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Next-generation genebanking: plant genetic resources management and utilization in the sequencing era

Published online by Cambridge University Press:  20 February 2014

Rob van Treuren  and
Theo J. L. van Hintum
Rob van Treuren*
Affiliation:
Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research Centre, PO Box 16, NL-6700 AA Wageningen, The Netherlands
Theo J. L. van Hintum
Affiliation:
Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research Centre, PO Box 16, NL-6700 AA Wageningen, The Netherlands
*
* Corresponding author. E-mail: [email protected]
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Abstract

Advances in sequencing technologies have made it possible to analyse large amounts of germplasm against low production costs, which has opened the door to screen genebank collections more efficiently for DNA sequence variation. The present study explores how these developments may affect the operations of genebanks and, consequently, how genebank agendas may change. It is argued that the new developments are more likely to have an impact on the user-oriented activities than the housekeeping operations of genebanks. To better facilitate the user community, genebanks may have to strengthen their core business, in particular, by improving quality management procedures and by providing access to a wider diversity of a crop's gene pool. In addition, genebanks may have to provide novel services, such as the introduction of specific user-oriented collection types, including research populations and genetically purified lines, and the development of novel information services, including plant genetic resources portals that should guide users to the information and materials of specific interest. To improve their user-oriented services, genebanks need to increase their communication and collaboration with the user community and to develop strategic alliances with this sector.

Keywords

genebank servicesgenomicsgermplasm utilizationnext-generation sequencing
Type
Research Article
Information
Plant Genetic Resources , Volume 12 , Issue 3 , December 2014 , pp. 298 - 307
Copyright
Copyright © NIAB 2014 

