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Discovery of small RNAs in wheat: a survey

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Abstract

Several studies related to plant-environment interactions have persistently conveyed the detrimental effects of changing environment on crop productivity. Additionally, alarming rise in population growth has necessitated substantial increase in food production to ensure global food security. World-wide, wheat is a staple dietary crop for humans. Like other crop systems, productivity of wheat is largely dependent on its growth and development, which in turn, is regulated by environmental conditions, including abiotic and biotic stress factors. Under natural conditions, plants are exposed to a multitude of abiotic stresses, either simultaneously or sequentially, which exacerbates their adverse effects. It is therefore necessary to understand the mechanism of stress response in wheat, so that suitable strategies are devised for enhancement of stress tolerance. In this context, concerted research efforts involving breeding programs as well as transgenic development are needed for developing improved and locally adapted wheat varieties. In the recent years, small RNAs, 21–24 nucleotides (nt) long non-coding RNAs, have emerged as crucial regulators of gene expression changes that modulate physiological responses against environmental challenges. In this review, an attempt has been made to present the progress done in the field of wheat small RNAs genomics. An anecdote of small RNA discoveries, their function and regulation during various biotic, abiotic stresses and distinct stages of wheat development is compiled. This information would benefit wheat researchers in devising appropriate strategies for engineering plants with enhanced tolerance to different stress conditions.

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References

  • Achard, P., Herr, A., Baulcombe, D. C., & Harberd, N. P. (2004). Modulation of floral development by a gibberellin-regulated microRNA. Development, 131, 3357–3365.

    Article  CAS  PubMed  Google Scholar 

  • Akpinar, B. A., Kantar, M., & Budak, H. (2015). Root precursors of microRNAs in wild emmer and modern wheat show major differences in response to drought stress. Functional & Integrative Genomics, 15(5), 587–598.

    Article  CAS  Google Scholar 

  • Ben Rejeb, I., Pastor, V., & Mauch-Mani, B. (2014). Plant responses to simultaneous biotic and abiotic stress: Molecular mechanisms. Plants, 3(4), 458–475.

    Article  CAS  PubMed Central  Google Scholar 

  • Bhardwaj, A. R., Joshi, G., Pandey, R., Kukreja, B., Goel, S., Jagannath, A., et al. (2014). A genome-wide perspective of miRNAome in response to high temperature, salinity and drought stresses in Brassica juncea (Czern) L. PLoS ONE, 9(3), e92456.

    Article  PubMed  PubMed Central  Google Scholar 

  • Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G. L. A., D’Amore, R., Allen, A. M., et al. (2012). Analysis of the bread wheat genome using whole genome shotgun sequencing. Nature, 491(7426), 705–710.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cantu, D., Vanzetti, L. S., Sumner, A., Dubcovsky, M., Matvienko, M., Distelfeld, A., et al. (2010). Small RNAs, DNA methylation and transposable elements in wheat. BMC Genomics, 11, 408.

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen, F., Zhang, X., Zhang, N., Wang, S., Yin, G., Dong, Z., et al. (2015). Combined small RNA and degradome sequencing reveals novel miRNAs and their targets in the high-yield mutant wheat strain Yunong 3114. PLoS ONE, 10(9), e0137773. https://doi.org/10.1371/journal.pone.0137773.

    Article  PubMed  PubMed Central  Google Scholar 

  • Chu, Z., Chen, J., Xu, H., Dong, Z., Chen, F., & Cui, D. (2016). Identification and comparative analysis of microRNA in wheat (Triticum aestivum L.) callus derived from mature and immature embryos during in vitro culture. Frontiers in Plant Science, 7, 1302. https://doi.org/10.3389/fpls.2016.01302.

    PubMed  PubMed Central  Google Scholar 

  • Combier, J.-P., Frugier, F., de Billy, F., Boualem, A., El-Yahyaoui, F., Moreau, S., et al. (2006). MtHAP2-1 is a key transcriptional regulator of symbiotic nodule development regulated by microRNA169 in Medicago truncatula. Genes & Development, 20, 3084–3088.

