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Increased long-distance interactions related to heterotic expression in Arabidopsis hybrids

ABSTRACT: In plants, the genomic structure of hybrids changed compared with their parents. However, the effects of genomic structure changes on heterotic expression in hybrids remain elusive. By comparing interspecific hybrids between Col×C24 and their backcross C24×Col in Arabidopsis with Hi-C analysis, we found that the three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents. The compartment strength related to the increased A-B compartment interactions decreased in hybrids. In the boundaries of topologically associated domains (TADs) like regions in hybrids, the values of Interchromosomal Fraction of Interactions (ICF) and Distal-to-Local [log2] (DLR) were higher than or close to the highest value of their parents. While in the hybrids of CURLY LEAF (clf) mutants, which affects the long-distance interactions, the heterosis phenotype disappeared and the ICF and DLR in hybrids were lower than their parents. In addition, compared with the clf mutant, the differential expressed genes located in TAD boundaries and loop regions in the wild type changed more obviously. In the long-distance interaction and the loop region between WT and clf, there were obvious differences in the functional enrichment for DEGs. The genes with cell cycle and mitotic related process were specifically enriched in clf. By analyzing ChIP-seq data, we found that the enrichment of H3K27me3 were higher in the hybrids in WT, which may lead to more long-distance interactions. Our findings may therefore propose a new epigenetic explanation of the heterotic expression in Arabidopsis hybrids and provide new insights into crop breeding and yield increasing.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE221446 | GEO | 2024/03/24

REPOSITORIES: GEO

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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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Increased long-distance interactions related to heterotic expression in Arabidopsis hybrids

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