TraitCapture: Genomic and environment modelling of plant phenomic data

Current Opinion in Plant Biology

Volumn 18, Issue 1, 2014, Pages 73-79

  Brown, Tim B ^a   Cheng, Riyan ^a   Sirault, Xavier R R ^b   Rungrat, Tepsuda ^a   Murray, Kevin D ^a   Trtilek, Martin ^a,b,c,d   Furbank, Robert T ^b   Badger, Murray ^a,d   Pogson, Barry J ^a,d   Borevitz, Justin O ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b CSIRO   (Australia)

^c Photon Systems Instruments   (Czech Republic)

^d LA TROBE UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DATA BASE; ENVIRONMENT; GENETICS; GENOMICS; PHENOTYPE; PLANT; PROCEDURES; QUANTITATIVE TRAIT;

DATABASES AS TOPIC; ENVIRONMENT; GENOMICS; PHENOTYPE; PLANTS; QUANTITATIVE TRAIT, HERITABLE;

EID: 84896108501     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2014.02.002     Document Type: Review

References (50)

1. Tester M., Langridge P. Breeding technologies to increase crop production in a changing world. Science 2010, 327:818-822.
2. Cline W.R. Global Warming and Agriculture: Impact Estimates by Country 2007, Peterson Institute.
3. Cooper M., van Eeuwijk F.A., Hammer G.L., Podlich D.W., Messina C. Modeling QTL for complex traits: detection and context for plant breeding. Curr Opin Plant Biol 2009, 12:231-240.
4. Furbank R.T., Tester M. Phenomics-technologies to relieve the phenotyping bottleneck. Trends Plant Sci 2011, 16:635-644.
5. Munns R., James R.A., Sirault X.R., Furbank R.T., Jones H.G. New phenotyping methods for screening wheat and barley for beneficial responses to water deficit. J Exp Bot 2010, 61:3499-3507.
6. Yu J., et al. Genic and non-genic contributions to natural variation of quantitative traits in maize. Genome Res 2012, 22(12):2436-2444.
7. Zhang X., Hause R.J., Borevitz J.O. Natural genetic variation for growth and development revealed by high-throughput phenotyping in Arabidopsis thaliana. G3 (Bethesda) 2012, 2:29-34.
8. Topp C.N., Iyer-Pascuzzi A.S., Anderson J.T., Lee C.R., Zurek P.R., Symonova O., Zheng Y., Bucksch A., Mileyko Y., Galkovskyi T., Moore B.T., Harer J., Edelsbrunner H., Mitchell-Olds T., Weitz J.S., Benfey P.N. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. Proc Natl Acad Sci USA 2013, 110:E1695-E1704.
9. Li Y., et al. PODD: an ontology-driven data repository for collaborative phenomics research. The Role of Digital Libraries in a Time of Global Change 2010, 179-188. Springer, Berlin, Heidelberg.
10. Li Y., Cheng R., Spokas K., Palmer A., Borevitz J. Genetic variation for life history sensitivity to seasonal warming in Arabidopsis thaliana. Genetics 2014, 196(2):569-577. 10.1534/genetics.113.157628.
11. Spokas K., Forcella F. Estimating hourly incoming solar radiation from limited meteorological data. Weed Sci 2006, 54:182-189.
12. Rankine C.J., Sanchez-Azofeifa A., do Espirito-Santo M.M., Viera M.T.S. Optical wireless sensor networks observe leaf phenology and photosynthetic radiation interception in a Brazilian tropical dry forest. Geoscience and Remote Sensing Symposium (IGARSS) 2012, 6914-6915. IEEE International.
13. Anderson Karen, Gaston Kevin J. Lightweight unmanned aerial vehicles will revolutionize spatial ecology. Front Ecol Environ 2013, 11:138-146. 10.1890/120150.
14. Brown, Timothy B., Zimmermann C., Panneton W., Noah N., Borevitz J. High-resolution, time-lapse imaging for ecosystem-scale phenotyping in the field. High Throughput Phenotyping in Plants. Methods in Molecular Biology 2011, Springer, New York. J. Normanly (Ed.).
15. Losos J.B., Arnold S.J., Bejerano G., Brodie E.D., Hibbett D., et al. Evolutionary biology for the 21st century. PLoS Biol 2013, 11:e1001466.
16. Atwell S., Huang Y.S., Vilhjalmsson B.J., Willems G., Horton M., Li Y., Meng D., Platt A., Tarone A.M., Hu T.T., et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 2010, 465:627-631.
17. Wang M., Jiang N., Jia T., Leach L., Cockram J., Comadran J., Shaw P., Waugh R., Luo Z. Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor Appl Genet 2012, 124:233-246.
18. Tian F., Bradbury P.J., Brown P.J., Hung H., Sun Q., Flint-Garcia S., Rocheford T.R., McMullen M.D., Holland J.B., Buckler E.S. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 2011, 43:159-162.
19. Ranc N., Munos S., Xu J., Le Paslier M.C., Chauveau A., Bounon R., Rolland S., Bouchet J.P., Brunel D., Causse M. Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. G3 (Bethesda) 2012, 2:853-864.
20. Huang X., Wei X., Sang T., Zhao Q., Feng Q., Zhao Y., et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 2010, 42:961-967.
21. Kang H.M., Sul J.H., Zaitlen N.A., Kong S.-Y., Freimer N.B., Sabatti C., Eskin E., et al. Variance component model to account for sample structure in genome-wide association studies. Nat Genet 2010, 42:348-354.
22. Zhang Z., Ersoz E., Lai C.-Q., Todhunter R.J., Tiwari H.K., Gore M.A., Bradbury P.J., Yu J., Arnett D.K., Ordovas J.M., et al. Mixed linear model approach adapted for genome-wide association studies. Nat Genet 2010, 42:355-360.
