Variant phasing and haplotypic expression from long-read sequencing in maize

Haplotype phasing maize genetic variants is important for genome interpretation, population genetic analysis and functional analysis of allelic activity. We performed an isoform-level phasing study using two maize inbred lines and their reciprocal crosses, based on single-molecule, full-length cDNA...

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Bibliographic Details
Published in:Communications biology 2020-02, Vol.3 (1), p.78-78, Article 78
Main Authors: Wang, Bo, Tseng, Elizabeth, Baybayan, Primo, Eng, Kevin, Regulski, Michael, Jiao, Yinping, Wang, Liya, Olson, Andrew, Chougule, Kapeel, Buren, Peter Van, Ware, Doreen
Format: Article
Language:English
Subjects:
38/39
45/91
631/114/2164
631/449/1870
Alleles
Biology
Biomedical and Life Sciences
Endosperm
Genes
Genetic analysis
Genetic crosses
Genetic diversity
Genomes
Haplotypes
Hybrids
Inbreeding
Isoforms
Life Sciences
Population genetics
Single-nucleotide polymorphism
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Summary:Haplotype phasing maize genetic variants is important for genome interpretation, population genetic analysis and functional analysis of allelic activity. We performed an isoform-level phasing study using two maize inbred lines and their reciprocal crosses, based on single-molecule, full-length cDNA sequencing. To phase and analyze transcripts between hybrids and parents, we developed IsoPhase. Using this tool, we validated the majority of SNPs called against matching short-read data from embryo, endosperm and root tissues, and identified allele-specific, gene-level and isoform-level differential expression between the inbred parental lines and hybrid offspring. After phasing 6907 genes in the reciprocal hybrids, we annotated the SNPs and identified large-effect genes. In addition, we identified parent-of-origin isoforms, distinct novel isoforms in maize parent and hybrid lines, and imprinted genes from different tissues. Finally, we characterized variation in cis- and trans-regulatory effects. Our study provides measures of haplotypic expression that could increase accuracy in studies of allelic expression. Bo Wang et al. report an isoform-level phasing study in maize using long-read cDNA sequencing and a new method, IsoPhase, to annotate allele-specific, gene-level and isoform-level expression. They identify novel gene isoforms, imprinted genes, and variation in cis- and trans-regulatory effects.
ISSN:2399-3642
2399-3642
DOI:10.1038/s42003-020-0805-8