Mixed model analysis combining disease ratings and DNA sequences to determine host range of Uromyces salsolae for biological control of Russian thistle

Biological Control

Volumn 49, Issue 1, 2009, Pages 68-76

  Berner, D K ^a   Bruckart, W L ^a   Cavin, C A ^a   Michael, J L ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Animal model; BLUP; Classical biological control; Disease prediction; GDATA; Henderson's mixed model equations; Host range testing; Invasive weeds; MME; Plant pathogens; PROC MIXED; Quartet puzzling; Reduced animal model; Relationship matrix; Rust fungus; Salsola tragus; SAS; Uromyces salsolae

Indexed keywords

ANIMALIA; FUNGI; SALSOLA; SALSOLA TRAGUS; UREDINALES; UROMYCES SALSOLAE;

EID: 60749119971     PISSN: 10499644     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biocontrol.2009.01.001     Document Type: Article

References (41)

1. Akhani H., Edwards G., and Roalson E.H. Diversification of the old world Salsoleae s.I. (Chenopodiaceae): molecular phylogenetic analysis of nuclear and chloroplast data sets and a revised classification. International Journal of Plant Science 168 (2007) 931-956
2. Bridge P.D., Roberts P.J., Spooner B.M., and Panchal G. On the unreliability of published DNA sequences. New Phytologist 160 (2003) 43-48
3. Briese D.T., and Walker A. A new perspective on the selection of test plants for evaluating the host-specificity of weed biological control agents: the case of Deuterocampta quadrijuga, a potential insect control agent of Heliotropium amplexicaule. Biological Control 25 (2002) 273-287
4. Crompton C.W., and Bassett I.J. The biology of Canadian weeds. 65. Salsola pestifer A. Nels. Canadian Journal of Plant Science 65 (1985) 379-388
5. Farr, D.F., Rossman, A.Y., Palm, M.E., McCray, E.B. (n.d.) 2006. Fungal Databases, Systematic Botany and Mycology Laboratory, ARS, USDA. Retrieved March 17, 2006. Available from: .
6. Felsenstein J. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5 (1989) 164-166
7. Garcia-Jacas N., Garnatje T., Susanna A., and Vilatersana R. Tribal and subtribal delimitation and phylogeny of the Cardueae (Asteraceae): a combined nuclear and chloroplast DNA analysis. Molecular Phylogenetics and Evolution 22 (2002) 51-64
8. Gaskin J.F., Ryan F.J., Hrusa G.F., and Londo J.P. Genotype diversity of Salsola tragus and potential origins of a previously unidentified invasive Salsola from California and Arizona. Madroño 53 (2006) 244-251
9. Harville D.A. Extension of the Gauss-Markov theorem to include the estimation of random effects. Annals of Statistics 4 (1976) 384-395
10. Harville D.A. Maximum likelihood approaches to variance component estimation and to related problems. Journal of the American Statistician Association 72 (1977) 320-338
11. Henderson C.R. Best linear unbiased prediction under a selection model. Biometrics 31 (1975) 423-447
12. Henderson C.R. Best linear unbiased prediction of breeding values not in the model for records. Journal of Dairy Science 60 (1977) 783-787
13. Henderson C.R., and Quaas R.L. Multiple trait evaluation using relatives' records. Journal of Animal Science 43 (1976) 1188-1197
14. Hibbett D.S., et al. A higher-level phylogenetic classification of the fungi. Mycological Research 111 (2007) 509-547
15. Housworth E.A., Martins E.P., and Lynch M. The phylogenetic mixed model. The American Naturalist 163 (2004) 84-96
16. International Bull Evaluation Service 2007. Interbull Centre, P.O. Box 7023, SE-750 07 Uppsala, Sweden. Available from: (cited 18.12.2007).
17. Kartesz, J.T., Meacham, C.A. 1999. Synthesis of the North American Flora, Version 1.0., North Carolina Botanical Garden, Chapel Hill, N.C.
18. Kelch D.G., and Baldwin B.G. Phylogeny and ecological radiation of New World thistles (Cirsium, Cardueae-Compositae) based on ITS and ETS rDNA sequence data. Molecular Ecology 12 (2003) 141-151
19. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., and Higgins D.G. ClustalW2 and ClustalX version 2. Bioinformatics 23 (2007) 2947-2948
