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Unravelling the complex trait of seed quality: using natural variation through a combination of physiology, genetics and -omics technologies

  • Wilco Ligterink (a1), Ronny V.L. Joosen (a1) and Henk W.M. Hilhorst (a1)

Seed quality is a complex trait that is the result of a large variety of developmental processes. The molecular-genetic dissection of these seed processes and their relationship with seed and seedling phenotypes will allow the identification of the regulatory genes and signalling pathways involved and, thus, provide the means to predict and enhance seed quality. Natural variation for seed-quality aspects found in recombinant inbred line (RIL) populations is a great resource to help unravel the complex networks involved in the acquisition of seed quality. Besides extensive phenotyping, RILs can also be profiled by -omics technologies, such as transcriptomics, proteomics and metabolomics in a sophisticated so-called generalized genetical genomics approach. This combined use of physiology, genetics and several -omics technologies, followed by advanced data analysis, allows the construction of regulatory networks involved in the various attributes of seed and seedling quality. This type of analysis of the genetic variation in RIL populations in combination with genome-wide association (GWA) studies will allow a relatively rapid identification of genes that are responsible for quality-related traits of seeds and seedlings. New developments in several -omics technologies, especially the fast-evolving next-generation sequencing techniques, will make a similar system-wide approach more applicable to non-model species in the near future and this will be a huge boost for the potential to breed for seed quality.

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Alonso-Blanco C. and Koornneef M. (2000) Naturally occurring variation in Arabidopsis: An underexploited resource for plant genetics. Trends in Plant Science 5, 2229.
Argyris J., Truco M., Ochoa O., Knapp S., Still D., Lenssen G., Schut J., Michelmore R. and Bradford K. (2005) Quantitative trait loci associated with seed and seedling traits in Lactuca. TAG Theoretical and Applied Genetics 111, 13651376.
Argyris J., Dahal P., Hayashi E., Still D.W. and Bradford K.J. (2008) Genetic variation for lettuce seed thermoinhibition is associated with temperature-sensitive expression of abscisic acid, gibberellin, and ethylene biosynthesis, metabolism, and response genes. Plant Physiology 148, 926947.
Armengaud P., Zambaux K., Hills A., Sulpice R., Pattison R.J., Blatt M.R. and Amtmann A. (2009) EZ-Rhizo: integrated software for fast and accurate measurement of root system architecture. Plant Journal 57, 945956.
Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M. and Sherlock G. (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nature Genetics 25, 2529.
Atwell S., Huang Y.S., Vilhjalmsson B.J., Willems G., Horton M., Li Y., Meng D., Platt A., Tarone A.M., Hu T.T., Jiang R., Muliyati N.W., Zhang X., Amer M.A., Baxter I., Brachi B., Chory J., Dean C., Debieu M., de Meaux J., Ecker J.R., Faure N., Kniskern J.M., Jones J.D.G., Michael T., Nemri A., Roux F., Salt D.E., Tang C., Todesco M., Traw M.B., Weigel D., Marjoram P., Borevitz J.O., Bergelson J. and Nordborg M. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465, 627631.
Bassel G.W., Lan H., Glaab E., Gibbs D.J., Gerjets T., Krasnogor N., Bonner A.J., Holdsworth M.J. and Provart N.J. (2011) Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proceedings of the National Academy of Sciences, USA 108, 97099714.
Baxter I., Brazelton J.N., Yu D., Huang Y.S., Lahner B., Yakubova E., Li Y., Bergelson J., Borevitz J.O., Nordborg M., Vitek O. and Salt D.E. (2010) A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter athkt1;1. PLoS Genetics 6, e1001193.
Bentsink L., Hanson J., Hanhart C.J., Blankestijn-de Vries H., Coltrane C., Keizer P., El-Lithy M., Alonso-Blanco C., de Andres M.T., Reymond M., van Eeuwijk F., Smeekens S. and Koornneef M. (2010) Natural variation for seed dormancy in Arabidopsis is regulated by additive genetic and molecular pathways. Proceedings of the National Academy of Sciences, USA 107, 42644269.
