High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements

Autoři: Cedar Warman aff001;  Kaushik Panda aff002;  Zuzana Vejlupkova aff001;  Sam Hokin aff003;  Erica Unger-Wallace aff004;  Rex A. Cole aff001;  Antony M. Chettoor aff003;  Duo Jiang aff005;  Erik Vollbrecht aff004;  Matthew M. S. Evans aff003;  R. Keith Slotkin aff002;  John E. Fowler aff001
Působiště autorů: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America aff001;  Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America aff002;  Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America aff003;  Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America aff004;  Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America aff005;  Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, United States of America aff006;  Interdepartmental Genetics, Iowa State University, Ames, Iowa, United States of America aff007;  Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America aff008
Vyšlo v časopise: High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. PLoS Genet 16(4): e1008462. doi:10.1371/journal.pgen.1008462
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008462


In flowering plants, gene expression in the haploid male gametophyte (pollen) is essential for sperm delivery and double fertilization. Pollen also undergoes dynamic epigenetic regulation of expression from transposable elements (TEs), but how this process interacts with gene expression is not clearly understood. To explore relationships among these processes, we quantified transcript levels in four male reproductive stages of maize (tassel primordia, microspores, mature pollen, and sperm cells) via RNA-seq. We found that, in contrast with vegetative cell-limited TE expression in Arabidopsis pollen, TE transcripts in maize accumulate as early as the microspore stage and are also present in sperm cells. Intriguingly, coordinate expression was observed between highly expressed protein-coding genes and their neighboring TEs, specifically in mature pollen and sperm cells. To investigate a potential relationship between elevated gene transcript level and pollen function, we measured the fitness cost (male-specific transmission defect) of GFP-tagged coding sequence insertion mutations in over 50 genes identified as highly expressed in the pollen vegetative cell, sperm cell, or seedling (as a sporophytic control). Insertions in seedling genes or sperm cell genes (with one exception) exhibited no difference from the expected 1:1 transmission ratio. In contrast, insertions in over 20% of vegetative cell genes were associated with significant reductions in fitness, showing a positive correlation of transcript level with non-Mendelian segregation when mutant. Insertions in maize gamete expressed2 (Zm gex2), the sole sperm cell gene with measured contributions to fitness, also triggered seed defects when crossed as a male, indicating a conserved role in double fertilization, given the similar phenotype previously demonstrated for the Arabidopsis ortholog GEX2. Overall, our study demonstrates a developmentally programmed and coordinated transcriptional activation of TEs and genes in pollen, and further identifies maize pollen as a model in which transcriptomic data have predictive value for quantitative phenotypes.

Klíčová slova:

Arabidopsis thaliana – Fertilization – Gene expression – Maize – Pollen – Seedlings – Seeds – Sperm


1. Yang W-C, Shi D-Q, Chen Y-H. Female gametophyte development in flowering plants. Annu Rev Plant Biol. 2010;61: 89–108. doi: 10.1146/annurev-arplant-042809-112203 20192738

2. Zhou L-Z, Juranić M, Dresselhaus T. Germline Development and Fertilization Mechanisms in Maize. Mol Plant. 2017;10: 389–401. doi: 10.1016/j.molp.2017.01.012 28267957

3. McCormick S. Male Gametophyte Development. Plant Cell. 1993;5: 1265–1275. doi: 10.1105/tpc.5.10.1265 12271026

4. Hafidh S, Fíla J, Honys D. Male gametophyte development and function in angiosperms: a general concept. Plant Reprod. 2016;29: 31–51. doi: 10.1007/s00497-015-0272-4 26728623

5. Dresselhaus T, Sprunck S, Wessel GM. Fertilization Mechanisms in Flowering Plants. Curr Biol. 2016;26: R125–39. doi: 10.1016/j.cub.2015.12.032 26859271

6. Zhou L-Z, Dresselhaus T. Chapter Seventeen—Friend or foe: Signaling mechanisms during double fertilization in flowering seed plants. In: Grossniklaus U, editor. Current Topics in Developmental Biology. Academic Press; 2019. pp. 453–496. doi: 10.1016/bs.ctdb.2018.11.013 30612627

7. Lausser A, Kliwer I, Srilunchang K-O, Dresselhaus T. Sporophytic control of pollen tube growth and guidance in maize. J Exp Bot. 2010;61: 673–682. doi: 10.1093/jxb/erp330 19926683

8. Mizukami AG, Inatsugi R, Jiao J, Kotake T, Kuwata K, Ootani K, et al. The AMOR Arabinogalactan Sugar Chain Induces Pollen-Tube Competency to Respond to Ovular Guidance. Curr Biol. 2016;26: 1091–1097. doi: 10.1016/j.cub.2016.02.040 27068416

