title: A unifying framework for bivalent multilocus linkage analysis of allotetraploids.
abstract: An allotetraploid has four paired sets of chromosomes derived from different diploid species, whose meiotic behavior is qualitatively different from the underlying diploids. According to a traditional view, meiotic pairing occurs only between homologous chromosomes, but new evidence indicates that homoeologous chromosomes may also pair to a lesser extent compared with homolog pairing. Here, we describe and assess a unifying analytical framework that incorporates differential chromosomal pairing into a multilocus linkage model. The preferential pairing factor is used to quantify the probability difference of pairing occurring between homologous chromosomes and homoeologous chromosomes. The unifying framework allows simultaneous estimation of the linkage, genetic interference and preferential pairing factor using commonly existing multiplex markers. We compared the unifying approach and traditional approaches assuming random chromosomal pairing by analyzing marker data collected in a full-sib family of tetraploid switchgrass, a bioenergy species whose diploid origins are undefined, but with subgenomes that are genetically well differentiated. The unifying framework provides a better tool for estimating the meiotic linkage and constructing a genetic map for allotetraploids.
authors.affiliation: Center for Computational Biology, Beijing Forestry University, Beijing 100083, China.
authors.forename: Xiaoxia
authors.initials: X
authors.lastname: Yang
authors.forename: Yafei
authors.initials: Y
authors.lastname: Lv
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Pang
authors.forename: Chunfa
authors.initials: C
authors.lastname: Tong
authors.forename: Zhong
authors.initials: Z
authors.lastname: Wang
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.forename: Sisi
authors.initials: S
authors.lastname: Feng
authors.forename: Christian M
authors.initials: CM
authors.lastname: Tobias
authors.forename: Rongling
authors.initials: R
authors.lastname: Wu
mesh_terms: D002874:Chromosome Mapping / Q000706:statistics & numerical data; D023902:Chromosome Pairing; D020090:Chromosome Segregation; D019295:Computational Biology; D003198:Computer Simulation; D008040:Genetic Linkage; D016013:Likelihood Functions; D008540:Meiosis / Q000235:genetics; D008957:Models, Genetic; D010944:Plants / Q000235:genetics*; D057891:Tetraploidy