Skip to main content

Advertisement

SpringerLink
Log in

Natural variation and genetic analysis of the tiller angle gene MsTAC1 in Miscanthus sinensis

  • Original Article
  • Published:
Planta Aims and scope Submit manuscript

Abstract

Biomass yield is an important target trait in Miscanthus breeding for desirable energy crops. Tiller angle is a key trait of plant architecture because it determines planting density and further influences biomass yield through affecting photosynthesis efficiency. TAC1, a major gene involved in tiller and leaf angle control in rice and maize, respectively, has been extensively studied. Nucleotide variation at this gene, MsTAC1, was investigated in 33 Miscanthus sinensis accessions collected from different areas in China, and one genotype of Miscanthus × giganteus. A total of 136 loci, including 129 single base substitutions and seven InDels, occurred within the MsTAC1 gene of 1,874 bp. The genetic diversity at MsTAC1 is characterized by high nucleotide diversity (π value) and high heterozygosity. Clustering analysis indicated that the phylogenetic tree of the 33 M. sinensis accessions was correlated with their geographical sites of origin. The neutrality test revealed no strong selection pressure on coding and non-coding region variations of the MsTAC1 gene in the accessions. Phenotype evaluations were conducted for tiller angle and five other traits in the Miscanthus panels in the first two growth years of 2009 and 2010. Analysis of variance showed significant phenotypic variations in the examined traits. Association analysis using 246 markers detected 88 loci associated with all the test traits in either 1 or 2 years, and 11 of the 88 were year reproducible and thus reliable. These associations indicate that the variation of MsTAC1 affects the phenotypic value of the tiller angle, tiller number and biomass yield, suggesting that allelic variation in MsTAC1 affects multiple traits and demonstrates its significance in Miscanthus breeding programs.

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
Fig. 5

Similar content being viewed by others

Abbreviations

TAC :

Tiller angle gene

Indel:

Insert and deletion

CDS:

Coding sequence

UTR:

Untranslated region

References

  • Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, Kruglyaket L (2004) Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol 2:e286

    Article  PubMed Central  PubMed  Google Scholar 

  • Alonso-Blanco C, Aarts MGM, Bentsink L, Keurentjes JJB, Reymond M, Vreugdenhil D, Koornneef M (2009) What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell 21:1877–1896

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE et al (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  CAS  PubMed  Google Scholar 

  • Chen YN, Fan XR, Song WJ, Yali Zhang Y, Xu GH (2012) Over-expression of OsPIN2 leads to increased tiller numbers, angle and shorter plant height through suppression of OsLAZY1. Plant Biotechnol J 10:139–149

    Article  CAS  PubMed  Google Scholar 

  • Clifton-Brown JC, Lewandowski I (2000) Overwintering problems of newly established Miscanthus plantations can be overcome by identifying genotypes with improved rhizome cold tolerance. New Phytol 148:287–294

    Article  Google Scholar 

  • Corre VL, Roux F, Reboud X (2002) DNA Polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is consistent with local selection for flowering time. Mol Biol Evol 19:1261–1271

    Article  PubMed  Google Scholar 

  • Dai LJ, Wang B, Zhao H, Peng JH (2013) Transferability of genomic simple sequence repeat and expressed sequence tag-simple sequence repeat markers from sorghum to Miscanthus sinensis, a potential biomass crop. Crop Sci 53:977–986

  • Doebley JB, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321

    Article  CAS  PubMed  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software SRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Hall TA (1999) Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecology Notes 2:618–620

  • Hastings A, Clifton-Brown J, Wattenbach M et al (2009a) The development of MISCANFOR, a new Miscanthus crop growth model: towards more robust yield predictions under different climatic and soil conditions. GCB Bioenerg 1:154–170

    Article  Google Scholar 

  • Hastings A, Clifton-Brown J, Wattenbach M et al (2009b) Future energy potential of Miscanthus in Europe. GCB Bioenerg 1:180–196

    Article  Google Scholar 

  • Heaton EA, Dohleman FG, Long SP (2009) Seasonal nitrogen dynamics of Miscanthus giganteus and Panicum virgatum. GCB Bioenerg 1:297–307

    Article  CAS  Google Scholar 

  • Jezowski S (2008) Yield traits of six clones of Miscanthus in the first 3 years following planting in Poland. Ind Crop Prod 27:65–68

    Article  Google Scholar 

  • Jiang JH, Tan LB, Zhu Z, Fu YC, Liu FX, Cai HW, Sun CQ (2012) Molecular evolution of the TAC1 Ggene from rice (Oryza sativa L.). J Genet Genomics 39:551–560

    Article  CAS  PubMed  Google Scholar 

  • Jin J, Huang W, Gao JP et al (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40:1365–1369

    Article  CAS  PubMed  Google Scholar 

  • Jørgensen U, Schwarz KU (2000) Why do basic research? A lesson from commercial exploitation of Miscanthus. New Phytol 148:190–193

    Article  Google Scholar 

  • Kovach MJ, Sweeney MT, McCouch SR (2007) New insights into the history of rice domestication. Trends Genet 23:578–587

    Article  CAS  PubMed  Google Scholar 

  • Ku L, Wei X, Zhang S et al (2011) Cloning and characterization of a putative TAC1 ortholog associated with leaf angle in maize (Zea mays L.). PLoS ONE 6:e20621