Borevitz J.O., Liang D., Plouffe D., Chang H.S., Zhu T., Weigel D., Berry C.C., Winzeler E. and Chory J. (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Research 13, 513523.
Bourgeois M., Jacquin F., Cassecuelle F., Savois V., Belghazi M., Aubert G., Quillien L., Huart M., Marget P. and Burstin J. (2011) A PQL (protein quantity loci) analysis of mature pea seed proteins identifies loci determining seed protein composition. Proteomics 11, 15811594.
Brachi B., Faure N., Horton M., Flahauw E., Vazquez A., Nordborg M., Bergelson J., Cuguen J. and Roux F. (2010) Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genetics 6, e1000940.
Buckler E. and Gore M. (2007) An Arabidopsis haplotype map takes root. Nature Genetics 39, 10561057.
Clerkx E.J.M., El-Lithy M.E., Vierling E., Ruys G.J., Blankestijn-De Vries H., Groot S.P.C., Vreugdenhil D. and Koornneef M. (2004) Analysis of natural allelic variation of Arabidopsis seed germination and seed longevity traits between the accessions Landsberg erecta and Shakdara, using a new recombinant inbred line population. Plant Physiology 135, 432443.
Dell'Aquila A. (2009) Digital imaging information technology applied to seed germination testing. A review. Agronomy for Sustainable Development 29, 213221.
Dias P., Brunel-Muguet S., Dürr C., Huguet T., Demilly D., Wagner M.-H. and Teulat-Merah B. (2011) QTL analysis of seed germination and pre-emergence growth at extreme temperatures in Medicago truncatula. Theoretical and Applied Genetics 122, 429444.
Dickson M.H. (1980) Genetic-aspects of seed quality. Hortscience 15, 771774.
Doganlar S., Frary A. and Tanksley S.D. (2000) The genetic basis of seed-weight variation: tomato as a model system. Theoretical and Applied Genetics 100, 12671273.
Foolad M.R., Zhang L.P. and Subbiah P. (2003) Genetics of drought tolerance during seed germination in tomato: inheritance and QTL mapping. Genome 46, 536545.
Foolad M.R., Subbiah P. and Zhang L. (2007) Common QTL affect the rate of tomato seed germination under different stress and nonstress conditions. International Journal of Plant Genomics 2007, 97386.
French A., Ubeda-Tomas S., Holman T.J., Bennett M.J. and Pridmore T. (2009) High-throughput quantification of root growth using a novel image-analysis tool. Plant Physiology 150, 17841795.
Galpaz N. and Reymond M. (2010) Natural variation in Arabidopsis thaliana revealed a genetic network controlling germination under salt stress. PLoS ONE 5, e15198.
Gupta V., Mathur S., Solanke A.U., Sharma M.K., Kumar R., Vyas S., Khurana P., Khurana J.P., Tyagi A.K. and Sharma A.K. (2009) Genome analysis and genetic enhancement of tomato. Critical Reviews in Biotechnology 29, 152181.
Hamblin M.T., Buckler E.S. and Jannink J.-L. (2011) Population genetics of genomics-based crop improvement methods. Trends in Genetics 27, 98106.
Harada J.J. (1997) Seed maturation and control of germination. pp. 545592 in Larkins B.; Vasil I. (Eds) Cellular and molecular biology of plant seed development. Dordrecht, Kluwer Academic Publishers.
Hilhorst H.W.M. and Toorop P.E. (1997) Review on dormancy, germinability, and germination in crop and weed seeds. Advances in Agronomy 61, 111165.
Huang X., Schmitt J., Dorn L., Griffith C., Effgen S., Takao S., Koornneef M. and Donohue K. (2010a) The earliest stages of adaptation in an experimental plant population: Strong selection on QTLs for seed dormancy. Molecular Ecology 19, 13351351.
Huang X., Wei X., Sang T., Zhao Q., Feng Q., Zhao Y., Li C., Zhu C., Lu T., Zhang Z., Li M., Fan D., Guo Y., Wang A., Wang L., Deng L., Li W., Lu Y., Weng Q., Liu K., Huang T., Zhou T., Jing Y., Lin Z., Buckler E.S., Qian Q., Zhang Q.F., Li J. and Han B. (2010b) Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics 42, 961967.
Ingvarsson P.K. and Street N.R. (2011) Association genetics of complex traits in plants. New Phytologist 189, 909922.
Jansen R.C. and Nap J.P. (2001) Genetical genomics: the added value from segregation. Trends in Genetics 17, 388391.
Jiménez-Gómez J.M., Wallace A.D. and Maloof J.N. (2010) Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoS Genetics 6, e1001100.
Joosen R.V., Ligterink W., Hilhorst H.W. and Keurentjes J.J. (2009) Advances in genetical genomics of plants. Current Genomics 10, 540549.
Joosen R.V., Kodde J., Willems L.A., Ligterink W., van der Plas L.H. and Hilhorst H.W. (2010) Germinator: a software package for high-throughput scoring and curve fitting of arabidopsis seed germination. Plant Journal 62, 148159.
Jordan M.C., Somers D.J. and Banks T.W. (2007) Identifying regions of the wheat genome controlling seed development by mapping expression quantitative trait loci. Plant Biotechnology Journal 5, 442453.
Keurentjes J.J.B. (2009) Genetical metabolomics: closing in on phenotypes. Current Opinion in Plant Biology 12, 223230.
Keurentjes J.J., Fu J., Terpstra I.R., Garcia J.M., van den Ackerveken G., Snoek L.B., Peeters A.J., Vreugdenhil D., Koornneef M. and Jansen R.C. (2007) Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proceedings of the National Academy of Sciences, USA 104, 17081713.
Kliebenstein D. (2009) Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs. Annual Review of Plant Biology 60, 93114.
Laubinger S., Zeller G., Henz S., Sachsenberg T., Widmer C., Naouar N., Vuylsteke M., Scholkopf B., Ratsch G. and Weigel D. (2008) At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biology 9, R112.
Li Y., Breitling R. and Jansen R.C. (2008) Generalizing genetical genomics: getting added value from environmental perturbation. Trends in Genetics 24, 518524.
Li Y., Breitling R., Snoek L.B., van der Velde K.J., Swertz M.A., Riksen J., Jansen R.C. and Kammenga J.E. (2010a) Global genetic robustness of the alternative splicing machinery in Caenorhabditis elegans. Genetics 186, 405410.
Li Y., Huang Y., Bergelson J., Nordborg M. and Borevitz J.O. (2010b) Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA 107, 2119921204.
Matsui A., Ishida J., Morosawa T., Mochizuki Y., Kaminuma E., Endo T.A., Okamoto M., Nambara E., Nakajima M., Kawashima M., Satou M., Kim J.-M., Kobayashi N., Toyoda T., Shinozaki K. and Seki M. (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant and Cell Physiology 49, 11351149.
McManus C.J., Coolon J.D., Duff M.O., Eipper-Mains J., Graveley B.R. and Wittkopp P.J. (2010) Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Research 20, 816825.
Metzker M.L. (2010) Sequencing technologies – the next generation. Nature Reviews Genetics 11, 3146.
Mockler T.C. and Ecker J.R. (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 115.
Montgomery S.B., Sammeth M., Gutierrez-Arcelus M., Lach R.P., Ingle C., Nisbett J., Guigo R. and Dermitzakis E.T. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773777.
Nesi N., Delourme R., Brégeon M., Falentin C. and Renard M. (2008) Genetic and molecular approaches to improve nutritional value of Brassica napus L. seed. Comptes Rendus Biologies 331, 763771.
Pickrell J.K., Marioni J.C., Pai A.A., Degner J.F., Engelhardt B.E., Nkadori E., Veyrieras J.B., Stephens M., Gilad Y. and Pritchard J.K. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768772.
Potokina E., Druka A., Luo Z., Wise R., Waugh R. and Kearsey M. (2008) Gene expression quantitative trait locus analysis of 16,000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. Plant Journal 53, 90101.
Potokina E., Druka A. and Kearsey M.J. (2009) Transcript profiling and expression level mapping. pp. 8192 in Somers D.J.; Langridge P.; Gustafson J.P. (Eds) Plant genomics. New York, Humana Press.
Powell A.A. (2006) Seed vigor and its assessment. pp. 603648 in Basra A.S. (Ed.) Handbook of seed science and technology. Binghamton, USA, Food Products Press.
Rockman M.V. and Kruglyak L. (2006) Genetics of global gene expression. Nature Reviews Genetics 7, 862872.
Salvi S. and Tuberosa R. (2005) To clone or not to clone plant QTLs: present and future challenges. Trends in Plant Science 10, 297304.
Shi C., Uzarowska A., Ouzunova M., Landbeck M., Wenzel G. and Lübberstedt T. (2007) Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population. BMC Genomics 8, 22.
Shriner D., Vaughan L.K., Padilla M.A. and Tiwari H.K. (2007) Problems with genome-wide association studies. Science 316, 18401842.
Sorkheh K., Malysheva-Otto L.V., Wirthensohn M.G., Tarkesh-Esfahani S. and Martínez-Gómez P. (2008) Linkage disequilibrium, genetic association mapping and gene localization in crop plants. Genetics and Molecular Biology 31, 805814.
Usadel B., Obayashi T., Mutwil M., Giorgi F.M., Bassel G.W., Tanimoto M., Chow A., Steinhauser D., Persson S. and Provart N.J. (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant, Cell & Environment 32, 16331651.
Vandecasteele C., Teulat-Merah B., Morere-LePaven M.C., Leprince O., LyVu B., Viau L., Ledroit L., Pelletier S., Payet N., Satour P., Lebras C., Gallardo K., Huguet T., Limami A.M., Prosperi J.M. and Buitink J. (2011) QTL analysis reveals a correlation between the ratio of sucrose/raffinose family oligosaccharides and seed vigour in Medicago truncatula. Plant, Cell & Environment 34, 14731487.
Varshney R.K., Nayak S.N., May G.D. and Jackson S.A. (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends in Biotechnology 27, 522530.
Vuylsteke M., Van Den Daele H., Vercauteren A., Zabeau M. and Kuiper M. (2006) Genetic dissection of transcriptional regulation by cDNA-AFLP. Plant Journal 45, 439446.
West M.A.L., Van Leeuwen H., Kozik A., Kliebenstein D.J., Doerge R.W., St. Clair D.A. and Michelmore R.W. (2006) High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Research 16, 787795.
West M.A.L., Kim K., Kliebenstein D.J., Van Leeuwen H., Michelmore R.W., Doerge R.W. and St. Clair D.A. (2007) Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics 175, 14411450.
Winter D., Vinegar B., Nahal H., Ammar R., Wilson G.V. and Provart N.J. (2007) An ‘Electronic Fluorescent Pictograph’ browser for exploring and analyzing large-scale biological data sets. PLoS ONE 2, e718.
Zeng D.L., Guo L.B., Xu Y.B., Yasukumi K., Zhu L.H. and Qian Q. (2006) QTL analysis of seed storability in rice. Plant Breeding 125, 5760.
Zhang J., Chiodini R., Badr A. and Zhang G. (2011) The impact of next-generation sequencing on genomics. Journal of Genetics and Genomics 38, 95109.
Zhang X. and Borevitz J.O. (2009) Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics 182, 943954.
Zhang X., Richards E.J. and Borevitz J.O. (2007) Genetic and epigenetic dissection of cis regulatory variation. Current Opinion in Plant Biology 10, 142148.
Zhang X., Byrnes J., Gal T., Li W.-H. and Borevitz J. (2008) Whole genome transcriptome polymorphisms in Arabidopsis thaliana. Genome Biology 9, R165.
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Seed Science Research
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