    Article  CAS  Google Scholar 

  • Debernardi, J. M., Lin, H., Chuck, G., Faris, J. D., & Dubcovsky, J. (2017). microRNA172 plays a crucial role in wheat spike morphogenesis and grain threshability. Development (Cambridge, England), 144(11), 1966–1975.

    Article  CAS  Google Scholar 

  • Dryanova, A., Zakharov, A., & Gulick, P. J. (2008). Data mining for miRNAs and their targets in the Triticeae. Genome, 51, 433–443.

    Article  CAS  PubMed  Google Scholar 

  • Giusti, L., Mica, E., Bertolini, E., De Leonardis, A. M., Faccioli, P., Cattivelli, L., et al. (2017). MicroRNAs differentially modulated in response to heat and drought stress in durum wheat cultivars with contrasting water use efficiency. Functional & Integrative Genomics, 17(2–3), 293–309.

    Article  CAS  Google Scholar 

  • Goswami, B., Mahi, G. S., & Saikia, U. S. (2006). Effect of few important climatic factors on phenology, growth and yield of rice and wheat—A review. Agricultural Reviews, 27(3), 223–228.

    Google Scholar 

  • Griffiths-Jones, S. (2004). The microRNA registry. Nucleic Acids Research, 32, D109–D111.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Griffiths-Jones, S., Grocock, R. J., van Dongen, S., Bateman, A., & Enright, A. J. (2006). miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Research, 34, D140–D144.

    Article  CAS  PubMed  Google Scholar 

  • Gupta, O. P., Meena, N. L., Sharma, I., & Sharma, P. (2014). Differential regulation of microRNAs in response to osmotic, salt and cold stresses in wheat. Molecular Biology Reports, 41, 4623–4629.

    Article  CAS  PubMed  Google Scholar 

  • Gupta, O. P., Permar, V., Koundal, V., Singh, U. D., & Praveen, S. (2012). MicroRNA regulated defense responses in Triticum aestivum L. during Puccinia graminis f. sp. tritici infection. Molecular Biology Reports, 39, 817–824.

    Article  CAS  PubMed  Google Scholar 

  • Han, R., Jian, C., Lv, J., Yan, Y., Chi, Q., Li, Z., et al. (2014). Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.). BMC Genomics, 15, 289.

    Article  PubMed  PubMed Central  Google Scholar 

  • Han, J., Kong, M., Xie, H., Sun, Q., Nan, Z., Zhang, Q., et al. (2013). Identification of miRNAs and their targets in wheat (Triticum aestivum L.) by EST analysis. Genetics and Molecular Research, 12, 3793.

    Article  CAS  PubMed  Google Scholar 

  • Han, Y., Luan, F., Zhu, H., Shao, Y., Chen, A., Lu, C., et al. (2009). Computational identification of microRNAs and their targets in wheat (Triticum aestivum L.). Science in China, Series C: Life Sciences, 52, 1091–1100.

    Article  CAS  Google Scholar 

  • Jin, W., Li, N., Zhang, B., Wu, F., Li, W., Guo, A., et al. (2008). Identification and verification of microRNA in wheat (Triticum aestivum). Journal of Plant Research, 121, 351–355.

    Article  CAS  PubMed  Google Scholar 

  • Johnson, C., Bowman, L., Adai, A. T., Vance, V., & Sundaresan, V. (2007). CSRDB: A small RNA integrated database and browser resource for cereals. Nucleic Acids Research, 35, D829–D833.

    Article  CAS  PubMed  Google Scholar 

  • Kantar, M., Akpınar, B. A., Valárik, M., Lucas, S. J., Doležel, J., Hernández, P., et al. (2012). Subgenomic analysis of microRNAs in polyploid wheat. Functional & Integrative Genomics, 12, 465–479.

