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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #374793
Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

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

Author
item WANG, BO - Cold Spring Harbor Laboratory
item TSENG, ELIZABETH - Pacific Biosciences Inc
item BAYBAYAN, PRIMO - Pacific Biosciences Inc
item ENG, KEVIN - Pacific Biosciences Inc
item REGULSKI, MICHAEL - Cold Spring Harbor Laboratory
item JIAO, YINPING - Cold Spring Harbor Laboratory
item WANG, LIYA - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item VAN BUREN, PETER - Cold Spring Harbor Laboratory
item Ware, Doreen

Submitted to: Communications Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/31/2020
Publication Date: 2/18/2020
Citation: Wang, B., Tseng, E., Baybayan, P., Eng, K., Regulski, M., Jiao, Y., Wang, L., Olson, A., Chougule, K., Van Buren, P., Ware, D. 2020. Variant phasing and haplotypic expression from long-read sequencing in maize. Communications Biology. 3(78). https://doi.org/10.1038/s42003-020-0805-8.
DOI: https://doi.org/10.1038/s42003-020-0805-8

Interpretive Summary: Haplotype refers to the combination of different alleles that can be found on a chromosome. Haplotype phasing is the statistical determination of haplotypes from genotype data. The ability to characterize these haplotypes is important for genome interpretation, population genetic analysis and functional analysis of allelic activity. In this study, we used long sequence molecules from corn, and used these to phase the haplotypes of corn hybrids. Using this approach we were able to phase 6907 genes, in these hybrids, annotate the SNPs and identified large-effect genes. In addition, we identified novel isoforms from the maize parent and hybrid lines, and genes that show parent of origin expression patterns in different tissues. Our study provides measures of haplotypic expression that could increase accuracy in studies of allelic expression.

Technical Abstract: 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. Our study provides measures of haplotypic expression that could increase accuracy in studies of allelic expression.