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Molecular Genetics and Genomics

, Volume 294, Issue 1, pp 35–45 | Cite as

Interspecific genetic maps in Miscanthus floridulus and M. sacchariflorus accelerate detection of QTLs associated with plant height and inflorescence

  • Chunxia Ge
  • Xin Ai
  • Shengfeng Jia
  • Yinqing Yang
  • Lu Che
  • Zili Yi
  • Cuixia ChenEmail author
Original Article
First Online:

Abstract

Miscanthus is recognized as a promising lignocellulosic crop for the production of bioethanol and bioproducts worldwide. To facilitate the identification of agronomical important traits and establish genetics knowledge, two genetic maps were developed from a controlled interspecific cross between M. floridulus and M. sacchariflorus. A total of 650 SSR markers were mapped in M. floridulus, spanning 19 linkage groups and 2053.31 cM with an average interval of 3.25 cM. The map of M. sacchariflorus comprised 495 SSR markers in 19 linkage groups covering 1684.86 cM with an average interval of 3.54 cM. The estimation on genome length indicated that the genome coverage of parental genetic maps were 93.87% and 89.91%, respectively. Eighty-eight bi-parental common markers were allowed to connect the two maps, and six pairs of syntenic linkage groups were recognized. Furthermore, quantitative trait loci (QTL) mapping of three agronomic traits, namely, plant height (PH), heading time (HT), and flowering time (FT), demonstrated that a total of 66 QTLs were identified in four consecutive years using interval mapping and multiple-QTL model. The LOD value of these QTLs ranged from 2.51 to 10.60, and the phenotypic variation explained varied from 9.50 to 37.10%. QTL cluster in syntenic groups MF19/MS7 contained six stable QTLs associated with PH, HT, and FT. In conclusion, we report for the first time the genetic mapping of biomass traits in M. floridulus and M. sacchariflorus. These results will be a valuable genetic resource, facilitating the discovery of essential genes and breeding of Miscanthus.

Keywords

Miscanthus Genetic map SSR QTL mapping Biomass 
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Notes

Acknowledgements

This work was supported by the National Natural Sciences Foundation of China (31271352 and 31071471).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical approval

The authors declare that this study complies with the current laws of the country in which the experiments were performed. This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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References

