, 215:65 | Cite as

Colinearity of putative flowering gene in both sugarcane and sorghum

  • Pattama Srinamngoen
  • Sontichai Chanprame
  • Nongluk Teinseree
  • Ismail DweikatEmail author


Sugarcane (Saccharum spp.) and sorghum (Sorghum spp.) have become increasingly important crops for biofuels production. Sugarcane has an autopolyploid complex genome, whereas sorghum has a diploid simple genome. Flowering is one of the sugar-related agronomic traits in both species. Here, we obtained cDNA of inflorescences at 0–15 cm from S. spontaneum using cDNA-amplified restriction fragment length polymorphisms to develop flower transcriptome profiling with 26 primer combinations. A total of 183 transcript-derived fragments (TDFs) were screened and 96 TDFs were sequenced. Out of 96 TDFs, 26 were selected as putative flowering genes to study collinearity with the sorghum genome. For gene collinearity, a genetic linkage map with 169 SSR co-dominant markers and 12 TDF marker loci were mapped to 14 linkage groups collectively spanning 1077.8 cM and corresponding to the 10 sorghum chromosomes. Interestingly, 9 TDF marker loci could be mapped to 5 linkage groups. In this study, we successfully identified the homologous location of sugarcane flowering TDFs in the sorghum genome and found that 4DS_1X and 2DS_3E TDFs may serve as candidate specific markers linked to flowering in both sorghum and sugarcane.


Collinearity RILs SSR cDNA-AFLP Sugarcane Sorghum 



We gratefully acknowledge Grants from the National Science and Technology Development Agency, Assoc. Prof. Dr.Julapark Chunwong for providing Joinmap® mapping Program and Dr.Sompong Chankaew for helpful advice on the analysis of the genetic linkage map.

