Statistical methods for data analysis in the complete classification Cultivar × Crop Management × Location × Year (G×M×L×Y) from PVTS
Wiesław Mądry
wieslaw_madry@sggw.ed.plKatedra Doświadczalnictwa i Bioinformatyki, Szkoła Główna Gospodarstwa Wiejskiego, Warszawa (Poland)
Adriana Derejko
Katedra Doświadczalnictwa i Bioinformatyki, Szkoła Główna Gospodarstwa Wiejskiego, Warszawa (Poland)
Abstract
Postregistration Experiments are conducted since 1998 as part of the Post-registration Variety Testing System (PVTS). In this system series of varietal and varietal-agronomic experiments are performed. Experiments in PVTS represent the last stage in the implementation of biological progress to agricultural practice. PVTS is coordinated by the Research Centre for Cultivar Testing in terms of design and methodology. The implementation of a series of experiments in PVTS is held throughout the country in environments (Cultivar Testing Stations) representing well the spatial variability of agro-ecosystems in the major growing areas of the particular plant species in Poland. In this paper the theoretical basis is proposed, as well as classical, adapted and adequately developed statistical methods, i.e. the combined analysis of variance, multiple comparison, AMMI analysis and cluster analysis are presented. Moreover, the usefulness of these methods for analyzing the data in the complete classification of Cultivar × Crop Management × Location Year, coming from PVTS is presented.
Keywords:
mixed linear ANOVA model, combined analysis of variance, AMMI, cluster analysis, PVTSReferences
Annicchiarico P. 2002 a. Defining adaptation strategies and yield stability targets in breeding programmes In: Kang M. S. (Ed.) Quantitative genetics, genomics and plant breeding. CAB, Wallingford, UK: 165 — 183.
Google Scholar
Annicchiarico P. 2002 b. Genotype-environment interactions: challenges and opportunities for plant breeding and cultivar recommendations. FAO Plant Production and Protection Paper No. 174. Food and Agriculture Organization, Rome.
Google Scholar
Annicchiarico P. 2009. Coping with and exploiting genotype × environment interactions. In: Ceccarelli S., Guimarães E. P., Weltzien E. (eds). Plant Breeding and Farmer Participation. Food and Agricultural Organization, Rome: 519 — 564.
Google Scholar
Annicchiarico P., Bellah F., Chiari T. 2006. Repeatable genotype × location interaction and its exploitation by conventional and GIS-based cultivar recommendation for durum wheat in Algeria. Eur. J. Agron. 24: 70 — 81.
Google Scholar
Annicchiarico P., Chiapparino E., Perenzin M. 2010 a. Response of common wheat varieties to organic and conventional production systems across Italian locations and implications for selection. Field Crops Res. 116: 230 — 238.
Google Scholar
Annicchiarico P., Scotti C., Carelli M., Pecetti L. 2010 b. Questions and avenues for lucerne improvement. Czech J. Genet. Plant Breed. 46: 1 — 13.
Google Scholar
Annicchiarico P., Iannucci A. 2008. Adaptation strategy, germplasm type and adaptive traits for field pea improvement in Italy based on variety responses across climatically contrasting environments. Field Crops Res. 108: 133 — 142.
Google Scholar
Annicchiarico P., Pecetti L., Abdelguerfi A., Bouizgaren A., Carroni A. M., Hayek T., M’Hammadi Bouzina M., Mezni M. 2011. Adaptation of landrace and variety germplasm and selection strategies for lucerne in the Mediterranean basin. Field Crops Res. 120: 283 — 291.
Google Scholar
Basford K. E., Cooper M. 1998. Genotype × environment interactions and some considerations of their implications for wheat breeding in Australia. Aust. J. Agric. Res. 49: 153 — 174.
Google Scholar
Brancourt-Hulmel M., Doussinault G., Lecomte C., Berard P., Le Buaec B., Trottet M. 2003. Genetic improvement of agronomic traits of winter wheat cultivars released in France from 1946 to 1992. Crop Sci. 43: 37 — 45.
Google Scholar
Bujak H., Tratwa G. 2011. Ocena stabilności plonowania odmian pszenicy ozimej na podstawie doświadczeń porejestrowych w Polsce. Biul. IHAR 260/261: 69 — 79.
Google Scholar
Caliński T., Czajka S., Kaczmarek Z, Krajewski P. 1998. SERGEN 4 — Analysis of series of variety trials and plant genetic or breeding experiments. Institute of Plant Genetics, Polish Academy of Sciences, and Department of Mathematical and Statistical Methods, Agricultural University, Poznań, Poland.
Google Scholar
Cooper, M., DeLacy I. H., Basford K. E. 1996. Relationships among analytical methods used to study genotypic adaptation in multienvironment trials. in M. Cooper and G. L. Hammer (ed.) Plant adaptation and crop improvement. CABI, Wallingford, UK: 193 — 224.
