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Bayesian estimation and use of high-throughput remote sensing indices for quantitative genetic analyses of leaf growth

Baker, RobertL., Leong, WenFung, An, Nan, Brock, MarcusT., Rubin, MatthewJ., Welch, Stephen, Weinig, Cynthia
Theoretical and applied genetics 2018 v.131 no.2 pp. 283-298
Bayesian theory, Brassica rapa, agronomy, biologists, carbon, carbon dioxide fixation, chlorophyll, data collection, gas exchange, genetic analysis, growth models, heritability, inbred lines, leaves, ontogeny, photochemistry, photosynthesis, plant breeders, reflectance, remote sensing, spatial data
KEY MESSAGE: We develop Bayesian function-valued trait models that mathematically isolate genetic mechanisms underlying leaf growth trajectories by factoring out genotype-specific differences in photosynthesis. Remote sensing data can be used instead of leaf-level physiological measurements. Characterizing the genetic basis of traits that vary during ontogeny and affect plant performance is a major goal in evolutionary biology and agronomy. Describing genetic programs that specifically regulate morphological traits can be complicated by genotypic differences in physiological traits. We describe the growth trajectories of leaves using novel Bayesian function-valued trait (FVT) modeling approaches in Brassica rapa recombinant inbred lines raised in heterogeneous field settings. While frequentist approaches estimate parameter values by treating each experimental replicate discretely, Bayesian models can utilize information in the global dataset, potentially leading to more robust trait estimation. We illustrate this principle by estimating growth asymptotes in the face of missing data and comparing heritabilities of growth trajectory parameters estimated by Bayesian and frequentist approaches. Using pseudo-Bayes factors, we compare the performance of an initial Bayesian logistic growth model and a model that incorporates carbon assimilation (A ₘₐₓ) as a cofactor, thus statistically accounting for genotypic differences in carbon resources. We further evaluate two remotely sensed spectroradiometric indices, photochemical reflectance (pri2) and MERIS Terrestrial Chlorophyll Index (mtci) as covariates in lieu of A ₘₐₓ, because these two indices were genetically correlated with A ₘₐₓ across years and treatments yet allow much higher throughput compared to direct leaf-level gas-exchange measurements. For leaf lengths in uncrowded settings, including A ₘₐₓ improves model fit over the initial model. The mtci and pri2 indices also outperform direct A ₘₐₓ measurements. Of particular importance for evolutionary biologists and plant breeders, hierarchical Bayesian models estimating FVT parameters improve heritabilities compared to frequentist approaches.