title: A model framework for identifying genes that guide the evolution of heterochrony.
abstract: Heterochrony, the phylogenic change in the time of developmental events or rate of development, has been thought to play an important role in producing phenotypic novelty during evolution. Increasing evidence suggests that specific genes are implicated in heterochrony, guiding the process of developmental divergence, but no quantitative models have been instrumented to map such heterochrony genes. Here, we present a computational framework for genetic mapping by which to characterize and locate quantitative trait loci (QTLs) that govern heterochrony described by four parameters, the timing of the inflection point, the timing of maximum acceleration of growth, the timing of maximum deceleration of growth, and the length of linear growth. The framework was developed from functional mapping, a dynamic model derived to map QTLs for the overall process and pattern of development. By integrating an optimality algorithm, the framework allows the so-called heterochrony QTLs (hQTLs) to be tested and quantified. Specific pipelines are given for testing how hQTLs control the onset and offset of developmental events, the rate of development, and duration of a particular developmental stage. Computer simulation was performed to examine the statistical properties of the model and demonstrate its utility to characterize the effect of hQTLs on population diversification due to heterochrony. By analyzing a genetic mapping data in rice, the framework identified an hQTL that controls the timing of maximum growth rate and duration of linear growth stage in plant height growth. The framework provides a tool to study how genetic variation translates into phenotypic innovation, leading a lineage to evolve, through heterochrony.
authors.affiliation: Beijing Key Laboratory of Ornamental Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China rwu@phs.psu.edu zqx@bjfu.edu.cn.
authors.forename: Lidan
authors.initials: L
authors.lastname: Sun
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China rwu@phs.psu.edu zqx@bjfu.edu.cn.
authors.forename: Meixia
authors.initials: M
authors.lastname: Ye
authors.affiliation: Center for Statistical Genetics, The Pennsylvania State University rwu@phs.psu.edu zqx@bjfu.edu.cn.
authors.forename: Han
authors.initials: H
authors.lastname: Hao
authors.affiliation: Center for Statistical Genetics, The Pennsylvania State University.
authors.forename: Ningtao
authors.initials: N
authors.lastname: Wang
authors.affiliation: Center for Statistical Genetics, The Pennsylvania State University.
authors.forename: Yaqun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Beijing Key Laboratory of Ornamental Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China.
authors.forename: Tangren
authors.initials: T
authors.lastname: Cheng
authors.affiliation: Beijing Key Laboratory of Ornamental Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China rwu@phs.psu.edu zqx@bjfu.edu.cn.
authors.forename: Qixiang
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCenter for Statistical Genetics, The Pennsylvania State University rwu@phs.psu.edu zqx@bjfu.edu.cn.
authors.forename: Rongling
authors.initials: R
authors.lastname: Wu
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D014644:Genetic Variation; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D010944:Plants / Q000235:genetics; D040641:Quantitative Trait Loci
keywords: developmental timing; functional mapping; growth rate; heterochrony; phylogeny; quantitative trait loci