Google Scholar
Cooper M., Woodruff D. R., Phillips I. G., Basford K. E., Gilmour A. R. 2001. Genotype-by-management interactions for grain yield and grain protein concentration of wheat. Field Crops Res. 69: 47 — 67.
Google Scholar
Crossa J., Cornelius P. L. 2002. Linear-bilinear models for the analysis of genotype-environment interaction In: Kang M.S. (Ed.) Quantitative genetics, genomics and plant breeding. CAB, Wallingford, UK: 305 — 322.
Google Scholar
Crossa J., Cornelius P. L., Yan W. 2002. Biplots of linear-bilinear models for studying crossover genotype x environment interaction Crop Sci. 42: 619 — 633.
Google Scholar
Crossa J., Franco J. 2004. Statistical methods for classifying genotypes. Euphytica 137: 19 — 37.
Google Scholar
Crossa J., Vargas M., Joshi A.K. 2010. Linear, bilinear, and linear-bilinear fixed and mixed models for analyzing genotype x environment interaction in plant breeding and agronomy. Can. J. Plant Sci. 90:561 — 574.
Google Scholar
de la Vega A. J., Chapman S. C. 2006. Defining sunflower selection strategies for a highly heterogeneous target population of environments. Crop Sci. 46: 136 — 144.
Google Scholar
De Vita P., Mastrangelo A. M., Matteu L., Mazzucotelli E., Virzi N., Palumbo M., Lo Storto M., Rizza F., Cattivelli L. 2010. Genetic improvement effects on yield stability in durum wheat genotypes grown in Italy. Field Crops Res. 119: 68 — 77.
Google Scholar
Derejko A., Mądry W., Gozdowski D., Rozbicki J., Golba J., Piechociński M., Studnicki M. 2011. Wpływ odmian, miejscowości i intensywności uprawy oraz ich interakcji na plon pszenicy ozimej w doświadczeniach PDO. Biul. IHAR 259: 131 — 146.
Google Scholar
Ebdon J. S., Gauch H. G. 2002. Additive main effect and multiplicative interactions analysis of national turfgrass performance trials. Interpretation of genotype x environment interactions. Crop Sci. 42: 489 — 496.
Google Scholar
Elandt R. 1964. Statystyka matematyczna w zastosowaniu do doświadczalnictwa rolniczego. PWN, Warszawa.
Google Scholar
Gauch H. G. 1992. Statistical analysis of regional yield trials. AMMI analysis of factorial designs. Elsevier Science, New York.
Google Scholar
Gauch H. G. 2006. Statistical analysis of yield trials by AMMI and GGE. Crop Sci. 46: 1488 — 1500.
Google Scholar
Gauch H. G., Piepho H.P., Annicchiarico P. 2008. Statistical analysis of yield trials by AMMI and GGE: Further considerations. Crop Sci. 48: 866 — 889.
Google Scholar
Gauch H. G., Zobel R. W. 1996. AMMI analysis of yield trials. In: M. S. Kang, H. G. Gauch (Ed.) Genotype by environment interaction. CRC Press, Boca Raton: 85 — 122.
Google Scholar
Gauch H. G., Zobel R. W. 1997. Identifying mega-environments and targeting genotypes. Crop Sci. 37: 311 — 326.
Google Scholar
Johnson R. A., Wichern D. W. 2002. Applied multivariate statistical analysis. Prentice-Hall, Inc. Upper Saddle River, NJ, USA.
Google Scholar
Kang M. S. 1993. Simultaneous selection for yield and stability in crop performance trials: Consequences for growers. Agron. J. 85: 754 — 57.
Google Scholar
Kang M. S. 1998. Using genotype-by environment interaction for crop cultivar development. Adv. Agron. 62: 199 — 253.
Google Scholar
Kang M. S. 2002. Genotype-environment interaction: Progress and prospects In: Kang M.S. (Ed.), Quantitative genetics, genomics and plant breeding, CAB International Wallingford, UK: 221 — 243.
Google Scholar
Krzanowski W. J. 1988. Principles of multivariate analysis: a users’ perspective. Oxford University Press, Oxford.
Google Scholar
Ma B. L., Yan W., Dwyer L. M., Fregeau-Reid J., Voldeng H. D., Dion Y., Nass H. 2004. Graphic analysis of genotype, environment, nitrogen fertilizer, and their interactions on spring wheat yield. Agron. J. 96: 169 — 180.
Google Scholar
Mądry W. 2003. Analiza statystyczna miar stabilności na podstawie danych w klasyfikacji genotypy × środowiska. Część II Model mieszany Shukli i model regresji łącznej. Coll. Biom. 33: 207 — 220.
Google Scholar
Mądry W., Paderewski J., Gozdowski D., Drzazga T. 2011. Adaptive yield response of winter wheat cultivars across environments in Poland using joint AMMI and cluster analyses. Intern. J. Plant Prod. 5: 299 — 310.
Google Scholar
Mądry W., Paderewski J., Rozbicki J., Gozdowski D., Golba J., Piechociński M., Studnicki M., Derejko A. 2012. Plonowanie odmian pszenicy ozimej w różnych środowiskach- jednoroczna seria PDOiR. Biul. IHAR 263:189 — 204.