  1. Atienza SG, Satovic Z, Peterson KK, Dolstra O (2002) Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers. Theor Appl Genet 105:946–952CrossRefGoogle Scholar
  2. Atienza SG, Satovic Z, Petersen KK, Dolstra O, Martin A (2003a) Identification of QTLs associated with yield and its components in Miscanthus sinensis Anderss. Euphytica 132:353–361CrossRefGoogle Scholar
  3. Atienza SG, Ramirez MC, Martin A (2003b) Mapping QTLs controlling flowering date in Miscanthus sinensis Anderss. Cereal Res Commun 31:265–271Google Scholar
  4. Atienza SG, Satovic Z, Petersen KK, Dolstra O, Martin A (2003c) Identification of QTLs influencing agronomic traits in Miscanthus sinensis Anderss. I. Total height, flag-leaf height and stem diameter. Theor Appl Genet 107:123–129CrossRefGoogle Scholar
  5. Atienza SG, Satovic Z, Petersen KK, Dolstra O, Martin A (2003d) Identification of QTLs influencing combustion quality in Miscanthus sinensis Anderss. II. Chlorine and potassium content. Theor Appl Genet 107:857–863CrossRefGoogle Scholar
  6. Atienza SG, Satovic Z, Petersen KK, Dolstra O, Martin A (2003e) Influencing combustion quality in Miscanthus sinensis Anderss.: identification of QTLs for calcium, phosphorus and sulphur content. Plant Breed 122:141–145CrossRefGoogle Scholar
  7. Barling A, Swaminathan K, Mitros T, James BT, Morris J, Ngamboma O, Hall MC, Kirkpatrick J, Alabady M, Spence AK, Hudson ME, Rokhsar DS, Moose SP (2013) A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes. BMC Genom 14:864CrossRefGoogle Scholar
  8. Bowers JE, Abbey C, Anderson S, Chang C, Draye X, Hoppe AH, Jessup R, Lemke C, Lennington J, Li Z, Lin Y, Liu S, Luo L, Marler BS, Ming R, Mitchell SE, Qiang D, Reischmann K, Schulze SR, Skinner DN, Wang Y, Kresovich S, Schertz KF, Paterson AH (2003) A high-density genetic recombination map of sequence-tagged sites for Sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics 165:367–386Google Scholar
  9. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Sanchez Villeda H, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD (2009) The genetic architecture of maize flowering time. Science 325:714–718CrossRefGoogle Scholar
  10. Chae WB, Hong SJ, Gifford JM, Rayburn AL, Sacks EJ, Juvik JA (2014) Plant morphology genome size and SSR markers differentiate five distinct taxonomic groups among accessions in the genus Miscanthus. GCB Bioenergy 6:646–660CrossRefGoogle Scholar
  11. Chakravarti A, Lasher LK, Reefer JE (1991) A maximum likelihood method for estimating genome length using genetic linkage data. Genetics 128:175–182Google Scholar
  12. Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murigneux A, Charcosset A (2004) Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 168:2169–2185CrossRefGoogle Scholar
  13. Chen SL, Renvoize SA (2006) Miscanthus. In: Wu ZY (ed) Flora of China, 3rd edn. Flora of China, Beijing, pp 581–583Google Scholar
  14. Clark LV, Brummer JE, Głowacka K, Hall MC, Heo K, Peng JH, Yamada T, Yoo JH, Yu CY, Zhao H, Long SP, Sacks EJ (2014) A footprint of past climate change on the diversity and population structure of Miscanthus sinensis. Ann Bot 114:97–107CrossRefGoogle Scholar
  15. Dong H, Liu S, Clark LV, Sharma S, Gifford JM, Juvik JA, Lipka AE, Sacks EJ (2017) Genetic mapping of biomass yield in three interconnected Miscanthus populations. GCB Bioenergy.  https://doi.org/10.1111/gcbb.12472 Google Scholar
  16. Fishman L, Kelly AJ, Morgan E, Willis JH (2001) A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics 159:1701–1716Google Scholar
  17. Ge C, Liu X, Liu S, Xu J, Li H, Cui T, Y Y, Chen M, Yu W, Chen C (2017) Miscanthus sp.: genetic diversity and phylogeny in China. Plant Mol Biol Rep 35:600–610CrossRefGoogle Scholar
  18. Gifford JM, Chae WB, Swaminathan K, Moose SP, Juvik JA (2015) Mapping the genome of Miscanthus sinensis for QTL associated with biomass productivity. GCB Bioenergy 7:797–810CrossRefGoogle Scholar
  19. Greef MJ, Deuter M, Jung C, Schondelmaier J (1997) Genetic diversity of European Miscanthus species revealed by AFLP fingerprinting. Genet Res Crop Evol 44:185–195CrossRefGoogle Scholar
  20. Hall MC, Willis JH (2005) Transmission ratio distortion in intraspecific hybrids of Mimulus guttatus: implications for genomic divergence. Genetics 170:375–386CrossRefGoogle Scholar
  21. Heaton EA, Voigt T, Long SP (2004) A quantitative review comparing the yields of two candidate C4 perennial biomass crops in relation to nitrogen, temperature and water. Biomass Bioenerg 27:21–30CrossRefGoogle Scholar
  22. Heaton EA, Dohleman FG, Long SP (2008) Meeting US biofuel goals with less land: the potential of Miscanthus. Glob Change Biol 14:2000–2014CrossRefGoogle Scholar
  23. Higgins RH, Thurber CS, Assaranurak I, Brown PJ (2014) Multiparental mapping of plant height and flowering time QTL in partially isogenic sorghum families. G3 (Genes Genom Genet) 4:1593–1602Google Scholar
  24. Hodkinson TR, Chase MW, Renvoize SA (2002a) Characterization of a genetic resource collection for Miscanthus (Saccharinae, Andropogoneae, Poaceae) using AFLP and ISSR PCR. Ann Bot 89:627–636CrossRefGoogle Scholar
  25. Hodkinson TR, Chase MW, Lledo MD, Salamin N, Renvoize SA (2002b) Phylogenetics of Miscanthus, Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers. J Plant Res 115:381–392CrossRefGoogle Scholar
  26. Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136:1447–1455Google Scholar
  27. Jensen E, Farrar K, Thomasjones S, Hastings A, Donnison I, Cliftonbrown J (2011) Characterization of flowering time diversity in Miscanthus species. GCB Bioenergy 3:387–400CrossRefGoogle Scholar
  28. Kim C, Zhang D, Auckland SA, Rainville LK, Jakob K, Kronmiller B, Sacks EJ, Deuter M, Paterson AH (2012) SSR-based genetic maps of Miscanthus sinensis. and M. sacchariflorus, and their comparison to sorghum. Theor Appl Genet 124:1325–1338CrossRefGoogle Scholar
  29. Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199Google Scholar
  30. Linde-Laursen I (1993) Cytogenetic analysis of Miscanthus ‘Giganteus’ an interspecific hybrid. Hereditas 119:297–300CrossRefGoogle Scholar
  31. Liu S, Clark LV, Swaminathan K, Gifford JM, Juvik JA, Sacks EJ (2015) High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe. GCB Bioenergy 8:616–630CrossRefGoogle Scholar
  32. Lu H, Romero-Severson J, Bernardo R (2002) Chromosomal regions associated with segregation distortion in maize. Theor Appl Genet 105:622–628CrossRefGoogle Scholar
  33. Ma XF, Jensen E, Alexandrov N, Troukhan M, Zhang L, Thomas-Jones S, Farrar K, Clifton-Brown J, Donnison I, Swaller T, Flavell R (2012) High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis. PLoS One 7:e33821CrossRefGoogle Scholar
  34. Mace ES, Buhariwalla HK, Crouch JH (2003) A high-throughput DNA extraction protocol for tropical molecular breeding programs. Plant Mol Biol Rep 21:459–460CrossRefGoogle Scholar
  35. Mannai YE, Shehzad T, Okuno K (2012) Mapping of QTLs underlying flowering time in sorghum [Sorghum bicolor (l.) moench]. Breed Sci 62:151–159CrossRefGoogle Scholar
  36. Manrique-Carpintero NC, Coombs JJ, Veilleux RE, Buell CR, Douches DS (2016) Comparative analysis of regions with distorted segregation in three diploid populations of potato. G3-Genes Genom Genet 6:2617–2628Google Scholar
  37. Ming R, Liu SC, Lin YR, Silva JD, 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 150:1663–1682Google Scholar
  38. Rayburn AL, Crawford J, Rayburn CM, Juvik JA (2009) Genome size of three Miscanthus species. Plant Mol Biol Rep 27:184–188CrossRefGoogle Scholar
  39. Sang T, Zhu WX (2010) China’s bioenergy potential. GCB Bioenergy 3:79–90CrossRefGoogle Scholar
  40. Somerville C, Youngs H, Taylor C, Davis SC, Long SP (2010) Feedstocks for lignocellulosic biofuels. Science 329:790–792CrossRefGoogle Scholar
  41. Swaminathan K, Chae WB, Mitros T, Varala K, Xie L, Barling A, Glowacka K, Hall M, Jezowski S, Ming R, Hudson M, Juvik JA, Rokhsar DS, Moose SP (2012) A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. BMC Genom 13:142–158CrossRefGoogle Scholar
  42. Van Ooijen JW (2006) JoinMap4, software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, WageningenGoogle Scholar
  43. Van Ooijen JW (2009) MAPQTL® 6, software for the mapping of quantitative trait loci in experimental populations of diploid species. Kyazma BV, WageningenGoogle Scholar
  44. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78CrossRefGoogle Scholar
  45. Weijde TVD, Kamei CLA, Severing EI, Torres AF, Gomez LD, Dolstra O, Maliepaard CA, McQueen-Mason SJ, Visser RGF, Trindade LM (2017) Genetic complexity of Miscanthus cell wall composition and biomass quality for biofuels. BMC Genom 18:406CrossRefGoogle Scholar
  46. Xu S (2003) Theoretical basis of the beavis effect. Genetics 165:2259–2268Google Scholar
  47. Zhang D, Kong W, Robertson J, Goff VH, Epps E, Kerr A, Mills G, Cromwell J, Lugin Y, Phillips C, Paterson AH (2015) Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae). BMC Plant Biol 15:107CrossRefGoogle Scholar
  48. Zhao Y, Basak S, Fleener CE, Egnin M, Sacks EJ, Prakash CS, He G (2016) Genetic diversity of Miscanthus sinensis in US naturalized populations. GCB Bioenergy 9:965–972CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Chunxia Ge
    • 1
    • 2
  • Xin Ai
    • 4
  • Shengfeng Jia
    • 1
    • 2
  • Yinqing Yang
    • 1
    • 2
  • Lu Che
    • 3
  • Zili Yi
    • 5
  • Cuixia Chen
    • 1
    • 2
    Email author
  1. 1.State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianChina
  2. 2.College of AgronomyShandong Agricultural UniversityTaianChina
  3. 3.Network Information Technology CenterShandong Agricultural UniversityTaianChina
  4. 4.College of Horticulture and LandscapeHunan Agricultural UniversityChangshaChina
  5. 5.College of Bioscience and BiotechnologyHunan Agricultural UniversityChangshaChina

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