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.
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
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
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
Dangl JL, Jones JD. 2001. Plant pathogens and integrated defence responses to infection. Nature 411: 826–833
DeBolt S. 2010. Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol. Evol. 2: 441–453
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
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
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
French-Constant RH, Daborn PJ, Le Goff G. 2004. The genetics and genomics of insecticide resistance. Trends Genet. 20: 163–170
Flor HH. 1954. The genetics of host-parasite interaction in flax rust. Phytopathology 44: 488–488
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
Gachon CMM, Langlois-Meurinne M, Saindrenan P. 2005. Plant secondary metabolism glycosyltransferases: the emerging functional analysis. Trends Plant Sci. 10: 542–549
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
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
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
Kawano T. 2003. Roles of the reactive oxygen species-generating peroxidase reactions in plant defense and growth induction. Plant Cell Rep 21: 829–837
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
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
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.
Michael TP, VanBuren R. 2015. Progress, challenges and the future of crop genomes. Curr. Opin. Plant Biol. 24C: 71–81
Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD et al. 2014. The genome of Eucalyptus grandis. Nature 510: 356–362
Okumoto S, Pilot G. 2011. Amino acid export in plants: A missing link in nitrogen cycling. Mol. Plant 4: 453–463
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
Paterson AH, Freeling M, Tang HB, Wang XY. 2010. Insights from the Comparison of Plant Genome Sequences. Annu. Rev. Plant Biol. 61: 349–372
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N et al. 2005. InterProScan: protein domains identifier. Nucleic Acids Res. 33: W116–W120
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
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
Schmutz J, Cannon SB, Schlueter J, Ma JX, Mitros T et al. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463: 178–183
Tegeder M, Rentsch D. 2010. Uptake and Partitioning of Amino Acids and Peptides. Mol. Plant 3: 997–1011
The Tomato Genome Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635–641
UniProt Consortium. 2012. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 40: D71–D75
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
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
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
Yin X, van Laar HH. 2005. Crop Systems Dynamics: An Ecophysiological Model of Genotype-by-Environment Interactions (GECROS). Wageningen Academic Pub., Wageningen
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
Zhang JZ. 2003. Evolution by gene duplication: an update. Trends Ecol.Evol. 18: 292–298
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
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
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12892-015-0027-7