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li PJ, Wang YH, Qian Q et al (2007) LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17:402–410

    CAS  PubMed  Google Scholar 

  • Li Q, Li L, Yang XH et al (2010) Relationship, evolutionary fate and function of two maize co-orthologs of rice GW2 associated with kernel size and weight. BMC Plant Biol 10:143

    Article  PubMed Central  PubMed  Google Scholar 

  • Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    Article  CAS  PubMed  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Peng J, Richards DE, Hartley NM et al (1999) Green revolution genes encode mutant gibberellin response modulators. Nature 400:256–261

    Article  CAS  PubMed  Google Scholar 

  • Peng JH, Ronin YI, Fahima T, Röder MS, Li YC, Nevo E, Korol A (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100:2489–2494

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Price L, Bullard M, Lyons H et al (2004) Identifying the yield potential of Miscanthus × giganteus: an assessment of the spatial and temporal variability of M. × giganteus biomass productivity across England and Wales. Biomass Bioenerg 26:3–13

    Article  Google Scholar 

  • Pritchard JK, Wen X, Falush D (2009) Documentation for structure software: Version 2.3. http://pritch.bsd.uchicago.edu/structure.html

  • Robson P, Jensen E, Hawkins S, White SR, Kenobi K, Clifton-Brown J, Donnison I, Farrar K (2013) Accelerating the domestication of a bioenergy crop: identifying and modelling morphological targets for sustainable yield increase in Miscanthus. J Exp Bot 64:4143–4155

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Swaminathan K, Alabady MS, Varala K et al (2010) Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biol 11:R12–R29

    Article  PubMed Central  PubMed  Google Scholar 

  • Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101:11030–11035

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tan LB, Li XR, Liu FX et al (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40:1360–1364

    Article  CAS  PubMed  Google Scholar 

  • Wang ML, Barkley NA, Yu JK, Dean RE, Newman ML, Sorrells ME, Pederson GA (2005) Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation. Plant Genet Resour 3:45–57

    Article  CAS  Google Scholar 

  • Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276

    Article  CAS  PubMed  Google Scholar 

  • Xu M, Zhu L, Shou HX, Wu P (2005) A PIN1 family gene, OsPIN1, involved in auxin-dependent adventitious root emergence and tillering in rice. Plant Cell Physiol 46:1674–1681

    Article  CAS  PubMed  Google Scholar 

  • Yan J, Chen WL, Luo F et al (2012) Variability and adaptability of Miscanthus species evaluated for energy crop domestication. GCB Bioenerg 4:49–60

    Article  Google Scholar 

  • Yang X, Yan J, Shah T et al (2010) Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection. Theor Appl Genet 121:417–431

    Article  PubMed  Google Scholar 

  • Yu J, Pressoir G, Briggs WH et al (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208

    Article  CAS  PubMed  Google Scholar 

  • Yu BS, Lin ZW, Li HX et al (2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52:891–898

    Article  CAS  PubMed  Google Scholar 

  • Yu L, Ding GD, Huai ZX et al (2013) Natural variation of biomass yield and nutrient dynamics in Miscanthus. Field Crops Res 151:1–8

    Article  Google Scholar 

  • Zhao H, Yu JY, You FM, Luo MC, Peng JH (2011) Transferability of microsatellite markers from Brachypodium distachyon to Miscanthus sinensis, a potential biomass crop. J Integr Plant Biol 53:232–245

    Article  CAS  PubMed  Google Scholar 

  • Zhao H, Li Q, He JR, Yu JG, Yang JP, Liu CZ, Peng JH (2013a) Genotypic variation of cell wall composition and its conversion efficiency in Miscanthus sinensis, a potential biomass feedstock crop in China. GCB Bioenerg. doi:10.1111/gcbb.12115

    Google Scholar 

  • Zhao H, Wang B, He JR, Yang JP, Pan L, Sun DF, Peng JH (2013b) Genetic diversity and population structure of Miscanthus sinensis germplasm in China. PLoS ONE 8:e75672

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgments

This study was supported by the National Natural Science Foundation of China (Grant No. 31100243 and 30870233). The authors kindly thank Prof. Hanhui Kuang at Huazhong Agricultural University for his advice to the work.

Author information

Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China

    Hua Zhao, Zexun Huai, Yingjie Xiao, Xiaohua Wang & Guangda Ding

  2. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China

    Hua Zhao, Yingjie Xiao & Junhua Peng

  3. Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China

    Jiangyan Yu

  4. Graduate University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China

    Jiangyan Yu

  5. Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523-1170, USA

    Junhua Peng

Authors
  1. Hua Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zexun Huai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yingjie Xiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xiaohua Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jiangyan Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Guangda Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Junhua Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Junhua Peng.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (TIFF 21 kb)

Suppl. Fig. S1 Population structure of 34 Miscanthus accessions based on 131 MsTAC1–derived SNP or InDel markers, and 115 SSRs. When K (the number of subgroups) was four, the 34 Miscanthus accessions were classified into four groups

Supplementary material 2 (DOCX 48 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhao, H., Huai, Z., Xiao, Y. et al. Natural variation and genetic analysis of the tiller angle gene MsTAC1 in Miscanthus sinensis . Planta 240, 161–175 (2014). https://doi.org/10.1007/s00425-014-2070-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00425-014-2070-x

Keywords

Search

Navigation