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Research paper | Open Access

Integrated transcriptome, small RNA, and degradome analysis to elucidate the regulation of rice seedling mesocotyl development during the passage from darkness to light

Yusong Lyua,b, Xiangjin Weia( ), Min Zhonga, Shipeng Niua, Shakeel Ahmada, Gaoneng Shaoa, Guiai Jiaoa, Zhonghua Shenga, Lihong Xiea, Shikai Hua, Yawen Wua, Shaoqing Tanga, Peisong Hua( )
State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China

Peer review under responsibility of Crop Science Society of China and Institute of Crop Science, CAAS.

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Abstract

The mesocotyl, a structure located between the basal part of the seminal root and the coleoptile node of seedlings, contributes to pushing the shoot tip through the soil surface, a function that is essential for the uniform emergence of direct-seeded rice. Its elongation is inhibited by light and induced in darkness. This investigation of an indica rice (P25) with vigorous mesocotyl elongation was aimed at identifying the “omics” basis of its light-induced growth inhibition. A transcriptomic comparison between mesocotyl tissues that had developed in the dark and then been exposed to light identified many differentially expressed genes (DEGs) and differentially abundant microRNAs (miRNAs). Degradome sequencing analysis revealed 27 negative miRNA-target pairs. A co-expression regulatory network was constructed based on the miRNAs, their corresponding targets, and DEGs with a common Gene Ontology term. It suggested that auxin and light, probably antagonistically, affect mesocotyl elongation by regulating polyamine oxidase activity.

Keywords

TranscriptomeOryza sativa. LMesocotylMicroRNAomeDegradome

References

[1]

W. Zhou, Z. Guo, J. Chen, J. Jiang, D. Hui, X. Wang, J. Sheng, L. Chen, Y. Luo, J. Zheng, S. Li, Y. Zhang, Direct seeding for rice production increased soil erosion and phosphorus runoff losses in subtropical China, Sci. Total Environ. 695 (2019) 133845.
Crossref Google Scholar
[2]

M. Farooq, K.H.M. Siddique, H. Rehman, T. Aziz, D.J. Lee, A. Wahid, Rice direct seeding: experiences, challenges and opportunities, Soil Till. Res. 111 (2) (2011) 87–98.
Crossref Google Scholar
[3]

H.S. Lee, K. Sasaki, J.W. Kang, T. Sato, W.Y. Song, S.N. Ahn, Mesocotyl elongation is essential for seedling emergence under deep-seeding condition in rice, Rice 10 (2017) 32.
Crossref Google Scholar
[4]

R. Nishimoto, Global trends in the crop protection industry, J. Pestic. Sci. 44 (2019) 141–147.
Crossref Google Scholar
[5]

M. Andrews, A. Douglas, A.V. Jones, C.E. Milburn, D. Porter, B.A. McKenzie, Emergence of temperate pasture grasses from different sowing depths: importance of seed weight, coleoptile plus mesocotyl length and shoot strength, Ann. Appl. Biol. 130 (1997) 549–560.
Crossref Google Scholar
[6]

M. Farooq, S.M.A. Barsa, A. Wahid, Priming of field-sown rice seed enhances germination, seedling establishment, allometry and yield, Plant Growth Regul. 49 (2006) 285–294.
Crossref Google Scholar
[7]

R.J.H. Sawers, P.J. Linley, P.R. Farmer, N.P. Hanley, D.E. Costich, M.J. Terry, T.P. Brutnell, Elongated mesocotyl1, a phytochrome-deficient mutant of maize, Plant Physiol. 130 (2002) 155–163.
Crossref Google Scholar
[8]

J. Luo, S.Q. Tang, P.S. Hu, A. Louis, G.A. Jiao, J. Tang, Analysis on factors affecting seedling establishment in rice, Rice Sci. 14 (2007) 27–32.
Crossref Google Scholar
[9]

M. Chen, J. Chory, C. Fankhauser, Light signal transduction in higher plants, Annu. Rev. Genet. 38 (2004) 87–117.
Crossref Google Scholar
[10]

J.F. Doebley, B.S. Gaut, B.D. Smith, The molecular genetics of crop domestication, Cell 127 (2006) 1309–1321.
Crossref Google Scholar
[11]

M. Iino, Inhibitory action of red light on the growth of the maize mesocotyl: evaluation of the auxin hypothesis, Planta 156 (1982) 388–395.
Crossref Google Scholar
[12]

M. Hohl, H. Greiner, P. Schopfer, The cryptic-growth response of maize coleoptiles and its relationship to H2O2-dependent cell-wall stiffening, Physiol. Plantarum 94 (1995) 491–498.
Crossref Google Scholar
[13]

S.X. Chen, P. Schopfer, Hydroxyl-radical production in physiological reactions - a novel function of peroxidase, Eur. J. Biochem. 260 (1999) 726–735.
Crossref Google Scholar
[14]