9. Higashiyama T, Takeuchi H. The mechanism and key molecules involved in pollen tube guidance. Annu Rev Plant Biol. 2015;66: 393–413. doi: 10.1146/annurev-arplant-043014-115635 25621518

10. Williams JH, Reese JB. Evolution of development of pollen performance. Curr Top Dev Biol. 2019;131: 299–336. doi: 10.1016/bs.ctdb.2018.11.012 30612621

11. Arthur KM, Vejlupkova Z, Meeley RB, Fowler JE. Maize ROP2 GTPase provides a competitive advantage to the male gametophyte. Genetics. 2003;165: 2137–2151. 14704193

12. Cole RA, Synek L, Zarsky V, Fowler JE. SEC8, a subunit of the putative Arabidopsis exocyst complex, facilitates pollen germination and competitive pollen tube growth. Plant Physiol. 2005;138: 2005–2018. doi: 10.1104/pp.105.062273 16040664

13. Huang JT, Wang Q, Park W, Feng Y, Kumar D, Meeley R, et al. Competitive Ability of Maize Pollen Grains Requires Paralogous Serine Threonine Protein Kinases STK1 and STK2. Genetics. 2017;207: 1361–1370. doi: 10.1534/genetics.117.300358 28986443

14. Kelliher T, Starr D, Richbourg L, Chintamanani S, Delzer B, Nuccio ML, et al. MATRILINEAL, a sperm-specific phospholipase, triggers maize haploid induction. Nature. 2017;542: 105–109. doi: 10.1038/nature20827 28114299

15. Gilles LM, Khaled A, Laffaire J-B, Chaignon S, Gendrot G, Laplaige J, et al. Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maize. EMBO J. 2017;36: 707–717. doi: 10.15252/embj.201796603 28228439

16. Liu C, Li X, Meng D, Zhong Y, Chen C, Dong X, et al. A 4-bp Insertion at ZmPLA1 Encoding a Putative Phospholipase A Generates Haploid Induction in Maize. Mol Plant. 2017;10: 520–522. doi: 10.1016/j.molp.2017.01.011 28179149

17. Zhong Y, Liu C, Qi X, Jiao Y, Wang D, Wang Y, et al. Mutation of ZmDMP enhances haploid induction in maize. Nat Plants. 2019;5: 575–580. doi: 10.1038/s41477-019-0443-7 31182848

18. Kelliher T, Starr D, Su X, Tang G, Chen Z, Carter J, et al. One-step genome editing of elite crop germplasm during haploid induction. Nat Biotechnol. 2019;37: 287–292. doi: 10.1038/s41587-019-0038-x 30833776

19. Honys D, Twell D. Comparative analysis of the Arabidopsis pollen transcriptome. Plant Physiol. 2003;132: 640–652. doi: 10.1104/pp.103.020925 12805594

20. Becker JD, Boavida LC, Carneiro J, Haury M, Feijó JA. Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome. Plant Physiol. 2003;133: 713–725. doi: 10.1104/pp.103.028241 14500793

21. Steffen JG, Kang I-H, Macfarlane J, Drews GN. Identification of genes expressed in the Arabidopsis female gametophyte: Female gametophyte-expressed genes. Plant J. 2007;51: 281–292. doi: 10.1111/j.1365-313X.2007.03137.x 17559508

22. Jones-Rhoades MW, Borevitz JO, Preuss D. Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins. PLoS Genet. 2007;3: 1848–1861. doi: 10.1371/journal.pgen.0030171 17937500

23. Chettoor AM, Givan SA, Cole RA, Coker CT, Unger-Wallace E, Vejlupkova Z, et al. Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes. Genome Biol. 2014;15: 414. doi: 10.1186/s13059-014-0414-2 25084966

24. Zhai J, Zhang H, Arikit S, Huang K, Nan G-L, Walbot V, et al. Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers. Proc Natl Acad Sci U S A. 2015;112: 3146–3151. doi: 10.1073/pnas.1418918112 25713378

25. Nelms B, Walbot V. Defining the developmental program leading to meiosis in maize. Science. 2019;364: 52–56. doi: 10.1126/science.aav6428 30948545

26. Begcy K, Nosenko T, Zhou L-Z, Fragner L, Weckwerth W, Dresselhaus T. Male Sterility in Maize after Transient Heat Stress during the Tetrad Stage of Pollen Development. Plant Physiol. 2019. doi: 10.1104/pp.19.00707 31378720

27. Chen J, Strieder N, Krohn NG, Cyprys P, Sprunck S, Engelmann JC, et al. Zygotic Genome Activation Occurs Shortly after Fertilization in Maize. Plant Cell. 2017;29: 2106–2125. doi: 10.1105/tpc.17.00099 28814645

28. Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, Feijó JA, et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell. 2009;136: 461–472. doi: 10.1016/j.cell.2008.12.038 19203581

