Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from Arabidopsis and Maize leaves

ABSTRACT: Many animal and plant species exhibit increased growth rates, reach larger sizes and, in the cases of crops and farm animals, produce higher yields when bred as hybrids between genetically differing strains, a phenomenon known as hybrid vigour or heterosis. Despite the importance of heterosis, and its extensive genetic analysis, there has been little understanding of its molecular basis. We aimed to determine whether characteristics of the leaf transcriptome, as an indicator of the innate functional genetic architecture of a plant line, could be used as markers to predict heterosis and the performance of hybrids, a methodology we term Association Transcriptomics. Relationships between transcript abundance of specific genes and the values of heterosis and heterosis-dependent traits were identified and mathematical models were constructed that relate gene expression characteristics in inbred lines of Arabidopsis thaliana and maize with vegetative biomass and for grain yield, respectively, in corresponding hybrids. Plants used for transcriptome analysis were grown from seeds for 2 weeks. Aerial parts above the coleoptiles were excised, weighed and frozen in liquid nitrogen. All plants were harvested as close as practicable to the middle of the photoperiod. Plants used for transcriptome analysis were grown from seeds for 2 weeks. Maize seeds were first imbibed in distilled water for 2 days in glasshouse conditions to break dormancy, before transfer to peat and sand P7 pots. They were grown in long day glass house conditions (16 hours photoperiod) at 22 degrees Celsius. Aerial parts above the coleoptiles were excised, weighed and frozen in liquid nitrogen. All plants were harvested as close as practicable to the middle of the photoperiod. Plants for yield trials were grown in the field at Clayton, NC, U.S.A. in 2005. Forty plants of each hybrid were grown in duplicate 0.0007 hectare plots.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Andreas Magusin

PROVIDER: E-GEOD-19785 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Hybrid plants and animals grow larger and more vigorously than the parents, a common phenomenon known as hybrid vigor or heterosis. Heterosis often correlates with the genetic distance between hybridizing parents, but the mechanism for this is largely unknown. We found that genetic distance was correlated with natural variation of stress responses under the control of the circadian clock. CIRCADIAN-CLOCK-ASSOCIATED1 (CCA1) and LATE-ELONGATED-HYPOCOTYL (LHY) or CCA1 alone mediate expression amplitudes and periods of these stress-responsive genes in stress and non-stress conditions. In Arabidopsis thaliana intraspecific hybrids, genome-wide expression of many biotic and abiotic stress-responsive genes was diurnally repressed to promote biomass heterosis, which is associated with several biomass quantitative trait loci (QTLs). Expression differences in four selected stress-responsive genes among ten ecotypes could be used to predict heterosis in their hybrids. Parent plants with larger expression differences between stress-responsive genes produced higher-vigor hybrids, while those with smaller differences produced lower-vigor hybrids. Stress-responsive genes were epigenetically repressed in the hybrids under normal conditions but induced during times of stress at certain times of the day, balancing the tradeoff between stress responses and growth. Consistently, repressing the stress genes in diploids increased growth vigor. We demonstrate how hybrids manipulate diurnal stress-responsive gene expression to enhance growth vigor. Both circadian and epigenetic regulation play key roles in the altered expression of stress-responsive genes in hybrids. Our findings provide a conceptual advance and mechanistic understanding of heterosis, as well as selection criteria for parents to be effectively used for producing high-yield hybrids. Examination of gene expression in Arabidopsis thaliana F1 hybrids between Col and C24 and 3 time points using mRNA-seq

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Expression data from Arabidopsis and Maize leaves

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