Y. Ono, D.W. Kim, K. Watanabe, A. Sasaki, M. Niitsu, T. Berberich, T. Kusano, Y. Takahashi, Constitutively and highly expressed Oryza sativa polyamine oxidases localize in peroxisomes and catalyze polyamine back conversion, Amino Acids 42 (2012) 867–876.
Crossref Google Scholar
[15]

Z.Y. Wang, M.Y. Bai, E. Oh, J.Y. Zhu, Brassinosteroid signaling network and regulation of photomorphogenesis, Annu. Rev. Genet. 46 (2012) 701–724.
Crossref Google Scholar
[16]

S.Y. Sun, T. Wang, L.L. Wang, X.M. Li, Y.C. Jia, C. Liu, X.H. Huang, W.B. Xie, X.L. Wang, Natural selection of a GSK3 determines rice mesocotyl domestication by coordinating strigolactone and brassinosteroid signaling, Nat. Commun. 9 (2018) 2523.
Crossref Google Scholar
[17]

Q. Xiong, B. Ma, X. Lu, Y.H. Huang, S.J. He, C. Yang, C.C. Yin, H. Zhao, Y. Zhou, W.K. Zhang, W.S. Wang, Z.K. Li, S.Y. Chen, J.S. Zhang, Ethylene-inhibited jasmonic acid biosynthesis promotes mesocotyl/coleoptile elongation of etiolated rice seedlings, Plant Cell 29 (2017) 1053–1072.
Crossref Google Scholar
[18]

S.W. Zhong, H. Shi, C. Xue, N. Wei, H.W. Guo, X.W. Deng, Ethylene-orchestrated circuitry coordinates a seedling's response to soil cover and etiolated growth, Proc. Natl. Acad. Sci. U. S. A. 111 (2014) 3913–3920.
Crossref Google Scholar
[19]

H. Shi, R.L. Liu, C. Xue, X. Shen, N. Wei, X.W. Deng, S.W. Zhong, Seedlings transduce the depth and mechanical pressure of covering soil using COP1 and ethylene to regulate EBF1/EBF2 for soil emergence, Curr. Biol. 26 (2016) 139–149.
Crossref Google Scholar
[20]

H. Shi, X. Shen, R.L. Liu, C. Xue, N. Wei, X.W. Deng, S.W. Zhong, The red light receptor phytochrome B directly enhances substrate-E3 ligase interactions to attenuate ethylene responses, Dev. Cell 39 (2016) 597–610.
Crossref Google Scholar
[21]

F.J. Feng, H.W. Mei, P.Q. Fan, Y.N. Li, X.Y. Xu, H.B. Wei, M. Yan, L.J. Luo, Dynamic transcriptome and phytohormone profiling along the time of light exposure in the mesocotyl of rice seedling, Sci. Rep. 7 (2017) 1–11.
Crossref Google Scholar
[22]

D.P. Bartel, MicroRNAs: genomics, biogenesis, mechanism, and function, Cell 116 (2004) 281–297.
Crossref Google Scholar
[23]

A.A. Bazzini, A.J. Giraldez, MicroRNAs sculpt gene expression in embryonic development: mew insights from plants, Dev. Cell 20 (2011) 3–4.
Crossref Google Scholar
[24]

M.W. Jones-Rhoades, D.P. Bartel, B. Bartel, MicroRNAs and their regulatory roles in plants, Annu. Rev. Plant Biol. 57 (2006) 19–53.
Crossref Google Scholar
[25]

L.I. Shukla, V. Chinnusamy, R. Sunkar, The role of microRNAs and other endogenous small RNAs in plant stress responses, Gene Regul. Mech. 1779 (2008) 743–748.
Crossref Google Scholar
[26]

J.W. Zhang, L.L. Chen, F. Xing, D.A. Kudrna, W. Yao, L.Z. Xiong, C.Y. Wu, Y.Z. Xing, D.X. Zhou, S.B. Yu, Y. Zhao, G.W. Wang, Y.S. Danowitz, R.A. Wing, Q.F. Zhang, Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63, Proc. Natl. Acad. Sci. U. S. A. 113 (2016) 5163–5171.
Crossref Google Scholar
[27]

J.M. Song, Y. Lei, C.C. Shu, Y.D. Ding, F. Xing, H. Liu, J. Wang, W.B. Xie, J.W. Zhang, L.L. Chen, Rice Information GateWay: a comprehensive bioinformatics platform for indica rice genomes, Mol. Plant 11 (2018) 505–507.
Crossref Google Scholar
[28]

Q.L. Lang, C.Z. Jin, L.Y. Lai, J.L. Feng, S.N. Chen, J.S. Chen, Tobacco microRNAs prediction and their expression infected with Cucumber mosaic virus and Potato virus X, Mol. Biol. Rep. 38 (2011) 1523–1531.
Crossref Google Scholar
[29]

