Skip to main content
SpringerLink
Log in

Low genetic diversity and functional constraint of miRNA genes participating pollen–pistil interaction in rice

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

Key message

In this study, we sequenced and analyzed the expression and evolution of rice miRNA genes participating pollen-pistil interaction that is crucial to rice yield.

Abstract

Pollen–pistil interaction is an essential reproductive process for all flowering plants. While microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNA levels in eukaryotic cells, there is little knowledge about which miRNAs involved in the early stages of pollen–pistil interaction in rice and how they evolve under this conserved process. In this study, we sequenced the small RNAs in rice from unpollinated pistil (R0), pistil from 5 min and 15 min after pollination, respectively, to identify known and novel miRNAs that are involved in this process. By comparing the corresponding mRNA-seq dataset, we identified a group of miRNAs with strong negative expression pattern with their target genes. Further investigation of all miRNA loci (MIRNAs) across 1083 public rice accessions revealed significantly reduced genetic diversity in MIRNAs with strong negative expression of their targets when comparing to those with little or no impact on targets during pollen–pistil interaction. Annotation of targets suggested that those MIRNAs with strong impact on targets were pronounced in cell wall related processes such as xylan metabolism. Additionally, plant conserved miRNAs, such as those with functions in gibberellic acid, auxin and nitrate signaling, were also with strong negative expression of their targets. Overall, our analyses identified key miRNAs participating pollen–pistil interaction and their evolutionary patterns in rice, which can facilitate the understanding of molecular mechanisms associated with seed setting.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Achard P, Herr A, Baulcombe DC, Harberd NP (2004) Modulation of floral development by a gibberellin-regulated microRNA. Development 131:3357–3365

    Article  CAS  PubMed  Google Scholar 

  • Allen RS, Li JY, Stahle MI, Dubroue A, Gubler F, Millar AA (2007) Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc Natl Acad Sci USA 104:16371–16376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arunkumar R, Josephs EB, Williamson RJ, Wright SI (2013) Pollen-specific, but Not sperm-specific, genes show stronger purifying selection and higher rates of positive selection than sporophytic genes in Capsella grandiflora. Mol Biol Evol 30:2475–2486

    Article  CAS  PubMed  Google Scholar 

  • Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995

    Article  CAS  PubMed  Google Scholar 

  • Bartel DP (2007) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 131:11–29. (Reprinted from Cell, vol 116, pg 281–297, 2004)

    Google Scholar 

  • Cammaerts S, Strazisar M, De Rijk P, Del Favero J (2015) Genetic variants in microRNA genes: impact on microRNA expression, function, and disease. Front Genet 6:186

    Article  PubMed  PubMed Central  Google Scholar 

  • Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301:336–338

    Article  CAS  PubMed  Google Scholar 

  • Chen XM (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21–44

    Article  PubMed  PubMed Central  Google Scholar 

  • Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, Su CL (2006) Regulation of phosphate homeostasis by MicroRNA in Arabidopsis. Plant Cell 18:412–421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cosgrove DJ (2000) Loosening of plant cell walls by expansins. Nature 407:321–326

    Article  CAS  PubMed  Google Scholar 

  • Debernardi JM, Rodriguez RE, Mecchia MA, Palatnik JF (2012) Functional specialization of the plant miR396 regulatory network through distinct microRNA–target interactions. Plos Genet 8:e1002419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong J, Kim ST, Lord EM (2005) Plantacyanin plays a role in reproduction in Arabidopsis. Plant Physiol 138:778–789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Friedlander MR, Mackowiak SD, Li N, Chen W, Rajewsky N (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 40:37–52

    Article  PubMed  Google Scholar 

  • Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34:D140–D144

    Article  CAS  PubMed  Google Scholar 

  • Guan Q, Lu X, Zeng H, Zhang Y, Zhu J (2013) Heat stress induction of mir398 triggers a regulatory loop that is critical for thermotolerance in arabidopsis. Plant J 74(5):840–851

    Article  CAS  PubMed  Google Scholar 

  • Guo HS, Xie Q, Fei JF, Chua NH (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 17:1376–1386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hahn MW, Kern AD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22:803–806

    Article  CAS  PubMed  Google Scholar 

  • Helwak A, Kudla G, Dudnakova T, Tollervey D (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 153:654–665

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu WJ, Harding SA, Lung J, Popko JL, Ralph J, Stokke DD, Tsai CJ, Chiang VL (1999) Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees. Nat Biotechnol 17:808–812

    Article  CAS  PubMed  Google Scholar 

  • Huang XH, Kurata N, Wei XH, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu KY, Lu HY, Li WJ, Guo YL, Lu YQ, Zhou CC, Fan DL, Weng QJ, Zhu CR, Huang T, Zhang L, Wang YC, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan XP, Xu Q, Dong GJ, Zhan QL, Li CY, Fujiyama A, Toyoda A, Lu TT, Feng Q, Qian Q, Li JY, Han B (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497–501

    Article  CAS  PubMed  Google Scholar 

  • Huang J, Li ZY, Zhao DZ (2016) Deregulation of the OsmiR160 target gene osarf18 causes growth and developmental defects with an alteration of auxin signaling in rice. Scientific Reports 6.