29. Schoft VK, Chumak N, Mosiolek M, Slusarz L, Komnenovic V, Brownfield L, et al. Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin. EMBO Rep. 2009;10: 1015–1021. doi: 10.1038/embor.2009.152 19680290

30. Calarco JP, Borges F, Donoghue MTA, Van Ex F, Jullien PE, Lopes T, et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell. 2012;151: 194–205. doi: 10.1016/j.cell.2012.09.001 23000270

31. Dooner HK, Wang Q, Huang JT, Li Y, He L, Xiong W, et al. Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions. Proc Natl Acad Sci U S A. 2019. doi: 10.1073/pnas.1903809116 30992374

32. He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. Elife. 2019;8. doi: 10.7554/eLife.42530 31135340

33. Martínez G, Slotkin RK. Developmental relaxation of transposable element silencing in plants: functional or byproduct? Curr Opin Plant Biol. 2012;15: 496–502. doi: 10.1016/j.pbi.2012.09.001 23022393

34. Martínez G, Panda K, Köhler C, Slotkin RK. Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nat Plants. 2016;2: 16030. doi: 10.1038/nplants.2016.30 27249563

35. Martinez G, Wolff P, Wang Z, Moreno-Romero J, Santos-González J, Conze LL, et al. Paternal easiRNAs regulate parental genome dosage in Arabidopsis. Nat Genet. 2018;50: 193–198. doi: 10.1038/s41588-017-0033-4 29335548

36. Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, et al. Improved maize reference genome with single-molecule technologies. Nature. 2017;546: 524–527. doi: 10.1038/nature22971 28605751

37. Lunardon A, Forestan C, Farinati S, Axtell MJ, Varotto S. Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses. Plant Physiol. 2016;170: 1535–1548. doi: 10.1104/pp.15.01205 26747286

38. Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, et al. Integration of omic networks in a developmental atlas of maize. Science. 2016;353: 814–818. doi: 10.1126/science.aag1125 27540173

39. Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK. Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biol. 2016;17: 170. doi: 10.1186/s13059-016-1032-y 27506905

40. Wolfgruber TK, Sharma A, Schneider KL, Albert PS, Koo D-H, Shi J, et al. Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic Loci shaped primarily by retrotransposons. PLoS Genet. 2009;5: e1000743. doi: 10.1371/journal.pgen.1000743 19956743

41. Anderson SN, Stitzer MC, Zhou P, Ross-Ibarra J, Hirsch CD, Springer NM. Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize. G3. 2019;9: 3673–3682. doi: 10.1534/g3.119.400431 31506319

42. Li Y, Segal G, Wang Q, Dooner HK. Gene Tagging with Engineered Ds Elements in Maize. In: Peterson T, editor. Plant Transposable Elements: Methods and Protocols. Totowa, NJ: Humana Press; 2013. pp. 83–99.

43. Warman C, Fowler JE. Custom built scanner and simple image processing pipeline enables low-cost, high-throughput phenotyping of maize ears. bioRxiv. 2019. p. 780650. doi: 10.1101/780650

44. Engel ML, Chaboud A, Dumas C, McCormick S. Sperm cells of Zea mays have a complex complement of mRNAs. Plant J. 2003;34: 697–707. 12787250

45. Engel ML, Holmes-Davis R, McCormick S. Green sperm. Identification of male gamete promoters in Arabidopsis. Plant Physiol. 2005;138: 2124–2133. doi: 10.1104/pp.104.054213 16055690

46. Mori T, Igawa T, Tamiya G, Miyagishima S-Y, Berger F. Gamete attachment requires GEX2 for successful fertilization in Arabidopsis. Curr Biol. 2014;24: 170–175. doi: 10.1016/j.cub.2013.11.030 24388850

47. Liao B-Y, Weng M-P. Unraveling the association between mRNA expressions and mutant phenotypes in a genome-wide assessment of mice. Proc Natl Acad Sci U S A. 2015;112: 4707–4712. doi: 10.1073/pnas.1415046112 25825715

48. Xu Z, Dooner HK. The maize aberrant pollen transmission 1 gene is a SABRE/KIP homolog required for pollen tube growth. Genetics. 2006;172: 1251–1261. doi: 10.1534/genetics.105.050237 16299389

49. Wilson-Sánchez D, Rubio-Díaz S, Muñoz-Viana R, Pérez-Pérez JM, Jover-Gil S, Ponce MR, et al. Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants. Plant J. 2014;79: 878–891. doi: 10.1111/tpj.12595 24946828

50. Rutter MT, Murren CJ, Callahan HS, Bisner AM, Leebens-Mack J, Wolyniak MJ, et al. Distributed phenomics with the unPAK project reveals the effects of mutations. Plant J. 2019. doi: 10.1111/tpj.14427 31155775

51. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002;418: 387–391. doi: 10.1038/nature00935 12140549

52. Berry DB, Guan Q, Hose J, Haroon S, Gebbia M, Heisler LE, et al. Multiple means to the same end: the genetic basis of acquired stress resistance in yeast. PLoS Genet. 2011;7: e1002353. doi: 10.1371/journal.pgen.1002353 22102822

53. Price MN, Deutschbauer AM, Skerker JM, Wetmore KM, Ruths T, Mar JS, et al. Indirect and suboptimal control of gene expression is widespread in bacteria. Mol Syst Biol. 2013;9: 660. doi: 10.1038/msb.2013.16 23591776

54. Helmann TC, Deutschbauer AM, Lindow SE. Genome-wide identification of Pseudomonas syringae genes required for fitness during colonization of the leaf surface and apoplast. Proc Natl Acad Sci U S A. 2019. doi: 10.1073/pnas.1908858116 31484768

55. Schnable JC. Genes and gene models, an important distinction. New Phytol. 2019. doi: 10.1111/nph.16011 31241760

56. Wang G, Jiang H, Del Toro de León G, Martinez G, Köhler C. Sequestration of a Transposon-Derived siRNA by a Target Mimic Imprinted Gene Induces Postzygotic Reproductive Isolation in Arabidopsis. Dev Cell. 2018;46: 696–705.e4. doi: 10.1016/j.devcel.2018.07.014 30122632

57. Borges F, Parent J-S, van Ex F, Wolff P, Martínez G, Köhler C, et al. Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis. Nat Genet. 2018;50: 186–192. doi: 10.1038/s41588-017-0032-5 29335544

58. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29: 15–21. doi: 10.1093/bioinformatics/bts635 23104886

59. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28: 511–515. doi: 10.1038/nbt.1621 20436464

60. Tian T, Liu Y, Yan H, You Q, Yi X, Du Z, et al. agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res. 2017;45: W122–W129. doi: 10.1093/nar/gkx382 28472432

61. Wimalanathan K, Friedberg I, Andorf CM, Lawrence-Dill CJ. Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER). Plant Direct. 2018;2: e00052. doi: 10.1002/pld3.52 31245718

62. Bushnell B. BBTools software package. URL http://sourceforge.net/projects/bbmap. 2014.

63. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30: 923–930. doi: 10.1093/bioinformatics/btt656 24227677

64. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15: 550. doi: 10.1186/s13059-014-0550-8 25516281

65. Gao H, Smith J, Yang M, Jones S, Djukanovic V, Nicholson MG, et al. Heritable targeted mutagenesis in maize using a designed endonuclease. Plant J. 2010;61: 176–187. doi: 10.1111/j.1365-313X.2009.04041.x 19811621

66. Vejlupkova Z, Fowler JE. Maize DNA preps for undergraduate students: a robust method for PCR genotyping. Maize Genetics Cooperation Newsletter. 2003;77: 24–25.

67. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9: 676–682. doi: 10.1038/nmeth.2019 22743772

68. Portwood JL 2nd, Woodhouse MR, Cannon EK, Gardiner JM, Harper LC, Schaeffer ML, et al. MaizeGDB 2018: the maize multi-genome genetics and genomics database. Nucleic Acids Res. 2019;47: D1146–D1154. doi: 10.1093/nar/gky1046 30407532

69. Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, et al. Araport: the Arabidopsis information portal. Nucleic Acids Res. 2015;43: D1003–9. doi: 10.1093/nar/gku1200 25414324

70. Cheng C-Y, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, Town CD. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J. 2017;89: 789–804. doi: 10.1111/tpj.13415 27862469

71. Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2019;47: D351–D360. doi: 10.1093/nar/gky1100 30398656

72. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305: 567–580. doi: 10.1006/jmbi.2000.4315 11152613

73. Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, et al. PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Res. 2018;46: D1190–D1196. doi: 10.1093/nar/gkx1002 29069403

74. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389–3402. doi: 10.1093/nar/25.17.3389 9254694

75. Vollbrecht E, Hake S. Deficiency analysis of female gametogenesis in maize. Dev Genet. 1995;16: 44–63.

76. Running MP, Clark SE, Meyerowitz EM. Chapter 15 Confocal Microscopy of the Shoot Apex. In: Galbraith DW, Bohnert HJ, Bourque DP, editors. Methods in Cell Biology. Academic Press; 1995. pp. 217–229.

77. Valdivia ER, Sampedro J, Lamb JC, Chopra S, Cosgrove DJ. Recent proliferation and translocation of pollen group 1 allergen genes in the maize genome. Plant Physiol. 2007;143: 1269–1281. doi: 10.1104/pp.106.092544 17220362

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