RESUMO
Understanding the impact of elevated CO2 (eCO2 ) in global agriculture is important given climate change projections. Breeding climate-resilient crops depends on genetic variation within naturally varying populations. The effect of genetic variation in response to eCO2 is poorly understood, especially in crop species. We describe the different ways in which Solanum lycopersicum and its wild relative S. pennellii respond to eCO2 , from cell anatomy, to the transcriptome, and metabolome. We further validate the importance of translational regulation as a potential mechanism for plants to adaptively respond to rising levels of atmospheric CO2 .
Assuntos
Dióxido de Carbono/metabolismo , Regulação da Expressão Gênica de Plantas , Biossíntese de Proteínas , Solanum/fisiologia , Transcriptoma , Biomassa , Mudança Climática , Produtos Agrícolas , Variação Genética , Metaboloma , Fotossíntese , Raízes de Plantas/anatomia & histologia , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/fisiologia , Polirribossomos , RNA Mensageiro/genética , RNA de Plantas/genética , Solanum/anatomia & histologia , Solanum/genética , Solanum/crescimento & desenvolvimentoRESUMO
Flooding due to extreme weather threatens crops and ecosystems. To understand variation in gene regulatory networks activated by submergence, we conducted a high-resolution analysis of chromatin accessibility and gene expression at three scales of transcript control in four angiosperms, ranging from a dryland-adapted wild species to a wetland crop. The data define a cohort of conserved submergence-activated genes with signatures of overlapping cis regulation by four transcription factor families. Syntenic genes are more highly expressed than nonsyntenic genes, yet both can have the cis motifs and chromatin accessibility associated with submergence up-regulation. Whereas the flexible circuitry spans the eudicot-monocot divide, the frequency of specific cis motifs, extent of chromatin accessibility, and degree of submergence activation are more prevalent in the wetland crop and may have adaptive importance.
Assuntos
Evolução Biológica , Inundações , Redes Reguladoras de Genes , Oryza/genética , Proteínas de Plantas/genética , Fatores de Transcrição/genética , Sítios de Ligação , Cromatina/genética , Regulação da Expressão Gênica de Plantas , Medicago truncatula/genética , Medicago truncatula/fisiologia , Família Multigênica , Oryza/fisiologia , Raízes de Plantas/fisiologia , Solanum/genética , Solanum/fisiologia , Estresse Fisiológico , SinteniaRESUMO
Genetic markers are essential when developing or working with genetically variable populations. Indel Group in Genomes (IGG) markers are primer pairs that amplify single-locus sequences that differ in size for two or more alleles. They are attractive for their ease of use for rapid genotyping and their codominant nature. Here, we describe a heuristic algorithm that uses a k-mer-based approach to search two or more genome sequences to locate polymorphic regions suitable for designing candidate IGG marker primers. As input to the IGG pipeline software, the user provides genome sequences and the desired amplicon sizes and size differences. Primer sequences flanking polymorphic insertions/deletions are produced as output. IGG marker files for three sets of genomes, Solanum lycopersicum/Solanum pennellii, Arabidopsis (Arabidopsis thaliana) Columbia-0/Landsberg erecta-0 accessions, and S. lycopersicum/S. pennellii/Solanum tuberosum (three-way polymorphic) are included.