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- Title
An open-pollinated design for mapping imprinting genes in natural populations.
- Authors
Lidan Sun; Xuli Zhu; Wenhao Bo; Fang Xu; Tangren Cheng; Qixiang Zhang; Rongling Wu
- Abstract
With the increasing recognition of its role in trait and disease development, it is crucial to account for genetic imprinting to illustrate the genetic architecture of complex traits. Genetic mapping can be innovated to test and estimate effects of genetic imprinting in a segregating population derived from experimental crosses. Here, we describe and assess a design for imprinting detection in natural plant populations. This design is to sample maternal plants at random from a natural population and collect open-pollinated (OP) seeds randomly from each maternal plant and germinate them into seedlings. A two-stage hierarchical platform is constructed to jointly analyze maternal and OP progeny markers. Through tracing the segregation and transmission of alleles from the parental to progeny generation, this platform allows parent-of-origin-dependent gene expression to be discerned, providing an avenue to estimate the effect of imprinting genes on a quantitative trait. The design is derived to estimate imprinting effects expressed at the haplotype level. Its usefulness and utilization were validated through computer simulation. This OP-based design provides a tool to detect the genomic distribution and pattern of imprinting genes as an important component of heritable variation that is neglected in traditional genetic studies of complex traits.
- Subjects
GENOMIC imprinting; GENE mapping; PLANT population genetics; HAPLOTYPES; COMPUTER simulation; POLLINATION; EXPECTATION-maximization algorithms
- Publication
Briefings in Bioinformatics, 2015, Vol 16, Issue 3, p449
- ISSN
1467-5463
- Publication type
Article
- DOI
10.1093/bib/bbu019