  • Jovelin R, Cutter AD (2014) Microevolution of nematode miRNAs reveals diverse modes of selection. Genome Biol Evol 6:3049–3063

    Article  PubMed  PubMed Central  Google Scholar 

  • Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42:D68–D73

    Article  CAS  PubMed  Google Scholar 

  • Li RQ, Li YR, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714

    Article  CAS  PubMed  Google Scholar 

  • Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang WX, Sunkar R (2010) Transcriptome-wide identification of microRNA targets in rice. Plant J 62:742–759

    Article  CAS  PubMed  Google Scholar 

  • Li XM, Sang YL, Zhao XY, Zhang XS (2013) High-throughput sequencing of small rnas from pollen and silk and characterization of miRNAs as candidate factors involved in pollen-silk interactions in maize. PLoS ONE 8(8):e72852

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li M, Wang K, Li SQ, Yang PF (2016) Exploration of rice pistil responses during early post-pollination through a combined proteomic and transcriptomic analysis. J Proteom 131:214–226

    Article  CAS  Google Scholar 

  • Liang H, Li WH (2009) Lowly expressed human MicroRNA genes evolve rapidly. Mol Biol Evol 26:1195–1198

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liang Y, Tan ZM, Zhu L, Niu QK, Zhou JJ, Li M, Chen LQ, Zhang XQ, Ye D (2013) MYB97, MYB101 and MYB120 function as male factors that control pollen tube-synergid interaction in Arabidopsis thaliana fertilization. PLoS Genet 9(11):e1003933

    Article  PubMed  PubMed Central  Google Scholar 

  • Llave C, Kasschau KD, Rector MA, Carrington JC (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell 14:1605–1619

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu Y, Chanroj S, Zulkifli L, Johnson MA, Uozumi N, Cheung A, Sze H (2011) Pollen tubes lacking a pair of K+ transporters fail to target ovules in Arabidopsis. Plant Cell 23:81–93

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mohammed J, Bortolamiol-Becet D, Flynt AS, Gronau I, Siepel A, Lai EC (2014) Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila. RNA 20:1195–1209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morea EGO, da Silva EM, Silva GFFE, Valente GT, Rojas CHB, Vincentz M, Nogueira FTS (2016) Functional and evolutionary analyses of the miR156 and miR529 families in land plants. BMC Plant Biol 16(1):1–1

    Article  Google Scholar 

  • Papp I, Mette MF, Aufsatz W, Daxinger L, Schauer SE, Ray A, van der Winden J, Matzke M, Matzke AJ (2003) Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol 132:1382–1390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reyes JL, Chua NH (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 49:592–606

    Article  CAS  PubMed  Google Scholar 

  • Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140

    Article  CAS  PubMed  Google Scholar 

  • Schwarz S, Grande AV, Bujdoso N, Saedler H, Huijser P (2008) The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis. Plant Mol Biol 67:183–195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R (2005) EXPANDER-an integrative program suite for microarray data analysis. BMC Bioinformat 6:232

    Article  Google Scholar 

  • Shi T, Dimitrov I, Zhang YL, Tax FE, Yi J, Gou XP, Li J (2015) Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication. Plant Mol Biol 89:253–261

    Article  CAS  PubMed  Google Scholar 

  • Shi T, Wang K, Yang P (2016) Ancient microRNA families that regulate transcription factors are preferentially preserved during plant radiation. Plant Signal Behav 11(12):e1261233

    Article  PubMed  Google Scholar 

  • Shi T, Wang K, Yang P (2017) The evolution of plant microRNAs—insights from a basal eudicot sacred lotus. Plant J 89(3):442–457

    Article  CAS  PubMed  Google Scholar 

  • Shivaprasad PV, Chen HM, Patel K, Bond DM, Santos BA, Baulcombe DC (2012) A microrna superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell 24(3):859–874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sun GH, Yan J, Noltner K, Feng JN, Li HT, Sarkis DA, Sommer SS, Rossi JJ (2009) SNPs in human miRNA genes affect biogenesis and function. RNA 15:1640–1651