23. Cheng R., Abney M., Palmer A.A., Skol A.D. QTLRel: an R package for genome-wide association studies in which relatedness is a concern. BMC Genet 2011, 12:66.
24. Lippert C., Listgarten J., Liu Y., Kadie C.M., Davidson R.I., Heckerman D. FaST linear mixed models for genome-wide association studies. Nat Methods 2011, 8:833-835.
25. Meyer K., Tier B. 'SNP Snappy': a strategy for fast genome-wide association studies fitting a full mixed model. Genetics 2012, 190:275-277.
26. Zhou X., Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nat Genet 2012, 44:821-824.
27. Seren Ü., Vilhjálmsson B.J., Horton M.W., Meng D., Forai P., Huang Y.S., Long Q., Segura V., Nordborg M. GWAPP: a web application for genome-wide association mapping in Arabidopsis. Plant Cell Online 2012, 24:4793-4805.
28. Grimm D., Greshake B., Kleeberger S., Lippert C., Stegle O., Schkopf B., Weigel D., Borgwardt K. easyGWAS: An integrated interspecies platform for performing genome-wide association studies 2012, arxiv:1212.4788.
29. Jiang C., Zeng Z.-B. Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 1995, 140:1111-1127.
30. Korol A.B., Ronin Y.I., Itskovich A.M., Peng J.H., Nevo E. Enhanced efficiency of quantitative trait loci mapping analysis based on multivariate complexes of quantitative traits. Genetics 2001, 157:789-1803.
31. Lund M.S., Sørensen P., Guldbrandtsen B., Sorensen D. Multitrait fine mapping of quantitative trait loci using combined linkage disequilibria and linkage analysis. Genetics 2003, 163:405-410.
32. Korte A., Vilhjalmsson B.J., Segura V., Platt A., Long Q., Nordborg M. A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nat Genet 2012, 44:1066-1071.
33. Korol A.B., Ronin Y.I., Kirzhner V.M. Interval mapping of quantitative trait loci employing correlated trait complexes. Genetics 1995, 140:1137-1147.
34. Cheng R., Borevitz J., Doerge R.W. Selecting informative traits for multivariate quantitative trait locus mapping helps to gain optimal power. Genetics 2013, 195:683-691.
35. Hanan J. Virtual plants: integrating architectural and physiological models. Environ Model Softw 1997, 12:35-42.
36. Godin C., Sinoquet H. Functional-structural plant modelling. New Phytol 2005, 166:705-708.
37. Vos J., Evers J.B., Buck-Sorlin G.H., Andrieu B., Chelle M., de Visser P.H. Functional-structural plant modelling: a new versatile tool in crop science. J Exp Bot 2010, 61:2101-2115.
38. Xu L., Henke M., Zhu J., Kurth W., Buck-Sorlin G. A functional-structural model of rice linking quantitative genetic information with morphological development and physiological processes. Ann Bot 2011, 107:817-828.
39. Li Y., Huang Y., Bergelson J., Nordborg M., Borevitz J.O. Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2010, 107:21199-21204.
40. De Vylder J., Vandenbussche F.J., Hu Y., Philips W., Van Der Straeten D. Rosette Tracker: an open source image analysis tool for automatic quantification of genotype effects. Plant Physiol 2012, 10.1104/pp.112.202762.
41. Moore C.R., Johnson L.S., Kwak I.-Y., Livny M., Broman K.W., Spalding E.P. High-throughput computer vision introduces the time axis to a quantitative trait map of a plant growth response. Genetics 2013, 195:1077-1086. 10.1534/genetics.113.153346.
42. Meijón Mónica, et al. Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis. Nat Genet 2014, 46:77-81.
43. Ansell P., Furbank R., Gunasekera K., Guo J., Benn D., Williams G., Sirault X. Flexible scientific data management for plant phenomics research. Proceeding of: 10th ESWC 2013 Semantics and Big Data 2013.
44. Paproki A., Sirault X., Berry S., Furbank R., Fripp J. A novel mesh processing based technique for 3D plant analysis. BMC Plant Biol 2012, 12:63.
45. Brachi B., Morris G., Borevitz J. Genome-wide assoc. studies in plants: the missing heritability is in the field. Genet Biol 2011, 12:232.
46. Chenu K., Deihimfard R., Chapman S.C. Large-scale characterization of drought pattern: a continent-wide modelling approach applied to the Australian wheatbelt-spatial and temporal trends. New Phytol 2013, 198:801-820.
47. Wilczek A.M., Roe J.L., Knapp M.C., Cooper M.D., Lopez-Gallego C., Martin L.J., Muir C.D., Sim S., Walker A., Anderson J., Egan J.F., Moyers B.T., Petipas R., Giakountis A., Charbit E., Coupland G., Welch S.M., Schmitt J. Effects of genetic perturbation on seasonal life history plasticity. Science 2009, 323:930-934.
48. Granier C., Vile D. Phenotyping and beyond: modelling the relationships between traits. Curr Opin Plant Biol 2014.
49. Pradal C., Dufour-Kowalski S., Boudon F., Fournier C., Godin C. OpenAlea: a visual programming and component-based software platform for plant modelling. Funct Plant Biol 2008, 35:751-760.
50. Fournier C., Andrieu B. ADEL-maize: an L-system based model for the integration of growth processes from the organ to the canopy. Application to regulation of morphogenesis by light availability. Agronomie 1999, 19:313-327. 10.1051/agro:19990311.