scholarly journals AMMI and GGE Biplot for genotype × environment interaction: a medoid–based hierarchical cluster analysis approach for high–dimensional data

2018 ◽  
Vol 55 (2) ◽  
pp. 97-121 ◽  
Author(s):  
Anderson Cristiano Neisse ◽  
Jhessica Letícia Kirch ◽  
Kuang Hongyu
Keyword(s):  
Cluster Analysis ◽  
Wheat Yield ◽  
Hierarchical Cluster ◽  
Environment Interaction ◽  
Gge Biplot ◽  
Spring Bread Wheat ◽  
Genotype Environment Interaction ◽  
Complex Process ◽  
Yield Trial ◽  
Selection Of

SummaryThe presence of genotype-environment interaction (GEI) influences production making the selection of cultivars in a complex process. The two most used methods to analyze GEI and evaluate genotypes are AMMI and GGE Biplot, being used for the analysis of multi environment trials data (MET). Despite their different approaches, both models complement each other in order to strengthen decision making. However, both models are based on biplots, consequently, biplot-based interpretation doesn’t scale well beyond two-dimensional plots, which happens whenever the first two components don’t capture enough variation. This paper proposes an approach to such cases based on cluster analysis combined with the concept of medoids. It also applies AMMI and GGE Biplot to the adjusted data in order to compare both models. The data is provided by the International Maize and Wheat Improvement Center (CIMMYT) and comes from the 14th Semi-Arid Wheat Yield Trial (SAWYT), an experiment concerning 50 genotypes of spring bread wheat (Triticum aestivum) germplasm adapted to low rainfall. It was performed in 36 environments across 14 countries. The analysis provided 25 genotypes clusters and 6 environments clusters. Both models were equivalent for the data’s evaluation, permitting increased reliability in the selection of superior cultivars and test environments.

Selection of environments using simultaneous clustering based on genotype × environment interaction

1994 ◽  
Vol 74 (2) ◽  
pp. 311-317 ◽  
Author(s):  
C. P. Baril ◽  
J-B. Denis ◽  
P. Brabant
Keyword(s):  
Cluster Analysis ◽  
Wheat Yield ◽  
Environment Interaction ◽  
Ge Interaction ◽  
Yield Data ◽  
Cluster Procedure ◽  
Genotype Environment Interaction ◽  
Series Of Experiments ◽  
The Common ◽  
Selection Of

Cluster analysis is used to classify genotypes and environments to decompose and interpret genotype × environment (GE) interaction. A simultaneous clustering method is applied to wheat-yield data collected over 8 yr in seven locations, with two agronomic treatments per location. This approach evidenced redundancies among the used environments constituting the Institut National de la Recherche Agronomique series of experiments in northern France. The aim is to reduce the number of environments without losing GE interaction. A graphical method based on the decreasing mean square of GE interaction is proposed to provide a cutting criterion of the cluster procedure. The comparison of groupings made independently for successive years suggested the removal of some environments, hence providing rational savings in the breeding program. Lastly, the simultaneous two-way clustering procedure is compared with the common one-way clustering procedure. Key words: Cluster analysis, genotype × environment interaction, pattern analysis, series of experiments, wheat

scholarly journals Analysis of yield stability of strawberry varieties and hybrids

2020 ◽  
Vol 25 ◽  
pp. 02014
Author(s):  
Vadim Lapshin ◽  
Valentina Yakovenko ◽  
Sergey Shcheglov
Keyword(s):  
Cluster Analysis ◽  
Hierarchical Cluster ◽  
Yield Stability ◽  
Environment Interaction ◽  
Multivariate Statistical ◽  
Genotype Environment Interaction ◽  
Yield Structure ◽  
Biological Yield ◽  
Factor Of Influence

