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Plant direct
Jul, 2022;6 (7): e425.

Keeping time in the dark: Potato diel and circadian rhythmic gene expression reveals tissue-specific circadian clocks.

Genevieve M Hoopes, Daniel Zarka, Ann Feke, Kaitlyn Acheson, John P Hamilton, David Douches, C Robin Buell, Eva M Farré
Author Information
  1. Genevieve M Hoopes: Department of Plant Biology Michigan State University East Lansing Michigan USA. ORCID
  2. Daniel Zarka: Department of Plant, Soil, and Microbial Sciences Michigan State University East Lansing Michigan USA.
  3. Ann Feke: Department of Plant Biology Michigan State University East Lansing Michigan USA. ORCID
  4. Kaitlyn Acheson: Department of Plant Biology Michigan State University East Lansing Michigan USA.
  5. John P Hamilton: Department of Plant Biology Michigan State University East Lansing Michigan USA. ORCID
  6. David Douches: Department of Plant, Soil, and Microbial Sciences Michigan State University East Lansing Michigan USA. ORCID
  7. C Robin Buell: Department of Plant Biology Michigan State University East Lansing Michigan USA. ORCID
  8. Eva M Farré: Department of Plant Biology Michigan State University East Lansing Michigan USA. ORCID
PMID: 35844780 DOI: 10.1002/pld3.425

Abstract

The circadian clock is an internal molecular oscillator and coordinates numerous physiological processes through regulation of molecular pathways. Tissue-specific clocks connected by mobile signals have previously been found to run at different speeds in tissues. However, tissue variation in circadian clocks in crop species is unknown. In this study, leaf and tuber global gene expression in cultivated potato under cycling and constant environmental conditions was profiled. In addition, we used a circadian-regulated luciferase reporter construct to study tuber gene expression rhythms. Diel and circadian expression patterns were present among 17.9% and 5.6% of the expressed genes in the tuber. Over 500 genes displayed differential tissue specific diel phases. Intriguingly, few core circadian clock genes had circadian expression patterns, while all such genes were circadian rhythmic in cultivated tomato leaves. Furthermore, robust diel and circadian transcriptional rhythms were observed among detached tubers. Our results suggest alternative regulatory mechanisms and/or clock composition is present in potato, as well as the presence of tissue-specific independent circadian clocks. We have provided the first evidence of a functional circadian clock in below-ground storage organs, holding important implications for other storage root and tuberous crops.

Keywords

Solanum tuberosum L. (potato) circadian clock diel gene expression luciferase luminescence tissue‐specific

