Skip to main content
Log in

Small-Scale duplication as a genomic signature for crop improvement

  • Review Article
  • Published:
Journal of Crop Science and Biotechnology Aims and scope Submit manuscript

Abstract

Next-generation sequencers (NGS) have enabled researchers to obtain a tremendous amount of genome sequence data from crops as well as from model plants. In combination of advances in assembly techniques of sequences, wide adoption of NGS has lowered the cost of whole genome sequencing, which has allowed the construction of reference genome sequences of various crops. Computational genomics based on reference genomes of crops could give an unprecedented opportunity for analysis of genomic structures for important traits, which would facilitate molecular breeding of crops. To elucidate the current research efforts on computational genomics, studies on small-scale duplication, which has been suggested as a genomic signature of the interaction between crop and environment, were reviewed. Computational genomics approach suggested that smallscale duplication including tandem and ectopic duplication was highly biased to gene families associated with environmental resistance. This indicated that genomic signature of small-scale duplication could be used to make reasonable inference to identify genome sequences associated with traits that would confer environmental resistance. Therefore, for the practical usage of published genomes to accelerate genome-assisted breeding, the structural analysis of the genomes to annotate the tandem/ectopic duplication traces are needed. Moreover, the features of tandem/ectopic duplicates for trait prediction can be exploited for the crop modeling approaches based on genome signatures.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815

    Article  Google Scholar 

  • Bolger ME, Weisshaar B, Scholz U, Stein N, Usadel B et al. 2014. Plant genome sequencing — applications for crop improvement. Curr. Opin. Biotechnol. 26: 31–37

    Article  CAS  PubMed  Google Scholar 

  • Cook DE, Lee TG, Guo X, Melito S, Wang K et al. 2012. Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 338: 1206–1209

    Article  CAS  PubMed  Google Scholar 

  • Dangl JL, Jones JD. 2001. Plant pathogens and integrated defence responses to infection. Nature 411: 826–833

    Article  CAS  PubMed  Google Scholar 

  • DeBolt S. 2010. Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol. Evol. 2: 441–453

    Article  PubMed Central  PubMed  Google Scholar 

  • Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S et al. 2015. The coffee genome hub: a resource for coffee genomes. Nucleic Acids Res. 43: D1028–1035

    Article  PubMed Central  PubMed  Google Scholar 

  • Diaz A, Zikhali M, Turner AS, Isaac P, Laurie DA. 2012. Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PLoS One 7: e33234

    Article  Google Scholar 

  • Du Z, Zhou X, Ling Y, Zhang Z, Su Z. 2010. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38: W64–70

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • French-Constant RH, Daborn PJ, Le Goff G. 2004. The genetics and genomics of insecticide resistance. Trends Genet. 20: 163–170

    Article  Google Scholar 

  • Flor HH. 1954. The genetics of host-parasite interaction in flax rust. Phytopathology 44: 488–488

    Google Scholar 

  • Freeling M. 2009. Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60: 433–453

    Article  CAS  PubMed  Google Scholar 

  • Gachon CMM, Langlois-Meurinne M, Saindrenan P. 2005. Plant secondary metabolism glycosyltransferases: the emerging functional analysis. Trends Plant Sci. 10: 542–549

    Article  CAS  PubMed  Google Scholar 

  • Goff SA, Ricke D, Lan TH, Presting G, Wang RL et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296: 92–100

    Article  CAS  PubMed  Google Scholar 

  • Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH. 2008. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 148: 993–1003

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kang YJ, Kim KH, Shim S, Yoon MY, Sun S et al. 2012. Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean. BMC Plant Biol. 12: 139

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kawano T. 2003. Roles of the reactive oxygen species-generating peroxidase reactions in plant defense and growth induction. Plant Cell Rep 21: 829–837

    CAS  PubMed  Google Scholar 

  • Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY. 2010. Rational association of genes with traits using a genomescale gene network for Arabidopsis thaliana. Nat. Biotechnol. 28: 149–156

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW. 2003. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15: 809–834

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mi HY, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD. 2010. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 38: D204–D210.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Michael TP, VanBuren R. 2015. Progress, challenges and the future of crop genomes. Curr. Opin. Plant Biol. 24C: 71–81

    Article  CAS  PubMed  Google Scholar 

  • Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD et al. 2014. The genome of Eucalyptus grandis. Nature 510: 356–362

    CAS  PubMed  Google Scholar 

  • Okumoto S, Pilot G. 2011. Amino acid export in plants: A missing link in nitrogen cycling. Mol. Plant 4: 453–463

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J et al. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551–556

    Article  CAS  PubMed  Google Scholar 

  • Paterson AH, Freeling M, Tang HB, Wang XY. 2010. Insights from the Comparison of Plant Genome Sequences. Annu. Rev. Plant Biol. 61: 349–372

    Article  CAS  PubMed  Google Scholar 

  • Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N et al. 2005. InterProScan: protein domains identifier. Nucleic Acids Res. 33: W116–W120

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rizzon C, Ponger L, Gaut BS. 2006. Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput. Biol. 2: 989–1000

    Article  CAS  Google Scholar 

  • Salentijn EMJ, Pereira A, Angenent GC, van der Linden CG, Krens F et al. 2006. Plant translational genomics: from model species to crops. Mol. Breed. 20: 1–13

    Article  Google Scholar 

  • Schmutz J, Cannon SB, Schlueter J, Ma JX, Mitros T et al. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463: 178–183

    Article  CAS  PubMed  Google Scholar 

  • Tegeder M, Rentsch D. 2010. Uptake and Partitioning of Amino Acids and Peptides. Mol. Plant 3: 997–1011

    Article  CAS  PubMed  Google Scholar 

  • The Tomato Genome Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635–641

    Article  Google Scholar 

  • UniProt Consortium. 2012. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 40: D71–D75

    Article  Google Scholar 

  • Varshney RK, Ribaut JM, Buckler ES, Tuberosa R, Rafalski JA et al. 2012. Can genomics boost productivity of orphan crops? Nat. Biotechnol. 30: 1172–1176

    CAS  Google Scholar 

  • Wilson D, Madera M, Vogel C, Chothia C, Gough J. 2007. The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res. 35: D308–313

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yang R, Jarvis DE, Chen H, Beilstein MA, Grimwood J et al. 2013. The reference genome of the halophytic plant Eutrema salsugineum. Front. Plant Sci. 4: 46

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yin X, van Laar HH. 2005. Crop Systems Dynamics: An Ecophysiological Model of Genotype-by-Environment Interactions (GECROS). Wageningen Academic Pub., Wageningen

    Google Scholar 

  • Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB et al. 2011. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480: 520–524

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zhang JZ. 2003. Evolution by gene duplication: an update. Trends Ecol.Evol. 18: 292–298

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yang Jae Kang.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kang, Y.J. Small-Scale duplication as a genomic signature for crop improvement. J. Crop Sci. Biotechnol. 18, 45–51 (2015). https://doi.org/10.1007/s12892-015-0027-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12892-015-0027-7

Keywords

Navigation