The profitability of strawberry cultivation is largely determined by the capacity and quality of the yield, depended on the features of the variety genotype. The aim of this work was to estimate the yield stability of varieties and hybrids by the methods of multivariate statistical analysis and identify the best genotypes. To solve this problem, we have used the two-factor analysis of variance and hierarchical cluster analysis according to the Ward’s method as well as the integral estimate of the differences between the values of yield. The results of the studies have shown that the genotype of the variety (hybrid) are makes a decisive factor of influence for variability of the yield structure signs from 17,1% (number of inflorescences) to 32,2% (number of berries). The «genotype × environment» interaction is comparable with the genotype influence, the share of influence of the year conditions of the year is insignificant. Cluster analysis according to complex of economic valuable signs allows us to identify the eight forms that the most adapted to the conditions of the Krasnodar Territory as 13-1-15, Florence, Roxana, 18-1-15, Asia, Onda, Kemia, Nelli from which the Roxana, Florence, 18-1-15, 13-1-15 have a high and steadily rising biological yield.

scholarly journals THE ANALYSIS OF GENOTYPE × ENVIRONMENT INTERACTION USING RAPESEED (BRASSICA NAPUS L.) BY GGE BIPLOT METHOD

2020 ◽  
Vol 51 (5) ◽  
pp. 1337-1349
Author(s):  
Motahhari & et al.
Keyword(s):  
Seed Yield ◽  
Agricultural Research ◽  
Environment Interaction ◽  
Block Designs ◽  
Gge Biplot ◽  
Ge Interaction ◽  
Brassica Napus L ◽  
Biplot Analysis ◽  
Genotype Environment Interaction ◽  
Selection Of

This study was aimed to asses seed yield performances of 16 rapeseed genotypes  in randomized complete block designs (RCBD) with three replications at four Agricultural Research Stations of cold and mid-cold regions over two years in Iran (2015-2017). GGE biplot analysis indicated that the first two components explained 83% of seed yield variations. Genotype, location and their interaction explained 18%, 52% and 30%of the total GE variation, respectively. In this research, a graphically represented GGE biplot analysis enabled selection of stable and high-yielding genotypes for all investigated locations, as well as genotypes with specific adaptability. The GGE biplot analysis was adequate in explaining GE interaction for seed yield in rapeseed. It can be concluded that genotypes G2, G4 and G13 had the highest mean seed yield and stability in four investigated locations. For specific adaptability, G13 was recommended for Isfahan, Karaj and Kermanshah and G4 for Mashhad.

scholarly journals l.240 ADAPTABILITY AND STABILITY OF Coffea arabica LINES IN THE WESTERN AMAZON

2019 ◽  
Vol 14 (2) ◽  
pp. 240
Author(s):  
Carolina Augusto de Souza ◽  
Alexsandro Lara Teixeira ◽  
Josemar Dávila Torres ◽  
Camila Andrade Silva ◽  
Marcelo Curitiba Espindula ◽  
...  
Keyword(s):  
Low Temperatures ◽  
Coffea Arabica ◽  
Environment Interaction ◽  
Gge Biplot ◽  
Early Maturation ◽  
Genotype Environment Interaction ◽  
The Mean ◽  
Low Altitude ◽  
Set Up ◽  
Selection Of

Growing Coffea arabica in regions of the Western Amazon is limited by early maturation and by its limited adaptation to regions of low altitude and high temperature. The aim in this study was to quantify the genotype × environment interaction of C. arabica lines in four different environments of the Western Amazon, seeking to assist selection of new lines with greater adaptability and stability for the region. In the months of December 2012 and January 2013, four competitive trials were set up in municipalities of the states of Rondônia and Acre. Each trial was composed of 21 lines and 4 reference cultivars evaluated as controls recommended for planting in the southeast region. In combined analysis, significant differences were not detected between the cultivars and controls; the mean yield of hulled coffee was 12.05 bags ha-1. The Alta Floresta Do Oeste environment has higher yield and is the only environment favorable for growing C. arabica; that environment is differentiated from the others through its higher altitudes and low temperatures. Through GGE biplot analyses, lines 12 and 13, identified as H514-7-10-6-9 and H514-7-10-6-2-3-9, were found to have results superior to the controls in the municipality of Alta Floresta Do Oeste, RO. The gain from selection of 56% obtained from line G12 and the gain of 46% obtained from line G13 show performance superior to the best control. The germplasm studied does not have genetic variability that contributes to selection of plants for adaptation to the low altitude and high temperatures in the amazonic region.

