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Related Experiment Video

Updated: Dec 28, 2025

Discrimintion and Mapping of the Primary and Processed Transcripts in Maize Mitochondrion Using a Circular RT-PCR-based Strategy
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Variant phasing and haplotypic expression from long-read sequencing in maize.

Bo Wang1, Elizabeth Tseng2, Primo Baybayan2

  • 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.

Communications Biology
|February 20, 2020
PubMed
Summary
This summary is machine-generated.

This study introduces IsoPhase for isoform-level haplotype phasing in maize, improving genetic variant analysis and understanding allele-specific expression in hybrids and parents.

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Area of Science:

  • Plant genetics
  • Genomics
  • Molecular biology

Background:

  • Haplotype phasing is crucial for maize genetic interpretation and functional analysis.
  • Understanding allelic activity requires accurate phasing of genetic variants.

Purpose of the Study:

  • To develop and apply a novel tool, IsoPhase, for isoform-level haplotype phasing in maize.
  • To analyze transcripts and identify allele-specific expression in maize inbred lines and their hybrids.

Main Methods:

  • Single-molecule, full-length cDNA sequencing of two maize inbred lines and their reciprocal crosses.
  • Development and application of the IsoPhase tool for phasing and transcript analysis.
  • Validation of SNPs against short-read data and identification of differential expression.

Main Results:

  • IsoPhase successfully phased 6907 genes in reciprocal hybrids.
  • Identified allele-specific, gene-level, and isoform-level differential expression.
  • Discovered parent-of-origin isoforms, novel isoforms, imprinted genes, and characterized cis/trans-regulatory effects.

Conclusions:

  • The study provides accurate measures of haplotypic expression in maize.
  • Enhanced accuracy in allelic expression studies is achievable with this method.
  • IsoPhase is a valuable tool for maize genetic and functional genomics research.