Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling

Autoři: Gezahegn Girma aff001;  Satoshi Natsume aff003;  Anna Vittoria Carluccio aff001;  Hiroki Takagi aff003;  Hideo Matsumura aff003;  Aiko Uemura aff003;  Satoru Muranaka aff004;  Hiroko Takagi aff004;  Livia Stavolone aff001;  Melaku Gedil aff001;  Charles Spillane aff002;  Ryohei Terauchi aff003;  Muluneh Tamiru aff003
Působiště autorů: Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria aff001;  Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland aff002;  Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan aff003;  Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Japan aff004
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: 10.1371/journal.pone.0216912


Dioecy (distinct male and female individuals) and scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are largely unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata), generating 20,236 unique tags. Of these, 13,901 were represented by a minimum of 10 tags. A total 88 tags were significantly differentially expressed in male, female and monoecious plants, of which 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of three candidate genes.

We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two consecutive years. Over 85% of accessions were either male or non-flowering, less than 15% were female, while monoecious plants were rare. Intensity of flowering varied between male and female plants, with the former flowering more abundantly than the latter. Candidate genes identified in this study can be targeted for further validation and to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve efficiency of yam breeding.

Klíčová slova:

Flowering plants – Flowers – Gene expression – Gene regulation – Sequence databases – Sex determination – Expressed sequence tags analysis – Floral development


1. Scarcelli N, Barnaud A, Eiserhardt W, Treier UA, Seveno M, d’Anfray A, et al. A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons. PLoS ONE. 2011;6. doi: 10.1371/journal.pone.0019954

2. Mignouna H, Abang MAR. Yams. In: C K, editor. Genome mapping and molecular breeding in plants. vol. 3. Heidelberg, Berlin, New York, Tokyo: Springer; 2007. p. 271–96.

3. Terauchi R KG. Sex determination in Dioscorea tokoro, a wild yam species. In: C A, editor. Sex Determination in Plants. Oxford OX4 1RE, UK: BIOS; 1999.

4. Lebot V. Tropical root and tuber crops: cassava, sweet potato,yams and aroids. Wallingford, UK: CABI Publishers; 2009.

5. Aryal R, Ming R. Sex determination in flowering plants: Papaya as a model system. Plant Science. 2014; 217–218: 56–62. doi: 10.1016/j.plantsci.2013.10.018 24467896

6. Ming R, Bendahmane A, Renner SS. Sex Chromosomes in Land Plants. Annual Review of Plant Biology. 2011; 62:485–514. doi: 10.1146/annurev-arplant-042110-103914 21526970

7. Martin F, Sex Ratio and Sex Determination in Dioscorea. Journal of Heredity 1966; 57(3):95–99

8. Cormier F, Lawac F, Maledon E, Gravillon M-C, Nudol E, Mournet P, et al. A reference high-density genetic map of greater yam (Dioscorea alata L.). Theoretical and Applied Genetics. 2019; 132(6): 1733–1744. 30783744

9. Tamiru M, Natsume S, Takagi H, White B, Yaegashi H, Shimizu M, et al. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC Biology; 2017; 15:86. doi: 10.1186/s12915-017-0419-x 28927400

10. Simpson GG, Dean C. Arabidopsis, the Rosetta stone of flowering time? Science. 2002. p. 285–9. doi: 10.1126/science.296.5566.285 11951029

11. Ma H, DePamphilis C. The ABCs of floral evolution. Cell. 2000; 101:5–8. doi: 10.1016/S0092-8674(00)80618-2 10778850

12. Coen ES, Meyerowitz EM. The war of the whorls: genetic interactions controlling flower development. Nature. 1991; 353:31–7. doi: 10.1038/353031a0 1715520

13. Heijmans K, Morel P, Vandenbussche M. MADS-box genes and floral development: The dark side. Journal of Experimental Botany. 2012; 63(15):5397–404. doi: 10.1093/jxb/ers233 22915743

14. Su CL, Chen WC, Lee AY, Chen CY, Chang YCA, Chao YT, et al. A modified ABCDE model of flowering in orchids based on gene expression profiling studies of the moth orchid Phalaenopsis aphrodite. PLoS ONE. 2013; 8(11): e80462. doi: 10.1371/journal.pone.0080462 24265826

15. Spigler RB, Lewers KS, Main DS, Ashman TL. Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome. Heredity. 2008; 101:507–17. doi: 10.1038/hdy.2008.100 18797475

16. Jaligot E, Adler S, Debladis É, Beulé T, Richaud F, Ilbert P, et al. Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis. Annals of Botany. 2011; 108(8): 1453–62. doi: 10.1093/aob/mcq266 21224269

17. Acosta IF, Laparra H, Romero SP, Schmelz E, Hamberg M, Mottinger JP, et al. tasselseed1 is a lipoxygenase affecting jasmonic acid signaling in sex determination of maize. Science. 2009; 323:262–5. doi: 10.1126/science.1164645 19131630

18. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial Analysis of Gene Expression. Science. 1995; 270:484–7. doi: 10.1126/science.270.5235.484 7570003

19. Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, et al. Using the transcriptome to annotate the genome. Nature Biotechnology. 2002; 20:508–12. doi: 10.1038/nbt0502-508 11981567

20. Gowda M, Jantasuriyarat C, Dean RA WG. Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiology. 2004; 134:890–7. doi: 10.1104/pp.103.034496 15020752

21. Nielsen KL, Høgh AL, Emmersen J. DeepSAGE—Digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucleic Acids Research. 2006; 34(19): e133. doi: 10.1093/nar/gkl714 17028099

22. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research. 2008; 18:1509–17. doi: 10.1101/gr.079558.108 18550803

23. Matsumura H, Yoshida K, Luo S, Kimura E, Fujibe T, Albertyn Z, et al. High-throughput superSAGE for digital gene expression analysis of multiple samples using next generation sequencing. PLoS ONE. 2010; 5(8):e12010 doi: 10.1371/journal.pone.0012010 20700453

24. IPGRI/IITA. Descriptors for yam (Dioscorea spp.). Interna- tional Institute of Tropical Agriculture, Ibadan, Nigeria/International Plant Genetic Resources Institute. Rome, Italy; 1997.

25. Dellaporta SL, Wood J, Hicks JB. A plant DNA minipreparation: Version II. Plant Molecular Biology Reporter.1983; 1(4):19–21. doi: 10.1007/BF02712670

26. Lê S, Josse J, Husson F. FactoMineR: An R Package for Multivariate Analysis. Journal of Statistical Software. 2008; 25:253–8.

27. R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL R Foundation for Statistical Computing, Vienna, Austria. 2013.

28. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (Oxford, England). 2010; 26:139–40. doi: 10.1093/bioinformatics/btp616 19910308

29. Livak KJ, Schmittgen TD. Analysis of Relative Gene Expression Data Using RealTime Quantitative PCR and the 22DDCT Method. Methods. 2001; 25, 402–408. doi: 10.1006/meth.2001.1262 11846609

30. Livak K. ABI Prism 7700 sequence detection system, User Bulletin 2. PE Applied Biosystems, Foster City, CA, U.S.A; 1997.

31. Zhao X, Zhang X, Guo X, Li S, Han L, Song Z, Wang Y, Li J. Identification and Validation of Reference Genes for qRT-PCR Studies of Gene Expression in Dioscorea opposita. BioMed Research International. 2016; 2016(1):1–13.

32. Hamadina EI, Craufurd PQ, Asiedu R. Flowering intensity in white yam (Dioscorea rotundata). Journal of Agricultural Science. 2009; 147:469–77.

33. Dansi A, Mignouna HD, Zoundjihékpon J, Sangare A, Asiedu R, Quin FM. Morphological diversity, cultivar groups and possible descent in the cultivated yams (Dioscorea cayenensis/D. rotundata) complex in Benin Republic. Genetic Resources and Crop Evolution. 1999; 46:371–88.

34. Hamon P, Toure B. Characterization of traditional yam varieties belonging to the Dioscorea cayenensis-rotundata complex by their isozymic patterns. Euphytica. 1990; 46:101–7.

35. Girma G, Hyma KE, Asiedu R, Mitchell SE, Gedil M, Spillane C. Next-generation sequencing based genotyping, cytometry and phenotyping for understanding diversity and evolution of Guinea yams. Theoretical and Applied Genetics. 2014; 127:1783–94. doi: 10.1007/s00122-014-2339-2 24981608

36. Micheli F, Holliger C, Goldberg R, Richard L. Characterization of the pectin methylesterase-like gene AtPME3: A new member of a gene family comprising at least 12 genes in Arabidopsis thaliana. Gene. 1998; 220:13–20. doi: 10.1016/s0378-1119(98)00431-4 9767082

37. Alexandersson E, Fraysse L, Sjövall-Larsen S, Gustavsson S, Fellert M, Karlsson M, et al. Whole gene family expression and drought stress regulation of aquaporins. Plant Molecular Biology. 2005; 59:469–84. doi: 10.1007/s11103-005-0352-1 16235111

38. Suzuki H, Sawada S, Watanabe K, Nagae S, Yamaguchi MA, Nakayama T, et al. Identification and characterization of a novel anthocyanin malonyltransferase from scarlet sage (Salvia splendens) flowers: An enzyme that is phylogenetically separated from other anthocyanin acyltransferases. Plant Journal. 2004; 38:994–1003. doi: 10.1111/j.1365-313X.2004.02101.x 15165190

39. Alonso JM, Granell A. A putative vacuolar processing protease is regulated by ethylene and also during fruit ripening in Citrus fruit. Plant Physiology. 1995; 109:541–7. doi: 10.1104/pp.109.2.541 7480346

40. Wang Y, Zhang W-Z, Song L-F, Zou J-J, Su Z, Wu W-H. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiology. 2008; 148:1201–11. doi: 10.1104/pp.108.126375 18775970

41. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, et al. A gene expression map of Arabidopsis thaliana development. Nature Genetics. 2005; 37:501–6. doi: 10.1038/ng1543 15806101