    Article  CAS  Google Scholar 

  • Kohli, D., Joshi, G., Deokar, A. A., Bhardwaj, A. R., Agarwal, M., Katiyar-Agarwal, S., et al. (2014). Identification and characterization of wilt and salt stress-responsive microRNAs in chickpea through high-throughput sequencing. PLoS ONE, 9(10), e108851.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar, D., Dutta, S., Kanodia, P., Prabhu, K. V., Kumar, M., & Mukhopadhyay, K. (2014). Discovery of novel leaf rust responsive microRNAs in wheat and prediction of their target genes. Journal of Nucleic Acids. https://doi.org/10.1155/2014/570176.

    PubMed  PubMed Central  Google Scholar 

  • Kumar, D., Dutta, S., Singh, D., Prabhu, K. V., Kumar, M., & Mukhopadhyay, K. (2017). Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis. Planta, 245(1), 161–182.

    Article  CAS  PubMed  Google Scholar 

  • Kumar, R. R., Pathak, H., Sharma, S. K., Kala, Y. K., Nirjal, M. K., Singh, G. P., et al. (2015). Novel and conserved heat-responsive microRNAs in wheat (Triticum aestivum L.). Functional & Integrative Genomics, 15(3), 323–348.

    Article  CAS  Google Scholar 

  • Kurtoglu, K. Y., Kantar, M., & Budak, H. (2014). New wheat microRNA using whole-genome sequence. Functional & Integrative Genomics, 14, 363–379.

    Article  CAS  Google Scholar 

  • Kurtoglu, K. Y., Kantar, M., Lucas, S. J., & Budak, H. (2013). Unique and conserved microRNAs in wheat chromosome 5D revealed by next-generation sequencing. PLoS ONE, 8, e69801.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lakhotia, N., Joshi, G., Bhardwaj, A. R., Katiyar-Agarwal, S., Agarwal, M., Jagannath, A., et al. (2014). Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing. BMC Plant Biology, 14, 6.

    Article  PubMed  PubMed Central  Google Scholar 

  • Li, A., Liu, D., Wu, J., Zhao, X., Hao, M., Geng, S., et al. (2014). mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat. The Plant Cell, 26(5), 1878–1900.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li, T., Ma, L., Geng, Y., Hao, C., Chen, X., & Zhang, X. (2015). Small RNA and degradome sequencing reveal complex roles of miRNAs and their targets in developing wheat grains. PLoS ONE, 10(10), e0139658.

    Article  PubMed  PubMed Central  Google Scholar 

  • Li, Y.-F., Zheng, Y., Jagadeeswaran, G., & Sunkar, R. (2013). Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches. Plant Science, 203–204, 17–24.

    Article  PubMed  Google Scholar 

  • Liu, H., Searle, I. R., Watson-Haigh, N. S., Baumann, U., Mather, D. E., Able, A. J., et al. (2015). Genome-wide identification of microRNAs in leaves and the developing head of four durum genotypes during water deficit stress. PLoS ONE, 10(11), e0142799.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lucas, S. J., & Budak, H. (2012). Sorting the wheat from the chaff: Identifying miRNAs in genomic survey sequences of Triticum aestivum chromosome 1AL. PLoS ONE, 7, e40859.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma, X., Xin, Z., Wang, Z., Yang, Q., Guo, S., Guo, X., et al. (2015). Identification and comparative analysis of differentially expressed miRNAs in leaves of two wheat (Triticum aestivum L.) genotypes during dehydration stress. BMC Plant Biology, 27(15), 21.

    Article  Google Scholar 

  • Meng, Y., Gou, L., Chen, D., Mao, C., Jin, Y., Wu, P., et al. (2011). PmiRKB: A plant microRNA knowledge base. Nucleic Acids Research, 39, D181–D187.

    Article  CAS  PubMed  Google Scholar 

  • Meng, F., Liu, H., Wang, K., Liu, L., Wang, S., Zhao, Y., et al. (2013). Development-associated microRNAs in grains of wheat (Triticum aestivum L.). BMC Plant Biology, 13, 140.

    Article  PubMed  PubMed Central  Google Scholar 

  • Middleton, C. P., Senerchia, N., Stein, N., Akhunov, E. D., Keller, B., Wicker, T., et al. (2014). Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS ONE, 9(3), e85761.

