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Reshaping of the maize transcriptome by domestication

ABSTRACT: Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. A wealth of archeological and population genetic data has established maize as a model system for studying domestication , genome evolution and the genetics and evolution of complex traits. We used expression profiling of 18,242 genes for 38 diverse maize genotypes and 18 teosinte genotypes to examine how domestication has re-shaped the transcriptome of maize seedlings. We detected evidence for more than 600 genes having significantly different expression levels in maize compared to teosinte as well as 800 genes with significantly altered co-expression profiles reflective of substantial rewiring of the transcriptome since domestication. These genes likely include loci with altered expression due to domestication. The genes with altered expression show a significant enrichment for genes located in regions that previous population genetic analyses have identified as having undergone a selective sweep during maize domestication; thirty-two genes previously identified as putative targets of selection also exhibit altered expression levels and co-expression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to out-crossed teosinte. These genes are over-represented for genes that function in response to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication and identifies several genes that may have contributed to the evolution of maize but also highlights the complementary information that can be gained by combining gene expression with population genetic analyses.

OTHER RELATED OMICS DATASETS IN: PRJNA144063

ORGANISM(S): Zea mays Zea mays subsp. parviglumis

PROVIDER: GSE30036 | GEO | 2012/04/01

SECONDARY ACCESSION(S): PRJNA144063

REPOSITORIES: GEO

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Project description:Different individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. In order to investigate the potential contribution of CNV and PAV to genomic diversity in maize we used array comparative genomic hybridization (CGH) to compare gene content and copy number variation among 25 diverse maize inbreds 14 genotypes of the wild ancestor of maize, teosinte. The microarray included multiple probes for each of the ~32,500 stringently filtered genes identified in the B73 reference genome. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3,410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes that are present in B73 but missing from the genome of several other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes and the majority of events are observed in both maize and teosinte suggesting that these reflect relatively old variants that are not associated with domestication or maize improvement. Many of the genes affected by CNV/PAV are either maize-specific or members of genes families suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. Many plant genomes are relatively large and contain the remnant of whole genome duplications which may provide the ability to tolerate high levels of structural variation. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation. 1-2 replications of 25 maize inbred and 14 teosinte genotypes were hybridized to an array designed from the ~32,400 genes in the maize B73 reference genome.

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Reshaping of the maize transcriptome by domestication

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