The Persistent Homology Mathematical Framework Provides Enhanced Genotype-to-Phenotype Associations for Plant Morphology
| Autor: | Washington Mio, Christopher N. Topp, Daniel H. Chitwood, Viktoriya Coneva, Margaret H. Frank, Mao Li |
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| Rok vydání: | 2018 |
| Předmět: |
0106 biological sciences
0301 basic medicine education.field_of_study Multivariate statistics Persistent homology Physiology fungi Population food and beverages Introgression Plant Science Biology Quantitative trait locus 01 natural sciences Phenotype 03 medical and health sciences 030104 developmental biology Evolutionary biology Plant morphology Genotype Genetics education 010606 plant biology & botany |
| Zdroj: | Plant Physiology. 177:1382-1395 |
| ISSN: | 1532-2548 0032-0889 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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