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vitkup D, Kharchenko P, Wagner A (2006) Influence of metabolic network structure and function on enzyme evolution. Genome Biol 7(5):R39

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang CY, Zhang SC, Yu Y, Luo YC, Liu Q, Ju CL, Zhang YC, Qu LH, Lucas WJ, Wang XJ, Chen YQ (2014) MiR397b regulates both lignin content and seed number in Arabidopsis via modulating a laccase involved in lignin biosynthesis. Plant Biotechnol J 12:1132–1142

    Article  CAS  PubMed  Google Scholar 

  • Wu HM, Cheung AY (2000) Programmed cell death in plant reproduction. Plant Mol Biol 44:267–281

    Article  PubMed  Google Scholar 

  • Wu L, Zhang QQ, Zhou HY, Ni FR, Wu XY, Qi YJ (2009) Rice microRNA effector complexes and targets. Plant Cell 21:3421–3435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie ZX, Kasschau KD, Carrington JC (2003) Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol 13:784–789

    Article  CAS  PubMed  Google Scholar 

  • Yan YS, Wang HC, Hamera S, Chen XY, Fang RX (2014) miR444a has multiple functions in the rice nitrate-signaling pathway. Plant J 78:44–55

    Article  CAS  PubMed  Google Scholar 

  • Yang J, Tian L, Sun MX, Huang XY, Zhu J, Guan YF, Jia QS, Yang ZN (2013) AUXIN RESPONSE FACTOR17 Is essential for pollen wall pattern formation in Arabidopsis. Plant Physiol 162:720–731

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang BH, Pan XP, Cobb GP, Anderson TA (2006) Plant microRNA: a small regulatory molecule with big impact. Dev Biol 289:3–16

    Article  CAS  PubMed  Google Scholar 

  • Zhang ZH, Yu JY, Li DF, Zhang ZY, Liu FX, Zhou X, Wang T, Ling Y, Su Z (2010) PMRD: plant microRNA database. Nucleic Acids Res 38:D806–D813

    Article  CAS  PubMed  Google Scholar 

  • Zhu Y, Skogerbo G, Ning QQ, Wang Z, Li BQ, Yang S, Sun H, Li YX (2012) Evolutionary relationships between miRNA genes and their activity. BMC Genom 13(1):718

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Natural Science Foundation of China (No. 31671775 and No. 31100230), the National Key Research and Development Program of China (2016YFD0100904) and the Open Research Fund of State Key Laboratory of Hybrid Rice, Wuhan University (No. KF201306). We thank Rebecca Njeri from Wuhan Botanical Garden, Chinese Academy of Sciences for revising the manuscript.

Author information

Authors and Affiliations

  1. Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China

    Kun Wang, Xin Wang, Ming Li, Tao Shi & Pingfang Yang

  2. College of Life Sciences, Wuhan University, Wuhan, China

    Kun Wang

  3. Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China

    Pingfang Yang

Authors
  1. Kun Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ming Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tao Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Pingfang Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

The experiment was designed by K. W. and P. Y. The experiment was performed by K. W. M. L. and X. W. performed some of the experiment. T. S. performed the analysis and wrote the manuscript.

Corresponding authors

Correspondence to Tao Shi or Pingfang Yang.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Fig. 1—Length distribution of small RNA sequences in R0 (A), R5 (B) and R15 (C) (JPG 322 KB)

Supplementary Fig. 2—Pollen-specific miRNAs are absent in pollinated pistil samples (R5 and R15) (JPG 99 KB)

Supplementary Fig. 3—Scatter plot of differential expression of miRNAs between samples (JPG 263 KB)

11103_2017_638_MOESM4_ESM.jpg

Supplementary Fig. 4—Stem-loop real-time PCR validation of the expression of 25 miRNAs during the three stages of pollen-pistil interaction. (A) Expression in sRNA-seq. (B) Expression in qRT-PCR experiment. Expression values in (A) and (B) for a selected miRNA across three samples were standardized to have mean 0.3333 and standard deviation 1. (C) Correlation coefficient of expression of each miRNAs between sRNA-seq and qRT-PCR (JPG 396 KB)

Supplementary Tables S1–S6 (XLSX 1198 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, K., Wang, X., Li, M. et al. Low genetic diversity and functional constraint of miRNA genes participating pollen–pistil interaction in rice. Plant Mol Biol 95, 89–98 (2017). https://doi.org/10.1007/s11103-017-0638-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11103-017-0638-0

Keywords

Search

Navigation