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Dark response genes: a group of endogenous pendulum/timing players in maize?

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Abstract

Main conclusion

Maize has a set of dark response genes, expression of which is influenced by multiple factor and varies with maize inbred lines but without germplasm specificity.

Abstract

The response to photoperiod is a common biological issue across the species kingdoms. Dark is as important as light in photoperiod. However, further in-depth understanding of responses of maize (Zea mays) to light and dark transition under photoperiod is hindered due to the lack of understanding of dark response genes. With multiple public “-omic” datasets of temperate and tropical/subtropical maize, 16 maize dark response genes, ZmDRGs, were found and had rhythmic expression under dark and light–dark cycle. ZmDRGs 6–8 were tandemly duplicated. ZmDRGs 2, 13, and 14 had a chromosomal collinearity with other maize genes. ZmDRGs 1–11 and 13–16 had copy-number variations. ZmDRGs 2, 9, and 16 showed 5′-end sequence deletion mutations. Some ZmDRGs had chromatin interactions and underwent DNA methylation and/or m6A mRNA methylation. Chromosomal histones associated with 15 ZmDRGs were methylated and acetylated. ZmDRGs 1, 2, 4, 9, and 13 involved photoperiodic phenotypes. ZmDRG16 was within flowering-related QTLs. ZmDRGs 1, 3, and 6–11 were present in cis-acting expression QTLs (eQTLs). ZmDRGs 1, 4, 6–9, 11, 12, and 14–16 showed co-expression with other maize genes. Some of ZmDRG-encoded ZmDRGs showed obvious differences in abundance and phosphorylation. Conclusion: Sixteen ZmDRGs 1–16 are associated with the dark response of maize. In the process of post-domestication and/or breeding, the ZmDRGs undergo the changes without germplasm specificity, including epigenetic modifications, gene copy numbers, chromatin interactions, and deletion mutations. In addition to effects by these factors, ZmDRG expression is influenced by promoter elements, cis-acting eQTLs, and co-expression networks.

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Abbreviations

CNV:

Copy-number variation

DAP1:

Day after pollination

DAP2:

Day after planting

DRP:

Dark response protein

eQTLs:

cis-Acting expression QTLs

QTLs:

Quantitative trait loci

GO:

Gene Ontology

DL:

Dark–light

PDIs:

Promoter proximal–distal interactions

PPIs:

Promoter proximal interactions

TD:

Total dark

ZmDRG :

Maize dark response gene

ZmDRG:

ZmDRG-Encoded protein

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Acknowledgements

This work was supported by the Guangxi Natural Science Fund Project (2017GXNSFEA198003) and the Science and Technology Major Project of Guangxi (Guike AA17204064).

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  1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, China

    Ming-You Dong, Ling Lei, Xian-Wei Fan & You-Zhi Li

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Dong, MY., Lei, L., Fan, XW. et al. Dark response genes: a group of endogenous pendulum/timing players in maize?. Planta 252, 1 (2020). https://doi.org/10.1007/s00425-020-03403-4

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