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References

AEGIS (2013) A European Genebank Integrated System. Available at http://aegis.cgiar.org/ (accessed April 2013)..Google Scholar
Agarwal, M, Shrivastava, N and Padh, H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports 27: 617–631.CrossRefGoogle ScholarPubMed
Avraham, S, Tung, CW, Ilic, K, Jaiswal, P, Kellogg, EA, McCouch, S, Pujar, A, Reiser, L, Rhee, SY, Sachs, MM, Schaeffer, M, Stein, L, Stevens, P, Vincent, L, Zapata, F and Ware, D (2008) The plant ontology database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research 36 (Suppl. 1): D449–D454.Google Scholar
Brachi, B, Morris, GP and Borevitz, JO (2011) Genome-wide association studies in plants: the missing heritability is in the field. Genome Biology 12: 232.CrossRefGoogle ScholarPubMed
CGN (2013) Plant Genetic Resources – CGN collection missions. Available at http://www.cgn.wur.nl.Google Scholar
CGP (2013) The Compositae Genome Project. Available at http://compgenomics.ucdavis.edu.Google Scholar
CGRFA (2012) Draft updated genebank standards: minimum standards for conservation of orthodox seeds. Food and Agriculture Organization of the United Nations, Rome, Italy. Available at http://www.fao.org/fileadmin/templates/agphome/documents/PGR/ITWG/ITWG5/dugbs-NFP-6jan2011.pdf.Google Scholar
Clark, MJ, Chen, R, Lam, HYK, Karczewski, KJ, Chen, R, Euskirchen, G, Butte, AJ and Snyder, M (2011) Performance comparison of exome DNA sequencing technologies. Nature Biotechnology 29: 908–914.Google Scholar
Cobb, JN, DeClerck, G, Greenberg, A, Clark, R and McCouch, S (2013) Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement. Theoretical and Applied Genetics 126: 867–887.Google Scholar
CoGePedia (2013) Sequenced plant genomes. Available at http://www.genomevolution.org (accessed March 2013).Google Scholar
Collard, BCY and Mackill, DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences 363: 557–572.CrossRefGoogle ScholarPubMed
Crop Wild Relatives and Climate Change (2013) Online resource. Available at http://www.cwrdiversity.org (accessed July 2013)..Google Scholar
Davey, JW and Blaxter, ML (2010) RADSeq: next-generation population genetics. Briefings in Functional Genomics 9: 416–423.CrossRefGoogle ScholarPubMed
Delseny, M, Hanb, B and Hsing, Y (2010) High-throughput DNA sequencing: the new sequencing revolution. Plant Science 179: 407–422.Google Scholar
Edwards, D and Batley, J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnology Journal 8: 2–9.Google Scholar
Egan, AN, Schlueter, J and Spooner, DM (2012) Applications of next-generation sequencing in plant biology. American Journal of Botany 99: 175–185.Google Scholar
Ekblom, R and Galindo, J (2011) Applications of next-generation sequencing in molecular ecology of non-model organisms. Heredity 107: 1–15.CrossRefGoogle ScholarPubMed
Elshire, RJ, Glaubitz, JC, Sun, Q, Poland, JA, Kawamoto, K, Buckler, ES and Mitchell, ES (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLOS ONE 6: e19379, doi:10.1371/journal.pone.0019379.Google Scholar
Engels, JMM and Maggioni, L (2012) AEGIS: a regionally based approach to PGR conservation. In: Maxted, N, Dulloo, ME, Ford-Lloyd, BV, Frese, L, Iriondo, J and Pinheiro de Carvalho, MAA (eds) Agrobiodiversity Conservation: Securing the Diversity of Crop Wild Relatives and Landraces. Wallingford, UK: CABI, pp. 321–326.Google Scholar
Engels, JMM and Visser, L (2003) A guide to effective management of germplasm collections. IPGRI Handbooks for Genebanks No. 6. Rome, Italy: IPGRI.Google Scholar
Furbank, RT and Tester, M (2011) Phenomics – technologies to relieve the phenotyping bottleneck. Trends in Plant Science 16: 635–644.CrossRefGoogle ScholarPubMed
Glaszmann, JC, Kilian, B, Upadhyaya, HD and Varshney, RK (2010) Accessing genetic diversity for crop improvement. Current Opinion in Plant Biology 13: 167–173.Google Scholar
Hall, N (2013) After the gold rush. Genome Biology 14: 115.Google Scholar
Hall, D, Tegström, C and Ingvarsson, PK (2010) Using association mapping to dissect the genetic basis of complex traits in plants. Briefings in Functional Genomics 9: 157–165.Google Scholar
Horner, DS, Pavesi, G, Castrignanò, T, D'Onorio De Meo, P, Liuni, S, Sammeth, M, Picardi, E and Pesole, G (2010) Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Briefings in Bioinformatics 11: 181–197.Google Scholar
Huang, X, Lu, T and Han, B (2013) Resequencing rice genomes: an emerging new era of rice genomics. Trends in Genetics 29: 225–232.CrossRefGoogle ScholarPubMed
Illumina (2013) Specification sheet HiSeq® 1500/2500 sequencing systems. Available at http://www.illumina.com (accessed March 2013).Google Scholar
Jannink, JL, Lorenz, AJ and Iwata, H (2010) Genomic selection in plant breeding: from theory to practice. Briefings in Functional Genomics 9: 166–177.Google Scholar
Jarvis, A, Lane, A and Hijmans, RJ (2008) The effect of climate change on crop wild relatives. Agriculture, Ecosystems & Environment 126: 13–23.Google Scholar
Jiao, Y, Zhao, H, Ren, L, Song, W, Zeng, B, Guo, J, Wang, B, Liu, Z, Chen, J, Li, W, Zhang, M, Xie, S and Lai, J (2012) Genome-wide genetic changes during modern breeding of maize. Nature Genetics 44: 812–817.CrossRefGoogle ScholarPubMed
Khoury, C, Laliberté, B and Guarino, L (2010) Trends in ex situ conservation of plant genetic resources: a review of global crop and regional conservation strategies. Genetic Resources and Crop Evolution 57: 625–639.Google Scholar
Kilian, B and Graner, A (2012) NGS technologies for analyzing germplasm diversity in genebanks. Briefings in Functional Genomics 11: 38–50.Google Scholar