Supplementary material

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  1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefGoogle Scholar
  2. Bachem CWB, van der Hoeven RS, de Bruijn SM, Vreugdenhil D, Zabeau M, Visser RGF (1996) Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J 9:745–753CrossRefGoogle Scholar
  3. Bhattramakki D, Dong J, Chhabra AK, Hart GE (2000) An integrated SSR and RFLP linkage map of sorghum bicolor (L.) Moench. Genome 43:988–1002CrossRefGoogle Scholar
  4. Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 11:113–116CrossRefGoogle Scholar
  5. Childs KL, Miller FR, Cordonnier-Pratt MM, Pratt LH, Morgan PW, Mullet JE (1997) The sorghum photoperiod sensitivity gene, Ma3, encodes a phytochrome B. Plant Physiol 113:611–619CrossRefGoogle Scholar
  6. Coelho CP, Costa Netto AP, Colasanti J, Chalfun-Junior A (2013) A proposed model for the flowering signaling pathway of sugarcane under photoperiodic control. Genet Mol Res 12:1347–1359CrossRefGoogle Scholar
  7. Coen ES, Meyerowiz EM (1991) The war of the whorls: genetic interactions controlling flower development. Nature 353:31–37CrossRefGoogle Scholar
  8. Coen ES, Romero JM, Doyle S, Elliott R, Murphy G, Carpenter R (1990) floricaula: a homeotic gene required for flower development in antirrhinum majus. Cell 63:1311–1322CrossRefGoogle Scholar
  9. Colasanti J, Coneva V (2009) Mechanisms of floral induction in grasses: something borrowed, something new. Plant Physiol 149:56–62CrossRefGoogle Scholar
  10. Durrant WE, Rowland O, Piedras P, Hammond-Kosack KE, Jones JDG (2000) cDNA-AFLP reveals a striking overlap in race-specific resistance and wound response gene expression profiles. Plant Cell 12:963–977CrossRefGoogle Scholar
  11. Dweikat I (2005) A diploid, interspecific, fertile hybrid from cultivated sorghum, Sorghum bicolor, and the Common Johnsongrass weed Sorghum halepense. Mol Breed 16:93–101CrossRefGoogle Scholar
  12. Glassop D, Rae AL, Bonnett GD (2014) Sugarcane flowering genes and pathway in relation to vegetative regression. Sugar Tech 16(3):235–240CrossRefGoogle Scholar
  13. Grivet L, Arruda P (2001) Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol 5:122–127CrossRefGoogle Scholar
  14. Grivet L, D’Hont A, Dufour P, Hamon P, Roques D, Glaszmann JC (1994) Comparative genome mapping of sugar cane with other species within the Andropogoneae tribe. Heredity 73:500–508CrossRefGoogle Scholar
  15. Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D’Eustachioc P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P (2016) Gramene database: navigating plant comparative genomics resources. Curr Plant Biol 7–8:10–15CrossRefGoogle Scholar
  16. Harry FC (1975) Flowering of sugarcane: mechanics and control. Technical Bulletin No.92. HAWAII Agricultural Experiment Station, University of HAWAIIGoogle Scholar
  17. He H, Yajing N, Huawen C, Xingjiao T, Xinli X, Weilun Y, Silan D (2012) cDNA-AFLP analysis of salt-inducible genes expression in Chrysanyhemum lavandulifolium under salt treatment. J Plant Physiol 169:410–420CrossRefGoogle Scholar
  18. Ivandic V, Hackett CA, Nevo E, Keith R, Thomas WTB, Forster BP (2002) Analysis of simple sequence repeats (SSRs) in wild barley from the fertile crescent: associations with ecology, geography and flowering time. Plant Mol Biol 48:511–527CrossRefGoogle Scholar
  19. Jaiswal P (2010) Gramene database: a hub for comparative plant genomics. Methods Mol Biol 678:247–275CrossRefGoogle Scholar
  20. Jordan DR, Mace EM, Henzell RG, Klein PE, Klein RR (2010) Molecular mapping and candidate gene identification of the Rf2 gene for pollen fertility restoration in sorghum [Sorghum bicolor (L.) Moench]. Theor Appl Genet 120:1279–1287CrossRefGoogle Scholar
  21. Julien R (1972) The photoperiodic control of flowering in Saccharum. Proc Int Soc Sugarcane Technol 14:323–333Google Scholar
  22. Kirsten B, Doebley JF (2005) Molecular evolution of FLORICAULA/LEAFY orthologs in the Andropogoneae (Poaceae). Mol Biol Evol 22(4):1082–1094CrossRefGoogle Scholar
  23. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175CrossRefGoogle Scholar
  24. Lekgari AL (2010) Genetic mapping of quantitative trait loci associated with bioenergy traits, and the assessment of genetic variability in sweet sorghum (Sorghum bicolor (L.). Moench). Ph.D. Dissertation, Agronomy and Horticulture, University of Nebraska, Lincoln, NEGoogle Scholar
  25. Mannai EY, Shehzad T, Okuno K (2012) Mapping of QTLs underlying flowering time in sorghum [Sorghum bicolorMoench (L.)]. Breed Sci 62:151–159CrossRefGoogle Scholar
  26. Menz MA, Klein RR, Mullet JE, Obert JA, Unruh NC, Klein PE (2002) A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP(R), RFLP and SSR markers. Plant Mol Biol 48:483–499CrossRefGoogle Scholar
  27. Ming R, Liu SC, Lin YR, da Silva J, Wilson W, Braga D, van Deynze A, Wenslaff TF, Wu KK, Moore PH, Burnquist W, Sorrells ME, Irvine JE, Paterson AH (1998) Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics 150(4):1663–1682PubMedPubMedCentralGoogle Scholar
  28. Murai K, Miyamae M, Kato H, Takumi S, Ogihara Y (2003) WAP1, a Wheat APETALA1 homolog, plays a central role in the phase transition from vegetative to reproductive growth. Plant Cell Physiol 44(12):1255–1265CrossRefGoogle Scholar
  29. Qin LHJ, Overmars Helder H, Popeijus J, van der Voort Rouppe, Groenink W, van Koert P, Schots A, Bakker J, Smant G (2000) An efficient cDNA AFLP-based strategy for the identification of putative pathogenicity factors from the potato cyst nematode Globodera rostochiensis. Mol Plant Microbe Interact 13:830–836CrossRefGoogle Scholar
  30. Salvi S, Corneti S, Bellotti M, Carraro N, Sanguineti MC, Castelletti S, Tuberosa R (2011) Genetic dissection of maize phenology using an intraspecific introgression library. BMC Plant Biol 11:4CrossRefGoogle Scholar
  31. Sanguinetti CJ, Dias NE, Simpson AJ (1994) Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques 17(5):914–921PubMedGoogle Scholar
  32. Swapna M, Singh PK (2008) Shoot apex development at various stages of flowering in sugarcane (Saccharum spp hybrid). Cytologia 73(2):173–177CrossRefGoogle Scholar
  33. Van Ooijen JW, Voorrips RE (2001) Joinmap 3.0 software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The NetherlandsGoogle Scholar
  34. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78CrossRefGoogle Scholar
  35. Vos P, Hogers R, Bleeker M, Reijans M, Van De Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23(21):4407–4414CrossRefGoogle Scholar
  36. Vuylsteke M, Pelema JD, VanEijk MJT (2007) Technology for DNA finger printing. Nat Protoc 2:1387–1398CrossRefGoogle Scholar
  37. Wang J, Roe B, Macmil S, Yu Q, Murray JE, Tang H, Chen C, Najar F, Wiley G, Bowers J, Sluys Marie-Anne V, Rokhsar DS, Hudson ME, Moose SP, Paterson AH, Ray MR (2010) Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. Genomic 11:261Google Scholar
  38. Weigel D, Alvarez J, Smyth DR, Yanofsky MF, Meyerowitz EM (1992) LEAFY controls floral meristem identity in Arabidopsis. Cell 69(5):843–859CrossRefGoogle Scholar
  39. Xie H, Ding D, Cui Z, Wu X, Hu Y, Liu Z, Li Y, Tang J (2010) Genetic analysis of the related traits of flowering and silk for hybrid seed production in maize. Genes Genomics 32:55–61CrossRefGoogle Scholar
  40. Yamaguchi N, Wu MF, Winter CM, Berns MC, Nole-Wilson S, Yamaguchi A, Coupland G, Krizek BA, Wagner D (2013) A molecular framework for auxin-mediated initiation of flower primordial. Dev Cell 24(3):271–282CrossRefGoogle Scholar
  41. Yang Z, Gu S, Wang X, Tang Z, Xu C (2008) Molecular evolution of the CPP-like gene family in plants: insights from comparative genomics of Arabidopsis and rice. J Mol Evol 67(3):266–277CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Pattama Srinamngoen
    • 1
    • 2
    • 3
  • Sontichai Chanprame
    • 1
    • 2
    • 4
  • Nongluk Teinseree
    • 1
    • 4
  • Ismail Dweikat
    • 5
    Email author
  1. 1.Center for Agricultural BiotechnologyKasetsart UniversityNakhon PathomThailand
  2. 2.Center of Excellence on Agricultural Biotechnology, Science and Technology, Postgraduate Education and Research Development OfficeCommission on Higher Education, Ministry of Education (AG-BIO/PERDO-CHE)BangkokThailand
  3. 3.Faculty of Science and ArtsBurapha UniversityChanthaburiThailand
  4. 4.Department of AgronomyFaculty of Agriculture at Kamphaeng Saen CampusNakhon PathomThailand
  5. 5.Department of Agronomy, Institute of Agricultural and Natural ResourcesUniversity of Nebraska-LincolnLincolnUSA

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