Funmap

Funmap identifies quantitative trait loci (QTL) associated with longitudinal or function-valued phenotypic traits by applying functional mapping to model growth trajectories, allometric scalings, and norms of reaction.

Key Features:

• Function-Valued Traits: Models continuous, infinite-dimensional traits that change over an independent variable, including growth trajectories, allometric scalings, and norms of reaction.
• Functional Mapping Strategy: Integrates mathematical relationships between traits or variables within the genetic mapping framework to analyze function-valued phenotypes.
• Logistic Mapping: Implements logistic (S-shaped) growth models based on the biological principle that growth over time follows exponential or sigmoidal patterns.
• Statistical Approach: Employs a logistic-mixture model with maximum-likelihood estimation executed via the Expectation-Maximization (EM) algorithm to estimate QTL positions, effects, and trajectory parameters.
• Enhanced Detection Power: Improves QTL detection power, parameter estimation precision, and localization resolution by reducing parameter count, leveraging pleiotropic QTL effects, and accounting for residual correlations across ages.
• Biological Hypotheses Testing: Enables testing of hypotheses about the genetic basis of quantitative variation and the role of development in evolution and domestication.

Scientific Applications:

• QTL mapping of growth trajectories: Maps loci affecting longitudinal phenotypes and other function-valued traits.
• Forest tree growth studies: Detects QTLs affecting stem growth in forest trees across developmental time points.
• Evolutionary and domestication research: Investigates how developmental genetic variation contributes to evolution and domestication.

Methodology:

Applies functional mapping using logistic (S-shaped) curve models and a logistic-mixture model, estimates parameters by maximum likelihood via the Expectation-Maximization (EM) algorithm, and accounts for residual correlations across ages while reducing parameter dimensionality.