Google Scholar
McIntosh M. S. 1983. Analysis of combined experiments. Agron. J. 75: 153 — 155.
Google Scholar
Mejza I. 1999. Planowanie serii doświadczeń dwuczynnikowych z rozszczepionymi jednostkami i analiza wyników. Roczniki Akademii Rolniczej w Poznaniu, vol. 301.
Google Scholar
Mintenko A. S., Smith S. R., Cattani D. J. 2002. Turfgrass evaluation of native grasses for the Northern Great Plains Region. Crop Sci. 42: 2018 — 2024.
Google Scholar
Mohammadi R., Amri A. 2013. Genotype × environment interaction and genetic improvement for yield and yield stability of rainfed durum wheat in Iran. Euphytica 192: 227 — 249.
Google Scholar
Mohammadi R., Sadeghzadeh D., Armion M., Amri A. 2011. Evaluation of durum wheat experimental lines under different climate and water regime conditions of Iran. Crop Pasture Sci. 62: 137 — 151.
Google Scholar
Quinn G. P., Keough M. J. 2003. Experimental design and data analysis for biologists. Cambridge University Press, Cambridge.
Google Scholar
Paderewski J. 2008. Przydatność modelu AMMI do badania reakcji roślin rolniczych na warunki środowiskowe. Praca doktorska, Wydział Rolnictwa i Biologii, SGGW.
Google Scholar
Paderewski J., Gauch H. G., Mądry W., Drzazga T., Rodrigues P. C. 2011. Yield response of winter wheat to agro-ecological conditions using additive main effects and multiplicative interaction and cluster analysis. Crop Sci. 51: 969 — 980.
Google Scholar
Pecetti L., Annicchiarico P., Abdelguerfi A., Kallida R., Mefti M., Porqueddu C., Simoes N., Volaire F., Lelievre F. 2011. Response of Mediterranean tall fescue cultivars to contrasting agricultural environments and implications for selection. J. Agron. Crop Sci. 197: 12 — 20.
Google Scholar
Pinnschmidt H. O., Hovmøller M. S. 2002. Genotype × environment interactions in the expression of net blotch resistance in spring and winter barley varieties. Euphytica 125: 227 — 243.
Google Scholar
Samonte S. O. Pb., Wilson L. T., McClung A. M., Medley C. 2005. Targeting cultivars onto rice growing environments using AMMI and SREG GGE biplot analyses. Crop Sci. 45: 2414 — 2424.
Google Scholar
Sivapalan S., O’Brien L., Ortiz-Ferrera G., Hollamby G.J., Barclay I., Martin P.J. 2000. An adaptation analysis of Australian and CIMMYT/ICARDA wheat germplasm in Australian production environments. Aust. J. Agric. Res. 51: 903 — 915.
Google Scholar
Smith A. B., Cullis B.R., Thompson R. 2005. The analysis of crop cultivar breeding and evaluation trials: an overview of current mixed model approaches. J. Agric. Sci. 143: 449 — 462.
Google Scholar
Steinberg W. J. 2011. Statistics Alive. SAGE Publications Inc.: 527 — 529.
Google Scholar
Stiller W. N., Reid P. E., Constable G. A. 2004. Maturity and leaf shape as traits influencing cotton cultivar adaptation to dryland conditions. Agron. J. 96: 656 — 664.
Google Scholar
van Eeuwijk F. A., Keizer L. C. E., Bakker J. J. 1995. Linear and bilinear models for the analysis of multi-environment trials: II. An application to data from the Dutch Maize Variety Trials. Euphytica 84: 9 — 22.
Google Scholar
Welham S. J., Gogel B. J., Smith A. B., Thompson R., Cullis B. R. 2010. A comparison of analysis methods for late stage variety evaluation trials. Aust. N. Z. J. Stat. 52: 125 — 149.
Google Scholar
Wójcik A. R., Laudański Z. 1989. Planowanie i wnioskowanie statystyczne w doświadczalnictwie. PWN.
Google Scholar
Yan W., M.S. Kang. 2003. GGE biplot analysis: A graphical tool for breeders, geneticists, and agronomists. CRC Press, Boca Raton, FL.
Google Scholar
Zhang Y., He Z., Zhang A., van Ginkel M., Pena R. J., Ye G. 2006. Pattern analysis on protein properties of Chinese and CIMMYT spring wheat cultivars sown in China and CIMMYT. Austr. J. Agric. Res. 57: 811 — 822.
Google Scholar
Authors
Wiesław Mądrywieslaw_madry@sggw.ed.pl
Katedra Doświadczalnictwa i Bioinformatyki, Szkoła Główna Gospodarstwa Wiejskiego, Warszawa Poland
Authors
Adriana DerejkoKatedra Doświadczalnictwa i Bioinformatyki, Szkoła Główna Gospodarstwa Wiejskiego, Warszawa Poland
Statistics
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