Knoll, J and Ejeta, G (2008) Marker-assisted selection for early-season cold tolerance in sorghum: QTL validation across populations and environments. Theoretical and Applied Genetics 116: 541–553.Google Scholar
Lee, HC, Lai, K, Lorenc, MT, Imelfort, M, Duran, C and Edwards, D (2012) Bioinformatics tools and databases for analysis of next-generation sequence data. Briefings in Functional Genomics 11: 12–24.CrossRefGoogle ScholarPubMed
Lister, R and Ecker, JR (2009) Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Research 19: 959–966.Google Scholar
Lorenz, AJ, Chao, S, Asoro, FG, Heffner, EL, Hayashi, T, Iwata, H, Smith, KP, Sorrells, ME and Jannink, JL (2011) Genomic selection in plant breeding: knowledge and prospects. In: Sparks, DL (ed.) Advances in Agronomy, vol. 110. San Diego, CA: Academic press, pp. 77–123.Google Scholar
Mauricio, R (2001) Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology. Nature Reviews Genetics 2: 370–381.Google Scholar
Maxted, N, Dulloo, E, Ford-Lloyd, BV, Iriondo, JM and Jarvis, A (2008) Gap analysis: a tool for complementary genetic conservation assessment. Diversity and Distributions 14: 1018–1030.CrossRefGoogle Scholar
Maxted, N, Kell, S, Ford-Lloyd, BV, Dulloo, ME and Toledo, A (2012) Toward the systematic conservation of global crop wild relative diversity. Crop Science 52: 774–785.CrossRefGoogle Scholar
McCouch, SR, McNally, KL, Wang, W and Sackville Hamilton, R (2012) Genomics of gene banks: a case study in rice. American Journal of Botany 99: 407–423.Google Scholar
Metzker, ML (2010) Sequencing technologies – the next generation. Nature Reviews Genetics 11: 31–46.CrossRefGoogle ScholarPubMed
Mir, RR and Varshney, RK (2012) Future prospects of molecular markers in plants. In: Henry, RJ (ed.) Molecular Markers in Plants. Oxford, UK: Blackwell Publishing, pp. 169–190.Google Scholar
Rafalski, JA (2010) Association genetics in crop improvement. Current Opinion in Plant Biology 13: 174–180.Google Scholar
Ramírez-Villegas, J, Khoury, C, Jarvis, A, Debouck, DG and Guarino, L (2010) A gap analysis methodology for collecting crop genepools: a case study with Phaseolus beans. PLOS ONE 5: e13497 , doi:10.1371/journal.pone.0013497 Google Scholar
Robertson, G, Hirst, M, Bainbridge, M, Bilenky, M, Zhao, Y, Zeng, T, Euskirchen, G, Bernier, B, Varhol, R, Delaney, A, Thiessen, N, Griffith, OL, He, A, Marra, M, Snyder, M and Jones, S (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods 4: 651–657.Google Scholar
Ruder, K and Winstead, ER (2013) A quick guide to sequenced genomes. Genome News Network. Available at http://www.genomenewsnetwork.org/ (accessed March 2013).Google Scholar
Shrestha, R, Matteis, L, Skofic, M, Portugal, A, McLaren, G, Hyman, G and Arnaud, E (2012) Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice. Frontiers in Physiology 3: 326.CrossRefGoogle ScholarPubMed
Spooner, D, van Treuren, R and de Vicente, MC (2005) Molecular Markers for Genebank Management. IPGRI Technical Bulletin No. 10 . Rome, Italy: International Plant Genetic Resources Institute.Google Scholar
Thormann, I, Yang, Q, Allender, C, Bas, N, Campbell, G, Dulloo, ME, Ebert, AW, Lohwasser, U, Pandey, C, Robertson, LD and Spellman, O (2013) Development of best practices for ex situ conservation of radish germplasm in the context of the crop genebank knowledge base. Genetic Resources and Crop Evolution 60: 1251–1262.Google Scholar
Thudi, M, Li, Y, Jackson, SA, May, GD and Varshney, RK (2012) Current state-of-art of sequencing technologies for plant genomics research. Briefings in Functional Genomics 11: 3–11.Google Scholar
Van Hintum, TJL and van Treuren, R (2002) Molecular markers: tools to improve genebank efficiency. Cellular and Molecular Biology Letters 7: 737–744.Google Scholar
Van Hintum, TJL, van de Wiel, CCM, Visser, DL, van Treuren, R and Vosman, B (2007) The distribution of genetic variation in a Brassica oleracea genebank collection related to the effects on diversity of regeneration, as measured with AFLPs. Theoretical and Applied Genetics 114: 777–786.CrossRefGoogle Scholar
Van Treuren, R, Coquin, P and Lohwasser, U (2012) Genetic resources collections of leafy vegetables (lettuce, spinach, chicory, artichoke, asparagus, lamb's lettuce, rhubarb and rocket salad): composition and gaps. Genetic Resources and Crop Evolution 59: 981–997.Google Scholar
Van Treuren, R, Engels, JMM, Hoekstra, R and van Hintum, TJL (2009) Optimization of the composition of crop collections for ex situ conservation. Plant Genetics Resources: Characterization and Utilization 7: 185–193.Google Scholar
Van Treuren, R, van der Arend, AJM and Schut, JW (2013) Distribution of downy mildew (Bremia Lactucae Regel) resistances in a genebank collection of lettuce and its wild relatives. Plant Genetics Resources: Characterization and Utilization 11: 15–25.Google Scholar
Van Treuren, R, van Hintum, TJL and van de Wiel, CCM (2008) Marker-assisted optimization of an expert-based strategy for the acquisition of modern lettuce varieties to improve a genebank collection. Genetic Resources and Crop Evolution 55: 319–330.Google Scholar
Varshney, RK, Nayak, SN, May, GD and Jackson, SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends in Biotechnology 27: 522–530.Google Scholar
Wallace, JG, Larsson, SJ and Buckler, ES (2013) Entering the second century of maize quantitative genetics. Heredity 112: 30–38 , doi:10.1038/hdy.2013.6 Google Scholar
Wang, Z, Gerstein, M and Snyder, M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10: 57–63.Google Scholar
Wetterstrand, KA (2013) DNA sequencing costs: data from the NHGRI Genome Sequencing Program (GSP). Available at http://www.genome.gov/sequencingcosts (accessed March 2013).Google Scholar
WUR (2013) 150 Tomato Genome ReSequencing Project. Available at http://www.tomatogenome.net/index.html.Google Scholar