Y. Zhang, J.B. Su, S. Duan, Y. Ao, J.R. Dai, J. Liu, P. Wang, Y.G. Li, B. Liu, D.R. Feng, J.F. Wang, H.B. Wang, A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes, Plant Methods 7 (2011) 30.
Crossref Google Scholar
[30]

J.H. Fu, J.F. Chu, X.H. Sun, J.D. Wang, C.Y. Yan, Simple, rapid, and simultaneous assay of multiple carboxyl containing phytohormones in wounded tomatoes by UPLC-MS/MS using single SPE purification and isotope dilution, Anal. Sci. 28 (2012) 1081–1087.
Crossref Google Scholar
[31]

A. Cona, F. Cenci, M. Cervelli, R. Federico, P. Mariottini, S. Moreno, R. Angelini, Polyamine oxidase, a hydrogen peroxide-producing enzyme, is up-regulated by light and down-regulated by auxin in the outer tissues of the maize mesocotyl, Plant Physiol. 131 (2003) 803–813.
Crossref Google Scholar
[32]

G.M. Rae, V.N. Uversky, K. David, M. Wood, DRM1 and DRM2 expression regulation: potential role of splice variants in response to stress and environmental factors in Arabidopsis, Mol. Genet. Genomics 289 (2014) 317–332.
Crossref Google Scholar
[33]

A. Yahalom, B.L. Epel, Z. Glinka, I.R. Macdonald, D.C. Gordon, A kinetic analysis of phytochrome controlled mesocotyl growth in maize seedlings, Plant Physiol. 84 (1987) 390–394.
Crossref Google Scholar
[34]

H. Shi, M. Lyu, Y. Luo, S. Liu, Y. Li, H. He, N. Wei, X.W. Deng, S. Zhong, Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors, Proc. Natl. Acad. Sci. U. S. A. 115 (2018) 6482–6487.
Crossref Google Scholar
[35]

C. Yang, B. Ma, S.J. He, Q. Xiong, K.X. Duan, C.C. Yin, H. Chen, X. Lu, S.Y. Chen, J.S. Zhang, MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIVE3-LIKE2 regulate ethylene response of roots and coleoptiles and negatively affect salt tolerance in rice, Plant Physiol. 169 (2015) 148–165.
Crossref Google Scholar
[36]

L. Wang, S. Sun, J. Jin, D. Fu, X. Yang, X. Weng, C. Xu, X. Li, J. Xiao, Q. Zhang, Coordinated regulation of vegetative and reproductive branching in rice, Proc. Natl. Acad. Sci. U. S. A. 112 (2015) 15504–15509.
Crossref Google Scholar
[37]

D. Huang, S. Wang, B. Zhang, K. Shang-Guan, Y. Shi, D. Zhang, X. Liu, K. Wu, Z. Xu, X. Fu, Y. Zhou, A gibberellin-mediated DELLA-NAC signaling cascade regulates cellulose synthesis in rice, Plant Cell 27 (2015) 1681–1696.
Crossref Google Scholar
[38]

T. Hewezi, T.R. Maier, D. Nettleton, T.J. Baum, The Arabidopsis microRNA396-GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection, Plant Physiol. 159 (2012) 321–335.
Crossref Google Scholar
[39]

J. Fina, R. Casadevall, H. AbdElgawad, E. Prinsen, M.N. Markakis, G.T.S. Beemster, P. Casati, UV-B inhibits leaf growth through changes in growth regulating factors and gibberellin levels, Plant Physiol. 174 (2017) 1110–1126.
Crossref Google Scholar
[40]

Y.R. Xie, Y. Liu, H. Wang, X.J. Ma, B.B. Wang, G.X. Wu, H.Y. Wang, Phytochrome-interacting factors directly suppress MIR156 expression to enhance shade-avoidance syndrome in Arabidopsis, Nat. Commun. 8 (2017) 348.
Crossref Google Scholar
[41]

S. Banerjee, N.F. Scherer, A.R. Dinner, Shape dynamics of growing cell walls, Soft Matter 12 (2016) 3442–3450.
Crossref Google Scholar
[42]

D.J. Cosgrove, Expansive growth of plant cell walls, Plant Physiol. Biochem. 38 (2000) 109–124.
Crossref Google Scholar
The Crop Journal
Volume 8 Issue 6,
December 2020
Pages 918-928
DOI: 10.1016/j.cj.2020.05.002
Cite this article:
Lyu Y, Wei X, Zhong M, et al. Integrated transcriptome, small RNA, and degradome analysis to elucidate the regulation of rice seedling mesocotyl development during the passage from darkness to light. The Crop Journal, 2020, 8(6): 918-928. https://doi.org/10.1016/j.cj.2020.05.002

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Received: 05 November 2019
Revised: 14 February 2020
Accepted: 30 May 2020
Published: 20 June 2020
© 2020 Crop Science Society of China and Institute of Crop Science, CAAS.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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