20. McLean, R.A. 1989. An introduction to general linear models. In: L.S.U. Department of Experimental Statistics, Applications of Mixed Models in Agriculture and Related Disciplines. Southern Cooperative Series Bulletin 343. Baton Rouge: Southern Regional Project S-189, pp. 9-38
21. McRae, T.A., Apiolaza, L.A., Dutkowski, G.W., Kerr, R.J., Pilbeam, D.J., Powell, M.B., Tier, B. 2003. TREEPLAN-A genetic evaluation system for forest trees. Stillwater, OK, USA, 27th Southern Forest Tree Improvement Conference, 25-27 June 2003. Available from: .
22. Nilsson R.H., Ryberg M., Kristiansson E., Abarenkov K., Karsson K.-H., and Koljalg U. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS ONE e59 (2006) 1-4
23. Page R.D.M. TREEVIEW: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12 (1996) 357-358
24. Penny, D., Hendy, M.D., Holland, B.R. 2007. Phylogenetics: parsimony, networks, and distance methods. In: Balding, D.J., Bishop, M., Cannings, C. (Eds.), Handbook of Statistical Genetics, third ed. (2 vols.) vol. 1. John Wiley & Sons, West Sussex, England, pp. 489-532.
25. Pyankov V.I., Artyusheva E.G., Edwards G.E., Black Jr. C.C., and Soltis P.S. Phylogenetic analysis of tribe Salsoleae (Chenopodiaceae) based on ribosomal ITS sequences: implications for the evolution of photosynthesis types. American Journal of Botany 88 (2001) 1189-1198
26. Rilke, S., 1999. Revision der Sektion Salsola s.l. der Gattung Salsola (Chenopodiaceae). Bibliotheca botanica, Heft 149. E. Schweizerbart'sche Verlagsbuchhandlung (Nagele u. Obermiller), Stuttgart, 189 p.
27. Saari L.L., Cotterman J.C., Smith W.F., and Primiani M.M. Sulfonylurea herbicide resistance in common chickweed, perennial ryegrass, and Russian thistle. Pesticide Biochemistry and Physiology 42 (1992) 110-118
28. ® 9.1.3. SAS Institute Inc., Cary, NC.
29. Saxton, A.M. 1998. A macro for converting mean separation output to letter groupings in Proc Mixed. In: Proceedings of 23rd SAS Users Group International, SAS Institute, Cary, NC, pp. 1243-1246.
30. Schabenberger O., and Pierce F.J. Contemporary Statistical Models for the Plant and Soil Sciences (2002), CRC Press, Boca Raton 738 pp
31. Schmidt H.A., Strimmer K., Vingron M., and von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 (2002) 502-504
32. Shah D.A., and Madden L.V. Nonparametric analysis of ordinal data in designed experiments. Phytopathology 94 (2004) 33-43
33. Strimmer K., and von Haeseler A. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Molecular Biology and Evolution 13 (1996) 964-969
34. USDA, APHIS. 2007. Technical Advisory Group for Biological Control Agents of Weeds Available from: .
35. USDA, ARS, National Genetic Resources Program. 2008. Germplasm Resources Information Network - (GRIN) [Online Database]. National Germplasm Resources Laboratory, Beltsville, Maryland. Available from: URL: (accessed 17.7.2008).
36. USDA, NRCS. 2008. The PLANTS Database. Available from: (accessed 3.1.2008). National Plant Data Center, Baton Rouge, LA 70874-4490 USA.
37. Wapshere A.J. A strategy for evaluating the safety of organisms for biological weed control. Annals of Applied Biology 77 (1974) 201-211
38. White T.J., Bruns T., Lee S., and Taylor J.W. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.A., Gelfand D.H., Sninsky J.J., and White T.J. (Eds). PCR Protocols: A Guide to Methods and Applications (1990), Academic Press, Inc., New York 315-322
39. Wilken D.H. Chenopodiaceae. In: Hickman J.C. (Ed). The Jepson Manual: Higher Plants of California (1993), Univ. California Press, Berkeley, CA 500-515
40. Young, F., Veseth, R., Thill, D., Schillinger, W., Ball, D., 1995. Managing Russian thistle under conservation tillage in crop-fallow rotations. In: Pacific Northwest Conservation Tillage Handbook. Pacific Northwest Extension Publications, PNW492, Washington State University, Pullman, 12 p.
41. Young J.A., and Evans R.A. Russian thistle-the weed that won the west. Weeds Today 16 (1985) 4-7