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

Bo Wang, Elizabeth Tseng, Primo Baybayan, Kevin Eng, Michael Regulski, Yinping Jiao, Liya Wang, Andrew Olson, Kapeel Chougule, Peter Van Buren, Doreen Ware

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


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.

Original languageEnglish
Article number78
JournalCommunications Biology
Issue number1
StatePublished - Dec 1 2020


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