An updated gene atlas for maize reveals organ-specific and stress-induced genes

Hoopes, Genevieve M.; Hamilton, John P.; Wood, Joshua C.; Esteban, Eddi; Pasha, Asher; Vaillancourt, Brieanne; Provart, Nicholas J.; Buell, C. Robin

doi:10.1111/tpj.14184

Title: An updated gene atlas for maize reveals organ-specific and stress-induced genes

Journal Article · Fri Dec 07 00:00:00 EST 2018 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.14184· OSTI ID:1609244

Hoopes, Genevieve M. ^[1]; Hamilton, John P. ^[1]; Wood, Joshua C. ^[1]; Esteban, Eddi ^[2]; Pasha, Asher ^[2]; Vaillancourt, Brieanne ^[1]; Provart, Nicholas J. ^[2]; Buell, C. Robin ^[1]

Michigan State Univ., East Lansing, MI (United States)
Univ. of Toronto, ON (Canada)

Maize (Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide. The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long-read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA-sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36 207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4154 organ-specific and 7704 differentially expressed (DE) genes following stress treatment. Gene co-expression network analyses revealed 12 modules associated with distinct biological processes containing 13 590 genes providing a resource for further association of gene function based on co-expression patterns. Presence–absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ-specific and stress-induced DE genes suggesting that PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average have significantly fewer co-expression network connections suggesting that a subset of PAVs may be on an evolutionary path to pseudogenization. Here, to facilitate use by the community, we developed the Maize Genomics Resource website (maize.plantbiology.msu.edu) for viewing and data-mining these resources and deployed two new views on the maize electronic Fluorescent Pictograph Browser (bar.utoronto.ca/efp_maize).

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Research Organization:: Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: FC02-07ER64494

OSTI ID:: 1609244

Journal Information:: The Plant Journal, Vol. 97, Issue 6; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 85 works

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59 BASIC BIOLOGICAL SCIENCES
plant sciences
Zea mays
B73
AGPv4
differential expression
co-expression
presence-absence variants
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