    Article  PubMed  PubMed Central  Google Scholar 

  • Nakano, M., Nobuta, K., Vemaraju, K., Tej, S. S., Skogen, J. W., & Meyers, B. C. (2006). Plant MPSS databases: Signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Research, 34, D731–D735.

    Article  CAS  PubMed  Google Scholar 

  • Palatnik, J. F., Allen, E., Wu, X., Schommer, C., Schwab, R., Carrington, J. C., et al. (2003). Control of leaf morphogenesis by microRNAs. Nature, 425, 257–263.

    Article  CAS  PubMed  Google Scholar 

  • Pandey, B., Gupta, O. P., Pandey, D. M., Sharma, I., & Sharma, P. (2013). Identification of new stress-induced microRNA and their targets in wheat using computational approach. Plant Signaling & Behavior, 8(5), e23932.

    Article  Google Scholar 

  • Pandey, R., Joshi, G., Bhardwaj, A. R., Agarwal, M., & Katiyar-Agarwal, S. (2014). A comprehensive genome-wide study on tissue-specific and abiotic stress-specific miRNAs in Triticum aestivum. PLoS ONE, 9, e95800.

    Article  PubMed  PubMed Central  Google Scholar 

  • Paola, D. D., Zuluaga, D. L., & Sonnante, G. (2016). The miRNAome of durum wheat: Isolation and characterisation of conserved and novel microRNAs and their target genes. BMC Genomics, 17, 505.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ragupathy, R., Ravichandran, S., Mahdi, S. R., Huang, D., Reimer, E., Domaratzki, M., et al. (2016). Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV. Scientific Reports, 6, 39373.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rhoades, M. W., Reinhart, B. J., Lim, L. P., Burge, C. B., Bartel, B., & Bartel, D. P. (2002). Prediction of plant microRNA targets. Cell, 110, 513–520.

    Article  CAS  PubMed  Google Scholar 

  • Seifert, F., Bössow, S., Kumlehn, J., Gnad, H., & Scholten, S. (2016). Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”. BMC Plant Biology, 16, 97.

    Article  PubMed  PubMed Central  Google Scholar 

  • Song, G., Zhang, R., Zhang, S., Li, Y., Gao, J., Han, X., et al. (2017). Response of microRNAs to cold treatment in the young spikes of common wheat. BMC Genomics, 18, 212.

    Article  PubMed  PubMed Central  Google Scholar 

  • Su, C., Yang, X., Gao, S., Tang, Y., Zhao, C., & Li, L. (2014). Identification and characterization of a subset of microRNAs in wheat (Triticum aestivum L.). Genomics, 103, 298–307.

    Article  CAS  PubMed  Google Scholar 

  • Sun, X., Dong, B., Yin, L., Zhang, R., Du, W., Liu, D., et al. (2013). PMTED: A plant microRNA target expression database. BMC Bioinformatics, 14, 174.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sun, F., Guo, G., Du, J., Guo, W., Peng, H., Ni, Z., et al. (2014). Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.). BMC plant biology, 14, 142.

    Article  PubMed  PubMed Central  Google Scholar 

  • Szczesniak, M. W., Deorowicz, S., Gapski, J., Kaczynski, L., & Makalowska, I. (2012). miRNEST database: An integrative approach in microRNA search and annotation. Nucleic Acids Research, 40, D198–D204.

    Article  CAS  PubMed  Google Scholar 

  • Tang, Z., Zhang, L., Xu, C., Yuan, S., Zhang, F., Zheng, Y., et al. (2012). Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male-sterile line by deep sequencing. Plant Physiology, 159, 721–738.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vaucheret, H. (2006). Post-transcriptional small RNA pathways in plants: Mechanisms and regulations. Genes & Development, 20, 759–771.

