期刊：
影响因子：
7.4
通讯作者：
Topp, Christopher N.
中科院分区：
文献类型：
--
作者：
Li, Mao;Frank, Margaret H.;Topp, Christopher N.
由于缺乏灵活有效的形态量化工具，阻碍了对植物形态遗传和环境条件的理解。在这里，我们表明，持久性同源性为基础的拓扑方法可以提高测量的变化，叶片形状，锯齿，和根结构。我们将这些方法应用于2D图像的叶片和根系在田间生长的植物的驯化的渐渗系群体的番茄（茄）。我们发现，与一些常用的常规性状分析方法相比，（1）基于持续同源性的方法能够更全面地捕捉形态变异，（2）这些方法能够以更大的标准化效应值区分基因型，并检测到更多的独特数量性状位点（QTL）;（3）多变量性状，无论是统计学上来源于单变量性状还是基于持续同源性的性状，都提高了我们理解表型遗传基础的能力;和（4）与传统性状或其多元衍生物相比，基于持续同源性的技术检测独特的QTL，表明以前未测量的形态学方面现在是可检测的。QTL结果进一步表明，形态的遗传贡献可以影响地上部和根部，揭示了番茄自然变异的多效性基础。持续同源性是一个通用的框架，以量化植物形态和发育过程，补充和扩展现有的方法。
Efforts to understand the genetic and environmental conditioning of plant morphology are hindered by the lack of flexible and effective tools for quantifying morphology. Here, we demonstrate that persistent-homology-based topological methods can improve measurement of variation in leaf shape, serrations, and root architecture. We apply these methods to 2D images of leaves and root systems in field-grown plants of a domesticated introgression line population of tomato (Solanum pennellii). We find that compared with some commonly used conventional traits, (1) persistent-homology-based methods can more comprehensively capture morphological variation; (2) these techniques discriminate between genotypes with a larger normalized effect size and detect a greater number of unique quantitative trait loci (QTLs); (3) multivariate traits, whether statistically derived from univariate or persistent-homology-based traits, improve our ability to understand the genetic basis of phenotype; and (4) persistent-homology-based techniques detect unique QTLs compared to conventional traits or their multivariate derivatives, indicating that previously unmeasured aspects of morphology are now detectable. The QTL results further imply that genetic contributions to morphology can affect both the shoot and root, revealing a pleiotropic basis to natural variation in tomato. Persistent homology is a versatile framework to quantify plant morphology and developmental processes that complements and extends existing methods.