42. Smirnova A, Leide J, Riederer M. Deficiency in a Very-Long-Chain Fatty Acid -Ketoacyl-Coenzyme A Synthase of Tomato Impairs Microgametogenesis and Causes Floral Organ Fusion. Plant Physiology. 2013; 161:196–209. doi: 10.1104/pp.112.206656 23144186

43. Ling H. Sequence analysis of GDSL lipase gene family in Arabidopsis thaliana. Pakistan Journal of Biological Sciences. 2008; 11:763–7. doi: 10.3923/pjbs.2008.763.767 18819574

44. Momose M, Itoh Y, Umemoto N, Nakayama M, Ozeki Y. Reverted glutathione S-transferase-like genes that influence flower color intensity of carnation (Dianthus caryophyllus L.) originated from excision of a transposable element. Breeding Science. 2013; 63:435–40. doi: 10.1270/jsbbs.63.435 24399917

45. Yoo SY, Kim Y, Kim SY, Lee JS, Ahn JH. Control of flowering time and cold response by a NAC-domain protein in Arabidopsis. PLoS ONE. 2007;2(7): e642. doi: 10.1371/journal.pone.0000642 17653269

46. Wang M, Yan J, Zhao J, Song W, Zhang X, Xiao Y, et al. Genome-wide association study (GWAS) of resistance to head smut in maize. Plant Science. 2012; 196:125–31. doi: 10.1016/j.plantsci.2012.08.004 23017907

47. Yang Y, Ma C, Xu Y, Wei Q, Imtiaz M, Lan H, et al. A Zinc Finger Protein Regulates Flowering Time and Abiotic Stress Tolerance in Chrysanthemum by Modulating Gibberellin Biosynthesis. The Plant Cell. 2014; 26:2038–54. doi: 10.1105/tpc.114.124867 24858937

48. Liu S, Han B. Differential expression pattern of an acidic 9/13-lipoxygenase in flower opening and senescence and in leaf response to phloem feeders in the tea plant. BMC Plant Biology. 2010; 10:228. doi: 10.1186/1471-2229-10-228 20969806

49. Fukuchi-Mizutani M, Ishiguro K, Nakayama T, Utsunomiya Y, Tanaka Y, Kusumi T, et al. Molecular and functional characterization of a rose lipoxygenase cDNA related to flower senescence. Plant Science. 2000; 160:129–37. 11164585

50. Ai-Hua S, Yin-Hua C, Zhi-Hui S, Xiao-Juan Z, Xue-Jun W, De-Zheng Q, et al. Identification of photoperiod-regulated gene in soybean and functional analysis in Nicotiana benthamiana. Journal of Genetics. 2014; 93:43–51. doi: 10.1007/s12041-014-0331-x 24840822

51. Oda A, Fujiwara S, Kamada H, Coupland G, Mizoguchi T. Antisense suppression of the Arabidopsis PIF3 gene does not affect circadian rhythms but causes early flowering and increases FT expression. FEBS Letters. 2004; 557:259–64. doi: 10.1016/s0014-5793(03)01470-4 14741378

52. Futamura N, Ishiiminami N, Hayashida N, Shinohara K. Expression of DnaJ homologs and Hsp70 in the Japanese willow (Salix gilgiana Seemen). Plant and Cell Physiology. 1999; 40:524–31. doi: 10.1093/oxfordjournals.pcp.a029573 10427775

53. Murase K, Shigenobu S, Fujii S, Ueda K, Murata T, Sakamoto A, Wada Y, Yamaguchi K, Osakabe Y, Osakabe K, Kanno A, Ozaki Y, Takayama S. MYB transcription factor gene involved in sex determination in Asparagus officinalis. Genes Cells. 2017; 22(1):115–123. doi: 10.1111/gtc.12453 27869347

54. Bi H, Wang M, Dong X, Ai X. Cloning and expression analysis of transketolase gene in Cucumis sativus L. Plant Physiology and Biochemistry. 2013; 70:512–21. doi: 10.1016/j.plaphy.2013.06.017 23860231

55. Nyaboga E, Tripathi JN, Manoharan R, Tripathi L. Agrobacterium-mediated genetic transformation of yam (Dioscorea rotundata): an important tool for functional study of genes and crop improvement. Fronteirs in Plant Science. 2014; 5:463. doi: 10.3389/fpls.2014.00463 25309562

Článek vyšel v časopise


2019 Číslo 9

Nejčtenější v tomto čísle

Tomuto tématu se dále věnují…


Zvyšte si kvalifikaci online z pohodlí domova

Ulcerative colitis_muž_břicho_střeva
Ulcerózní kolitida
nový kurz

Blokátory angiotenzinových receptorů (sartany)
Autoři: MUDr. Jiří Krupička, Ph.D.

Antiseptika a prevence ve stomatologii
Autoři: MUDr. Ladislav Korábek, CSc., MBA

Citikolin v neuroprotekci a neuroregeneraci: od výzkumu do klinické praxe nejen očních lékařů
Autoři: MUDr. Petr Výborný, CSc., FEBO

Zánětlivá bolest zad a axiální spondylartritida – Diagnostika a referenční strategie
Autoři: MUDr. Monika Gregová, Ph.D., MUDr. Kristýna Bubová

Všechny kurzy
Kurzy Doporučená témata