An open-pollinated design for mapping imprinting genes in natural populations

Lidan Sun, Xuli Zhu, Wenhao Bo, Fang Xu, Tangren Cheng, Qixiang Zhang, Rongling Wu

Research output: Contribution to journalArticle

10 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberbbu019
Pages (from-to)449-460
Number of pages12
JournalBriefings in bioinformatics
Volume16
Issue number3
DOIs
StatePublished - Aug 2 2014

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Chromosome Mapping
Genomic Imprinting
Genes
Mothers
Population
Seedlings
Computer Simulation
Haplotypes
Seeds
Alleles
Gene expression
Seed
Gene Expression
Computer simulation

All Science Journal Classification (ASJC) codes

  • Information Systems
  • Molecular Biology

Cite this

Sun, Lidan ; Zhu, Xuli ; Bo, Wenhao ; Xu, Fang ; Cheng, Tangren ; Zhang, Qixiang ; Wu, Rongling. / An open-pollinated design for mapping imprinting genes in natural populations. In: Briefings in bioinformatics. 2014 ; Vol. 16, No. 3. pp. 449-460.
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Sun, L, Zhu, X, Bo, W, Xu, F, Cheng, T, Zhang, Q & Wu, R 2014, 'An open-pollinated design for mapping imprinting genes in natural populations', Briefings in bioinformatics, vol. 16, no. 3, bbu019, pp. 449-460. https://doi.org/10.1093/bib/bbu019

An open-pollinated design for mapping imprinting genes in natural populations. / Sun, Lidan; Zhu, Xuli; Bo, Wenhao; Xu, Fang; Cheng, Tangren; Zhang, Qixiang; Wu, Rongling.

In: Briefings in bioinformatics, Vol. 16, No. 3, bbu019, 02.08.2014, p. 449-460.

Research output: Contribution to journalArticle

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