References

  1. PLoS Genet. 2008 Feb;4(2):e14 [PMID: 18248097]
  2. Elife. 2020 Sep 30;9: [PMID: 32996462]
  3. Genome Biol. 2014;15(12):550 [PMID: 25516281]
  4. Plant Physiol. 2016 Jan;170(1):528-39 [PMID: 26586835]
  5. PLoS One. 2010 Sep 23;5(9):e12887 [PMID: 20886102]
  6. Genome Biol. 2019 Nov 14;20(1):238 [PMID: 31727128]
  7. Plant Direct. 2022 Jul 12;6(7):e425 [PMID: 35844780]
  8. Plant Physiol. 2017 Jun;174(2):845-856 [PMID: 28520554]
  9. Curr Biol. 2019 Apr 1;29(7):1178-1186.e6 [PMID: 30905604]
  10. BMC Bioinformatics. 2008 Dec 29;9:559 [PMID: 19114008]
  11. Curr Biol. 2016 Apr 4;26(7):872-81 [PMID: 26972319]
  12. Plant Biotechnol J. 2018 Jan;16(1):197-207 [PMID: 28509353]
  13. Genetics. 2008 Sep;180(1):391-408 [PMID: 18723883]
  14. J Exp Bot. 2019 Oct 24;70(20):5703-5714 [PMID: 31328229]
  15. PLoS One. 2014 May 08;9(5):e96462 [PMID: 24809473]
  16. PLoS Biol. 2019 Aug 15;17(8):e3000407 [PMID: 31415556]
  17. Science. 2008 Dec 19;322(5909):1832-5 [PMID: 19095940]
  18. Proc Natl Acad Sci U S A. 2010 May 18;107(20):9458-63 [PMID: 20439704]
  19. Plant Cell Environ. 2014 Feb;37(2):439-50 [PMID: 23889235]
  20. Plant Physiol. 2003 May;132(1):365-71 [PMID: 12746541]
  21. Front Genet. 2019 Nov 29;10:1239 [PMID: 31850080]
  22. Plant Sci. 2014 Jul;224:20-6 [PMID: 24908502]
  23. Sci Adv. 2021 Jan 29;7(5): [PMID: 33514540]
  24. Nat Genet. 2016 Jan;48(1):89-93 [PMID: 26569124]
  25. Science. 2000 Dec 15;290(5499):2110-3 [PMID: 11118138]
  26. Plant Physiol. 2008 Feb;146(2):515-28 [PMID: 18083796]
  27. Plant Cell Environ. 2014 Jun;37(6):1351-63 [PMID: 24236539]
  28. J Biol Rhythms. 2017 Oct;32(5):380-393 [PMID: 29098954]
  29. Plant Physiol. 2020 Jun;183(2):765-779 [PMID: 32229608]
  30. Nature. 2013 Mar 14;495(7440):246-50 [PMID: 23467094]
  31. Nat Commun. 2015 Jul 06;6:7641 [PMID: 26144255]
  32. Genome Biol. 2008;9(8):R130 [PMID: 18710561]
  33. Plant Physiol. 2017 Jan;173(1):5-15 [PMID: 27688622]
  34. New Phytol. 2016 Oct;212(1):136-49 [PMID: 27240972]
  35. Dev Cell. 2018 Apr 9;45(1):101-113.e4 [PMID: 29576425]
  36. Biology (Basel). 2020 Dec 09;9(12): [PMID: 33317013]
  37. Annu Rev Genet. 2010;44:419-44 [PMID: 20809800]
  38. Plant Cell. 2015 Oct;27(10):2743-69 [PMID: 26432862]
  39. Bioinformatics. 2020 Feb 1;36(3):773-781 [PMID: 31384918]
  40. Nature. 2014 Nov 20;515(7527):419-22 [PMID: 25363766]
  41. Nat Plants. 2016 May 27;2(6):16074 [PMID: 27255838]
  42. Plant Physiol. 2016 Jan;170(1):310-24 [PMID: 26553650]
  43. PLoS One. 2014 Feb 13;9(2):e88844 [PMID: 24551177]
  44. PLoS One. 2011;6(6):e16907 [PMID: 21694767]
  45. Plant J. 2000 Jul;23(2):223-32 [PMID: 10929116]
  46. Cell. 2015 Sep 24;163(1):148-59 [PMID: 26406375]
  47. Nat Commun. 2019 Feb 13;10(1):737 [PMID: 30760717]
  48. Genome Res. 2003 Nov;13(11):2498-504 [PMID: 14597658]
  49. Plant Cell Physiol. 1998 Sep;39(9):905-13 [PMID: 9816675]
  50. Plant Mol Biol. 2002 Jun-Jul;49(3-4):373-85 [PMID: 12036261]
  51. Front Plant Sci. 2013 Feb 20;4:26 [PMID: 23429841]
  52. Bioinformatics. 2016 Nov 1;32(21):3351-3353 [PMID: 27378304]
  53. Plant Direct. 2020 Nov 18;4(11):e00286 [PMID: 33241173]
  54. Nat Genet. 2014 Sep;46(9):1034-8 [PMID: 25064008]
  55. Plant Cell Environ. 2015 Nov;38(11):2318-26 [PMID: 25850677]
  56. Physiol Plant. 2020 Jul;169(3):442-451 [PMID: 32303120]
  57. Nat Plants. 2020 Apr;6(4):416-426 [PMID: 32284549]
  58. Plant J. 2019 Apr;98(1):42-54 [PMID: 30552774]
  59. Nucleic Acids Res. 2012 Jan;40(Database issue):D1202-10 [PMID: 22140109]
  60. Nature. 2011 Jul 10;475(7355):189-95 [PMID: 21743474]
  61. Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9999-E10008 [PMID: 29087343]
  62. Gigascience. 2020 Sep 23;9(9): [PMID: 32964225]
  63. Front Plant Sci. 2016 Jul 27;7:1114 [PMID: 27512400]
  64. Plant J. 2015 Sep;83(6):1097-113 [PMID: 26216534]
  65. Nat Genet. 2014 Nov;46(11):1220-6 [PMID: 25305757]
  66. Photosynth Res. 2014 Feb;119(1-2):181-90 [PMID: 23529849]

Grants

  1. T32 GM110523/NIGMS NIH HHS
Journal Article
Article has an altmetric score of 15

Word Cloud

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