Skip to main content
SpringerLink
Log in
SpringerLink
Log in

CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses

  • Protocol
  • First Online:
Plant Genomics Databases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1533))

  • 1936 Accesses

Abstract

Conventional biparental quantitative trait locus (QTL) mapping has led to some successes in the identification of causal genes in many organisms. QTL likelihood intervals not only provide “prior information” for finer-resolution approaches such as GWAS but also provide better statistical power than GWAS to detect variants with low/rare frequency in a natural population. Here, we describe a new element of an ongoing effort to provide online resources to facilitate study and improvement of the important Saccharinae clade. The primary goal of this new resource is the anchoring of published QTLs for this clade to the Sorghum genome. Genetic map alignments translate a wealth of genomic information from sorghum to Saccharum spp., Miscanthus spp., and other taxa. In addition, genome alignments facilitate comparison of the Saccharinae QTL sets to those of other taxa that enjoy comparable resources, exemplified herein by rice.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Paterson AH, Lander ES, Hewitt JD et al (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335:721–726

    Article  CAS  PubMed  Google Scholar 

  2. Kover PX, Valdar W, Trakalo J et al (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5:e1000551

    Article  PubMed  PubMed Central  Google Scholar 

  3. Buckler ES, Holland JB, Bradbury PJ et al (2009) The genetic architecture of maize flowering time. Science 325:714–718

    Article  CAS  PubMed  Google Scholar 

  4. 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 

  5. Thornsberry JM, Goodman MM, Doebley J et al (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289

    Article  CAS  PubMed  Google Scholar 

  6. Yu J, Holland JB, McMullen MD et al (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551

    Article  PubMed  PubMed Central  Google Scholar 

  7. Myles S, Peiffer J, Brown PJ et al (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21:2194–2202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Heaton EA, Dohleman FG, Long SP (2008) Meeting US biofuel goals with less land: the potential of Miscanthus. Glob Chang Biol 14:2000–2014

    Article  Google Scholar 

  9. Lewandowski I, Scurlock JMO, Lindvall E et al (2003) The development and current status of perennial rhizomatous grasses as energy crops in the US and Europe. Biomass Bioenergy 25:335–361

    Article  Google Scholar 

  10. Lewandowski I, Clifton-brown JC, Scurlock JMO et al (2008) Miscanthus: European experience with a novel energy crop. Biomass Bioenergy 19:209–227

    Article  Google Scholar 

  11. Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556

    Article  CAS  PubMed  Google Scholar 

  12. Lin Y, Keith F, Paterson AH (1995) Comparative analysis of QTLs affecting plant height and maturity across the poaceae, in reference to an interspecific sorghum population. Genetics 141:391–411

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Paterson AH, Lin YR, Li Z et al (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic Loci. Science 269:1714–1718

    Article  CAS  PubMed  Google Scholar 

  14. Paterson AH, Schertz KF, Lin YR et al (1995) The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L.) Pers. Proc Natl Acad Sci U S A 92:6127–6131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ming R, Del Monte TA, Hernandez E et al (2002) Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes. Genome 45:794–803

    Article  CAS  PubMed  Google Scholar 

  16. Hu FY, Tao DY, Sacks E et al (2003) Convergent evolution of perenniality in rice and sorghum. Proc Natl Acad Sci U S A 100:4050–4054

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Feltus FA, Hart GE, Schertz KF et al (2006) Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations. Theor Appl Genet 112:1295–1305

    Article  CAS  PubMed  Google Scholar 

  18. Rong J, Feltus FA, Waghmare VN et al (2007) Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 176:2577–2588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Zhang D, Guo H, Kim C et al (2013) CSGRqtl, a comparative quantitative trait locus database for Saccharinae grasses. Plant Physiol 161:594–599

    Article  CAS  PubMed  Google Scholar 

  20. Ware D, Jaiswal P, Ni J et al (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Res 30:103–105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Wang X, Wang J, Jin D et al (2015) Genome alignment spanning major poaceae lineages reveals heterogeneous evolutionary rates and alters inferred dates for key evolutionary events. Mol Plant 8:885–898

    Article  CAS  PubMed  Google Scholar 

  22. Lee T-H, Tang H, Wang X et al (2013) PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res 41:D1152–D1158

    Article  CAS  PubMed  Google Scholar 

  23. Krzywinski M, Schein J, Birol I et al (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Youens-Clark K, Faga B, Yap IV et al (2009) CMap 1.01: a comparative mapping application for the Internet. Bioinformatics 25:3040–3042

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Stein LD, Mungall C, Shu S et al (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12:1599–1610

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Wang X, Shi X, Li Z et al (2006) Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics 7:447

    Article  PubMed  PubMed Central  Google Scholar 

  27. Quinby JR (1974) Sorghum improvement and the genetics of growth. Texas A&M University Press, College Station, TX

    Google Scholar 

  28. Rooney WL, Aydin S (1999) Genetic control of a photoperiod-sensitive response in sorghum bicolor (L.) moench. Crop Sci 39:397–400

    Article  Google Scholar 

  29. Zhang D, Kong W, Robertson J et al (2015) Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae). BMC Plant Biol 15:107

    Article  PubMed  PubMed Central  Google Scholar 

  30. Zhang D, Li J, Compton RO et al (2015) Comparative genetics of seed size traits in divergent cereal lineages represented by sorghum (Panicoidae) and rice (Oryzoidae). G3 (Bethesda, Md) 5:1117–1128

    Article  Google Scholar 

Download references

Acknowledgment

This work was supported by the Department of Energy-US Department of Agriculture Plant Feedstock Genomics program and the United Sorghum Checkoff Program (to A.H.P.).

Author information

Authors and Affiliations

  1. Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA

    Dong Zhang

  2. Plant Genome Mapping Laboratory (Dept #398), University of Georgia, 111 Riverbend Road, Rm 228, Athens, GA, 30602, USA

    Andrew H. Paterson

Authors
  1. Dong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrew H. Paterson
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Andrew H. Paterson .

Editor information

Editors and Affiliations

  1. PRI Bioscience, Biometris and Bioinformatics, Wageningen University & Research Wageningen, Wageningen, The Netherlands

    Aalt D.J van Dijk

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media New York

About this protocol

Cite this protocol

Zhang, D., Paterson, A.H. (2017). CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses. In: van Dijk, A. (eds) Plant Genomics Databases. Methods in Molecular Biology, vol 1533. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6658-5_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6658-5_15

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6656-1

  • Online ISBN: 978-1-4939-6658-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation