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

Seed Science Research

Volumn 22, Issue SUPPL. 1, 2012, Pages

  Ligterink, Wilco ^a   Joosen, Ronny V L ^a   Hilhorst, Henk W M ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

omics techno logies; genetical genomics; genome wide association studies; high throughput phenotyping; quantitative trait locus analysis; seed quality

Indexed keywords

EID: 84855769227     PISSN: 09602585     EISSN: None     Source Type: Journal    
DOI: 10.1017/S0960258511000328     Document Type: Review

References (68)

1. Alonso-Blanco, C. and Koornneef, M. (2000) Naturally occurring variation in Arabidopsis: An underexploited resource for plant genetics. Trends in Plant Science 5, 22-29. (Pubitemid 30445966)
2. 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 111,1365-1376. (Pubitemid 41634685)
3. 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, 926-947. (Pubitemid 352847549)
4. 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, 945-956.
5. 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, 25-29. (Pubitemid 30257031)
6. 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, 627-631.
7. 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 coordi-nated regulation of plant cellular phase transitions. Proceedings of the National Academy of Sciences, USA 108, 9709-9714.
8. 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. PLo S Genetics 6, e1001193.
9. 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, 4264-4269.
10. 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 poly-morphisms in complex genomes. Genome Research 13, 513-523. (Pubitemid 36395410)
11. 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, 1581-1594.
12. 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. PLo S Genetics 6, e1000940.
13. Buckler, E. and Gore, M. (2007) An Arabidopsis haplotype map takes root. Nature Genetics 39,1056-1057. (Pubitemid 47340639)
14. 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, 432-443. (Pubitemid 38653689)
15. Dell'Aquila, A. (2009) Digital imaging information techno-logy applied to seed germination testing. A review. Agronomy for Sustainable Development 29, 213-221.
16. 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, 429-444.
17. Dickson, M.H. (1980) Genetic-aspects of seed quality Hortscience 15, 771-774.
18. 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, 1267-1273. (Pubitemid 30427787)
19. 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, 536-545. (Pubitemid 37144152)
20. 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.
21. 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, 1784-1795.
22. Galpaz, N. and Reymond, M. (2010) Natural variation in Arabidopsis thaliana revealed a genetic network control-ling germination under salt stress. PLo S ONE 5, e15198.
23. 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 29,152-181.
24. Hamblin, M.T., Buckler, E.S. and Jannink, J.-L. (2011) Population genetics of genomics-based crop improve-ment methods. Trends in Genetics 27, 98-106.
25. Harada, J.J. (1997) Seed maturation and control of germina-tion. pp. 545-592 in Larkins, B.; Vasil, I. (Eds) Cellular and molecular biology of Plant seed development. Dordrecht, Kluwer Academic Publishers.
26. Hilhorst, H.W.M. and Toorop, P.E. (1997) Review on dormancy germinability and germination in crop and weed seeds. Advances in Agronomy 61,111-165.
27. 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 19,1335-1351.
28. 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 agro-nomic traits in rice landraces. Nature Genetics 42, 961-967.
29. Ingvarsson, P.K. and Street, N.R. (2011) Association genetics of complex traits in plants. New Phytologist 189, 909-922.
30. Jansen, R.C. and Nap, J.P. (2001) Genetical genomics: the added value from segregation. Trends in Genetics 17, 388-391. (Pubitemid 32545383)
31. 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. PLo S Genetics 6, e1001100.
32. Joosen, R.V., Ligterink, W., Hilhorst, H.W. and Keurentjes, J.J. (2009) Advances in genetical genomics of plants. Current Genomics 10, 540-549.
33. 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, 148-159.
34. 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, 442-453. (Pubitemid 46558329)
35. Keurentjes, JJ.B. (2009) Genetical metabolomics: closing in on phenotypes. Current Opinion in Plant Biology 12, 223-230.
36. 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, 1708-1713. (Pubitemid 46214655)
37. Kliebenstein, D. (2009) Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or e QTLs. Annual Review of Plant Biology 60, 93-114.
38. 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.
39. Li, Y., Breitling, R. and Jansen, R.C. (2008) Generalizing genetical genomics: getting added value from environ-mental perturbation. Trends in Genetics 24, 518-524.
40. 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, 405-410.
41. 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, 21199-21204.
42. 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 con-ditions using a tiling array. Plant and Cell Physiology 49, 1135-1149.
43. Mc Manus, 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 m RNA-seq. Genome Research 20, 816-825.
44. Metzker, M.L. (2010) Sequencing technologies - the next generation. Nature Reviews Genetics 11, 31-46.
45. Mockler, T.C. and Ecker, J.R. (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 1-15. (Pubitemid 39655686)
46. 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 popu-lation. Nature 464, 773-777.
47. 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, 763-771.
48. 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 vari-ation with RNA sequencing. Nature 464, 768-772.
49. 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, 90-101. (Pubitemid 350265242)
50. Potokina, E., Druka, A. and Kearsey, M.J. (2009) Transcript profiling and expression level mapping. pp. 81-92 in Somers, D.J.; Langridge, P.; Gustafson, J.P. (Eds) Plant genomics. New York, Humana Press.
51. Powell, A.A. (2006) Seed vigor and its assessment. pp. 603-648 in Basra, A.S. (Ed.) Handbook ofseed science and technology. Binghamton, USA, Food Products Press.
52. Rockman, M.V. and Kruglyak, L. (2006) Genetics of global gene expression. Nature Reviews Genetics 7, 862-872. (Pubitemid 44607102)
53. Salvi, S. and Tuberosa, R. (2005) To clone or not to clone plant QTLs: present and future challenges. Trends in Plant Science 10, 297-304. (Pubitemid 40793516)
54. Shi, C., Uzarowska, A., Ouzunova, M., Landbeck, M., Wenzel, G. and Lübberstedt, T. (2007) Identification of candidate genes associated with cell wall digestibility and e QTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population. BMC Genomics 8, 22.
55. Shriner, D., Vaughan, L.K., Padilla, M.A. and Tiwari, H.K. (2007) Problems with genome-wide association studies. Science 316, 1840-1842.
56. Sorkheh, K., Malysheva-Otto, L.V., Wirthensohn, M.G., Tarkesh-Esfahani, S. and Mart́nez-Gómez, P. (2008) Linkage disequilibrium, genetic association mapping and gene localization in crop plants. Genetics and Molecular Biology 31, 805-814.
57. 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, 1633-1651.
58. Vandecasteele, C., Teulat-Merah, B., Morere-Le Paven, M.C., Leprince, O., Ly Vu, 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 34,1473-1487.
59. 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 27,522-530.
60. Vuylsteke, M., Van Den Daele, H., Vercauteren, A., Zabeau, M. and Kuiper, M. (2006) Genetic dissection of transcriptional regulation by c DNA-AFLP. Plant Journal 45,439-446. (Pubitemid 43373725)
61. West, MA.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, 787-795. (Pubitemid 43830699)
62. 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 e QTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics 175, 1441-1450. (Pubitemid 46798243)
63. 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 largescale biological data sets. PLo S ONE 2, e718.
64. 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, 57-60.
65. Zhang, J., Chiodini, R., Badr, A. and Zhang, G. (2011) The impact of next-generation sequencing on genomics. Journal of Genetics and Genomics 38, 95-109.
66. Zhang, X. and Borevitz, J.O. (2009) Global analysis of allelespecific expression in Arabidopsis thaliana. Genetics 182, 943-954.
67. Zhang, X., Richards, E.J. and Borevitz, J.O. (2007) Genetic and epigenetic dissection of cis regulatory variation. Current Opinion in Plant Biology 10, 142-148. (Pubitemid 46330118)
68. Zhang, X., Byrnes, J., Gal, T., Li, W.-H. and Borevitz, J. (2008) Whole genome transcriptome polymorphisms in Arabidopsis thaliana. Genome Biology 9, R165.