1. Section of Molecular Cell and Developmental Biology,
2. Institute for Cellular and Molecular Biology,
3. Center for Computational Biology and Bioinformatics, and,
4. Section of Integrative Biology, The University of Texas at Austin, One University Station, A-4800, Austin, Texas 78712, USA
5. Department of Plant Genetics and Breeding, China Agricultural University, Yuanmingyuan Xilu No. 2, Beijing, 100094, China
6. These authors contributed equally to this work.
7. Present address: Department of Plant Genetics and Breeding, China Agricultural University, Yuanmingyuan Xilu No. 2, Beijing, 100094, China.

Correspondence to: Z. Jeffrey Chen^1,2,3,4 Correspondence and requests for materials should be addressed to Z.J.C. (Email: zjchen@mail.utexas.edu).

Abstract

Segregating hybrids and stable allopolyploids display morphological vigour^{1, 2, 3}, and Arabidopsis allotetraploids are larger than the parents Arabidopsis thaliana and Arabidopsis arenosa^{1, 4}—the mechanisms for this are unknown. Circadian clocks mediate metabolic pathways and increase fitness in animals and plants^{5, 6, 7, 8}. Here we report that epigenetic modifications of the circadian clock genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY)^{9, 10, 11} and their reciprocal regulators TIMING OF CAB EXPRESSION 1 (TOC1) and GIGANTEA (GI)^{10, 12, 13} mediate expression changes in downstream genes and pathways. During the day, epigenetic repression of CCA1 and LHY induced the expression of TOC1, GI and downstream genes containing evening elements¹⁴ in chlorophyll and starch metabolic pathways in allotetraploids and F₁ hybrids, which produced more chlorophyll and starch than the parents in the same environment. Mutations in cca1 and cca1 lhy and the daily repression of cca1 by RNA interference (RNAi) in TOC1::cca1(RNAi) transgenic plants increased the expression of downstream genes and increased chlorophyll and starch content, whereas constitutively expressing CCA1 or ectopically expressing TOC1::CCA1 had the opposite effect. The causal effects of CCA1 on output traits suggest that hybrids and allopolyploids gain advantages from the control of circadian-mediated physiological and metabolic pathways, leading to growth vigour and increased biomass.

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