Computational identification of genes modulating stem height–diameter allometry

Abstract

SummaryThe developmental variation in stem height with respect to stem diameter is related to a broad range of ecological and evolutionary phenomena in trees, but the underlying genetic basis of this variation remains elusive. We implement a dynamic statistical model, functional mapping, to formulate a general procedure for the computational identification of quantitative trait loci (QTLs) that control stem height–diameter allometry during development. Functional mapping integrates the biological principles underlying trait formation and development into the association analysis of DNA genotype and endpoint phenotype, thus providing an incentive for understanding the mechanistic interplay between genes and development. Built on the basic tenet of functional mapping, we explore two core ecological scenarios of how stem height and stem diameter covary in response to environmental stimuli: (i) trees pioneer sunlit space by allocating more growth to stem height than diameter and (ii) trees maintain their competitive advantage through an inverse pattern. The model is equipped to characterize ‘pioneering’ QTLs (pi QTLs) and ‘maintaining’ QTLs (mi QTLs) which modulate these two ecological scenarios, respectively. In a practical application to a mapping population of full‐sib hybrids derived from two Populus species, the model has well proven its versatility by identifying several pi QTLs that promote height growth at a cost of diameter growth and several mi QTLs that benefit radial growth at a cost of height growth. Judicious application of functional mapping may lead to improved strategies for studying the genetic control of the formation mechanisms underlying trade‐offs among quantities of assimilates allocated to different growth parts.

A Computational Model for Inferring QTL Control Networks Underlying Developmental Covariation

“…We start our model derivations by considering the developmental covariation between stem height growth and stem diameter growth as an example. In our previous study, we also used this example to map height-diameter allometry QTLs (Jiang et al, 2016). We recapitulate part of our previous procedure as a first step for our QTL network inference.…”

“…where H 0 is the stem height at an initiate time point at which stem height is measured; a H←D , b H←D , and We integrated H-D allometry equations into functional mapping through a multiplicative likelihood (Jiang et al, 2016). Let y i = (y i (1), …, y i (T)) and z i = (z i (1), …, z i (T)) denote stem height and diameter growth for individual i of a mapping population measured at a series of T time points, respectively.…”

“…Several studies have develop statistical approaches for mapping allometry quantitative trait loci (QTLs) that govern the developmental change of one trait as a function of another trait (Li et al, 2007;Huang et al, 2014). Stimulated by the importance of stem height-diameter allometry in tree genetics, we have extended these approaches to map different batteries of QTLs responsible for reciprocal changes of one trait with the other (Jiang et al, 2016). By analyzing genetic mapping data of stem height and diameter growth in Populus trees, our approach can map and detect the "pioneering" QTLs (piQTLs) that determine how height scales with diameter and "maintaining" QTLs (miQTLs) that determine how diameter scales with height.…”

Thinning Effects on the Tree Height–Diameter Allometry of Masson Pine (Pinus massoniana Lamb.)

“…Silvicultural thinning changes the canopy status of residual trees rapidly, which causes the remaining trees to suddenly have more growing space [102]. Consequently, these trees change their original growth pattern and use more growth resources for diameter growth to maintain their spatial advantage until the canopy again begins to close, after which the trees begin the next stage of space competition [103]. The sudden increase in diameter growth of retained trees after thinning supports this explanation.…”

Two‐stage identification ofSNPeffects on dynamic poplar growth

“…The genetic material used in this study was described in previous studies (Jiang et al ., ; Xu et al ., ), which is a full‐sib family derived from hybridization between two heterozygous parents of poplar (Populus) trees. The full‐sib family has been widely used as a mapping population for outcrossing species including trees (Grattapaglia et al ., ; Wu et al ., ; Lu et al ., ).…”