TY - JOUR
T1 - Variant phasing and haplotypic expression from long-read sequencing in maize
AU - Wang, Bo
AU - Tseng, Elizabeth
AU - Baybayan, Primo
AU - Eng, Kevin
AU - Regulski, Michael
AU - Jiao, Yinping
AU - Wang, Liya
AU - Olson, Andrew
AU - Chougule, Kapeel
AU - Buren, Peter Van
AU - Ware, Doreen
N1 - Funding Information:
This work was supported by USDA-SCA grant #51530311 and NSF Gramene grant #52930511. The authors thank Tim Mulligan for assistance with farming.
Publisher Copyright:
© 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.
PY - 2020/12/1
Y1 - 2020/12/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85079592821&partnerID=8YFLogxK
U2 - 10.1038/s42003-020-0805-8
DO - 10.1038/s42003-020-0805-8
M3 - Article
C2 - 32071408
AN - SCOPUS:85079592821
VL - 3
JO - Communications Biology
JF - Communications Biology
SN - 2399-3642
IS - 1
M1 - 78
ER -