title: A reciprocal cross design to map the genetic architecture of complex traits in apomictic plants.
abstract: Many higher plants of economic and biological importance undergo apomixis in which the maternal tissue of the ovule forms a seed, without experiencing meiosis and fertilization. This feature of apomixis has made it difficult to perform linkage mapping which relies on meiotic recombination. Here, we describe a computational model for mapping quantitative trait loci (QTLs) that control complex traits in apomictic plants. The model is founded on the mixture model-based likelihood in which maternal genotypes are dissolved into two possible components generated by meiotic and apomictic processes, respectively. The EM algorithm was implemented to discern meiotic and apomictic genotypes and, therefore, allow the marker-QTL linkage relationship to be estimated. By capitalizing on reciprocal crosses, the model is renovated to estimate and test imprinting effects of QTLs, providing a better gateway to characterize the genetic architecture of complex traits. The model was validated through computer simulation and further demonstrated for its usefulness by analyzing a real data for an apomictic woody plant. The model has for the first time provided a unique tool for genetic mapping in apomictic plants.
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
authors.forename: Danni
authors.initials: D
authors.lastname: Yin
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
authors.forename: Xuli
authors.initials: X
authors.lastname: Zhu
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
authors.forename: Libo
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.|Yuanpeng Genome Institute of Jiangsu, Nantong, Jiangsu, 226531, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural and Forestry University, Lin'an, Zhejiang, 311300, China.
authors.forename: Yanru
authors.initials: Y
authors.lastname: Zeng
authors.affiliation: Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.|Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.
authors.forename: Rongling
authors.initials: R
authors.lastname: Wu
mesh_terms: D060832:Apomixis / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D003433:Crosses, Genetic; D008040:Genetic Linkage; D018392:Genomic Imprinting; D005838:Genotype; D040582:Inheritance Patterns / Q000235:genetics; D016013:Likelihood Functions; D010944:Plants / Q000235:genetics*; D011336:Probability; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable
keywords: EM algorithm; apomixis; genetic imprinting; quantitative trait locus (QTL); reciprocal cross