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Methods ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Plant Sci. | doi: 10.3389/fpls.2019.01557

A computational model for inferring QTL control networks underlying developmental covariation

 Rongling Wu1,  Li B. Jiang2, Hexin Shi2,  Mengmeng Sang2, Chenfei Zheng2,  Zhu Xuli2,  Qixiang Zhang2 and Lidan Sun2*
  • 1Pennsylvania State University (PSU), United States
  • 2Beijing Forestry University, China

How one trait developmentally varies as a function of others shapes a spectrum of biological phenomena. Despite its importance to trait dissection, the understanding of whether and how genes mediate such developmental covariation is poorly understood. We integrate developmental allometry equations into the functional mapping framework to map specific QTLs that govern the correlated development of different traits. Based on evolutionary game theory, we assemble and contextualize these QTLs into an intricate but organized network coded by bidirectional, signed, and weighted QTL-QTL interactions. We use this approach to map shoot height-diameter allometry QTLs in an ornamental woody species, mei (Prunus mume). We detect “pioneering” QTLs (piQTLs) and “maintaining” QTLs (miQTLs) that determine how shoot height varies with diameter and how shoot diameter varies with height, respectively. The QTL networks inferred can visualize how each piQTL regulates others to promote height growth at a cost of diameter growth, how miQTL regulates others to benefit radial growth at a cost of height growth, and how piQTLs and miQTLs regulate each other to form a pleiotropic web of primary and secondary growth in trees. Our approach provides a unique gateway to explore the genetic architecture of developmental covariation, a widespread phenomenon in nature.

Keywords: Phenotypic covariation, developmental covariation, height-diameter allometry, Functional Mapping, QTL network, woody plant

Received: 02 Aug 2019; Accepted: 07 Nov 2019.

Copyright: © 2019 Wu, Jiang, Shi, Sang, Zheng, Xuli, Zhang and Sun. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Mx. Lidan Sun, Beijing Forestry University, Beijing, 100083, Beijing, China, sunlidan@bjfu.edu.cn