ArticleG3 (Bethesda, Md.)2015
Mapping Quantitative Trait Loci Underlying Function-Valued Traits Using Functional Principal Component Analysis and Multi-Trait Mapping.
Article in G3 (Bethesda, Md.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Genetics of behavioural evolution in giant mice from Gough Island.Proceedings. Biological sciences · 2023Article
- Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence.PLoS genetics · 2021Article
- Increased Power and Accuracy of Causal Locus Identification in Time Series Genome-wide Association in Sorghum.Plant physiology · 2020Article
- Functional QTL mapping and genomic prediction of canopy height in wheat measured using a robotic field phenotyping platform.Journal of experimental botany · 2020Article
- Integrating High-Throughput Phenotyping and Statistical Genomic Methods to Genetically Improve Longitudinal Traits in Crops.Frontiers in plant science · 2020Review
- Smoothing and extraction of traits in the growth analysis of noninvasive phenotypic data.Plant methods · 2020Article
- A Gaussian process model and Bayesian variable selection for mapping function-valued quantitative traits with incomplete phenotypic data.Bioinformatics (Oxford, England) · 2019Article
- Components of Water Use Efficiency Have Unique Genetic Signatures in the Model CPlant physiology · 2018Article
- A machine vision platform for measuring imbibition of maize kernels: quantification of genetic effects and correlations with germination.Plant methods · 2018Article
- Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria.PLoS genetics · 2017Article
- Candidate pathway association and genome-wide association approaches reveal alternative genetic architectures of carotenoid content in cultivated sunflower (Applications in plant sciencesArticle
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Authors and funding
4 authors.
Funding
Abstract
We previously proposed a simple regression-based method to map quantitative trait loci underlying function-valued phenotypes. In order to better handle the case of noisy phenotype measurements and accommodate the correlation structure among time points, we propose an alternative approach that maintains much of the simplicity and speed of the regression-based method. We overcome noisy measurements by replacing the observed data with a smooth approximation. We then apply functional principal component analysis, replacing the smoothed phenotype data with a small number of principal components. Quantitative trait locus mapping is applied to these dimension-reduced data, either with a multi-trait method or by considering the traits individually and then taking the average or maximum LOD score across traits. We apply these approaches to root gravitropism data on Arabidopsis recombinant inbred lines and further investigate their performance in computer simulations. Our methods have been implemented in the R package, funqtl.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.