    Article  CAS  Google Scholar 

  • Wang, Y., Li, H., Sun, Q., & Yao, Y. (2016). Characterization of small RNAs derived from tRNAs, rRNAs and snoRNAs and their response to heat stress in wheat seedlings. PLoS ONE, 11(3), e0150933.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang, Y., Sun, F., Cao, H., Peng, H., Ni, Z., Sun, Q., et al. (2012). TamiR159 directed wheat TaGAMYB cleavage and its involvement in anther development and heat response. PLoS ONE, 7(11), e48445.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang, B., Sun, Y. F., Song, N., Wei, J. P., Wang, X. J., Feng, H., et al. (2014). MicroRNAs involving in cold, wounding and salt stresses in Triticum aestivum L. Plant Physiology and Biochemistry, 80, 90–96.

    Article  CAS  PubMed  Google Scholar 

  • Wang, J.-W., Wang, L.-J., Mao, Y.-B., Cai, W.-J., Xue, H.-W., & Chen, X.-Y. (2005). Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. The Plant Cell, 17, 2204–2216.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wei, B., Cai, T., Zhang, R., Li, A., Huo, N., Li, S., et al. (2009). Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Functional & Integrative Genomics, 9, 499–511.

    Article  CAS  Google Scholar 

  • Xie, K., Shen, J., Hou, X., Yao, J., Li, X., Xiao, J., et al. (2012). Gradual increase of miR156 regulates temporal expression changes of numerous genes during leaf development in rice. Plant Physiology, 158, 1382–1394.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xin, M., Wang, Y., Yao, Y., Xie, C., Peng, H., Ni, Z., et al. (2010). Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biology, 10, 123.

    Article  PubMed  PubMed Central  Google Scholar 

  • Yao, Y., Guo, G., Ni, Z., Sunkar, R., Du, J., Zhu, J.-K., et al. (2007). Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol, 8, R96.

    Article  PubMed  PubMed Central  Google Scholar 

  • Yi, X., Zhang, Z., Ling, Y., Xu, W., & Su, Z. (2015). PNRD: A plant non-coding RNA database. Nucleic Acids Research, 43, D982–D989.

    Article  CAS  PubMed  Google Scholar 

  • Yin, Z., & Shen, F. (2010). Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum). Genetics and Molecular Research, 9, 1186–1196.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, B. H., Xiao Ping, P., Qing Lian, W., Cobb, G. P., & Anderson, T. A. (2005). Identification and characterization of new plant microRNAs using EST analysis. Cell Research, 15, 336–360.

    Article  PubMed  Google Scholar 

  • Zhang, Z., Yu, J., Li, D., Zhang, Z., Liu, F., Zhou, X., et al. (2010). PMRD: Plant microRNA database. Nucleic Acids Research, 38, D806–D813.

    Article  CAS  PubMed  Google Scholar 

  • Zhao, X. Y., Hong, P., Wu, J. Y., Chen, X. B., Ye, X. G., Pan, Y. Y., et al. (2016). The tae-miR408-mediated control of TaTOC1 genes transcription is required for the regulation of heading time in wheat. Plant Physiology, 170(3), 1578–1594.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou, G.-K., Kubo, M., Zhong, R., Demura, T., & Ye, Z.-H. (2007). Overexpression of miR165 affects apical meristem formation, organ polarity establishment and vascular development in Arabidopsis. Plant and Cell Physiology, 48, 391–404.

    Article  CAS  PubMed  Google Scholar 

  • Zhu, J.-K. (2002). Salt and drought stress signal transduction in plants. Annual Review of Plant Biology, 53, 247–273.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu, J.-K. (2016). Abiotic stress signaling and responses in plants. Cell, 167(2), 313–332.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

Research work in the laboratory of SKA and MA is supported by Grants from R & D Grant & DST-PURSE from University of Delhi and Department of Biotechnology, Government of India. RP and ARB are thankful to SGTB Khalsa College, University of Delhi and Ramjas College, University of Delhi, respectively, for financial support.

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Correspondence to Surekha Katiyar-Agarwal.

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Pandey, R., Bhardwaj, A.R., Agarwal, M. et al. Discovery of small RNAs in wheat: a survey. Ind J Plant Physiol. 22, 411–421 (2017). https://doi.org/10.1007/s40502-017-0338-4

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