title: A statistical design for testing apomictic diversification through linkage analysis.
abstract: The capacity of apomixis to generate maternal clones through seed reproduction has made it a useful characteristic for the fixation of heterosis in plant breeding. It has been observed that apomixis displays pronounced intra- and interspecific diversification, but the genetic mechanisms underlying this diversification remains elusive, obstructing the exploitation of this phenomenon in practical breeding programs. By capitalizing on molecular information in mapping populations, we describe and assess a statistical design that deploys linkage analysis to estimate and test the pattern and extent of apomictic differences at various levels from genotypes to species. The design is based on two reciprocal crosses between two individuals each chosen from a hermaphrodite or monoecious species. A multinomial distribution likelihood is constructed by combining marker information from two crosses. The EM algorithm is implemented to estimate the rate of apomixis and test its difference between two plant populations or species as the parents. The design is validated by computer simulation. A real data analysis of two reciprocal crosses between hickory (Carya cathayensis) and pecan (C. illinoensis) demonstrates the utilization and usefulness of the design in practice. The design provides a tool to address fundamental and applied questions related to the evolution and breeding of apomixis.
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural and Forestry University, Lin'an, Zhejiang 311300, China; Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA. Tel.: +1 717 531 2037; Fax: +1 717 531 0480; rwu@phs.psu.edu.
authors.forename: Yanru
authors.initials: Y
authors.lastname: Zeng
authors.forename: Wei
authors.initials: W
authors.lastname: Hou
authors.forename: Shuang
authors.initials: S
authors.lastname: Song
authors.forename: Sisi
authors.initials: S
authors.lastname: Feng
authors.forename: Lin
authors.initials: L
authors.lastname: Shen
authors.forename: Guohua
authors.initials: G
authors.lastname: Xia
authors.forename: Rongling
authors.initials: R
authors.lastname: Wu
mesh_terms: D000465:Algorithms; D060832:Apomixis / Q000235:genetics*; D001947:Breeding; D031325:Carya / Q000235:genetics; D019295:Computational Biology; D008040:Genetic Linkage; D014644:Genetic Variation; D008957:Models, Genetic; D015233:Models, Statistical; D018521:Plant Physiological Phenomena; D010944:Plants / Q000235:genetics*