Simultaneous selection of yield and yield stability in chickpea genotypes using the GGE biplot technique

2013 ◽  
Vol 61 (3) ◽  
pp. 185-194 ◽  
Author(s):  
E. Farshadfar
Keyword(s):  
Grain Yield ◽  
Principal Component ◽  
Environment Interaction ◽  
Gge Biplot ◽  
Yield Data ◽  
Genotype By Environment ◽  
Growing Seasons ◽  
Genotype Environment Interaction ◽  
The Mean ◽  
Selection Of

GGE biplot analysis is an effective method, based on principal component analysis (PCA), to fully explore multi-environment trials (METs). It allows visual examination of the relationships among the test environments, genotypes and the genotype-by-environment interactions (G×E interaction). The objective of this study was to explore the effect of genotype (G) and the genotype × environment interaction (GEI) on the grain yield of 20 chickpea genotypes under two different rainfed and irrigated environments for 4 consecutive growing seasons (2008–2011). The yield data were analysed using the GGE biplot method. The first mega-environment contained environments E1, E3, E4 and E6, with genotype G17 (X96TH41K4) being the winner; the second mega-environment contained environments E5, E7 and E8, with genotype G12 (X96TH46) being the winner. The E2 environment made up another mega-environment, with G19 (FLIP-82-115) the winner. The mean performance and stability of the genotypes indicated that genotypes G4, G16 and G20 were highly stable with high grain yield.

scholarly journals GGE-BIPLOT OF MULTIVARIATE INDEX TO SELECT MAIZE PROGENIES FOR EFFICIENT ASSOCIATION WITH Azospirillum brasiliense1

2021 ◽  
Vol 34 (4) ◽  
pp. 739-751
Author(s):  
FELIPE CECCON ◽  
LIVIA MARIA CHAMMA DAVIDE ◽  
MANOEL CARLOS GONÇALVES ◽  
ADRIANO DOS SANTOS ◽  
ELAINE PINHEIRO REIS LOURENTE
Keyword(s):  
Selection Index ◽  
High Yield ◽  
Environment Interaction ◽  
Gge Biplot ◽  
Mato Grosso ◽  
Genotype Environment Interaction ◽  
Two Cities ◽  
The Stability ◽  
Mato Grosso Do Sul ◽  
Selection Of

ABSTRACT Maize is widely cultivated in Brazil, and nitrogen is a major nutrient for its yield. Azospirillum brasiliense bacteria help in plant nutrient supply; however, maize-Azospirillum symbiosis is not very efficient and requires selection of genotypes with a more efficient association. Multivariate indexes facilitate selection using a single value, and GGE-biplot analysis enables the visualization of the genotype-environment interaction from this value. The present study aimed to select progenies that effectively associate with the bacteria and study the efficiency of progeny selection using a multivariate index observed in the GGE-biplot method. The experiments were conducted in two cities in the state of Mato Grosso do Sul. In a simple 16 × 16 lattice, 256 genotypes were evaluated in the presence and absence of diazotrophic bacteria. PH, SL, SD, FI, HGM, SS, and GY were measured for the construction of a selection index. Genotypes exhibited significant genotype–environment interactions for all evaluated traits, allowing their use in the selection index. High-yield genotypes were not those with the highest selection index values. The traits GY, SD, HGM, SS, SL, and PH contributed the most to the construction of the index. The no-till system may have contributed to the weaker response of maize inoculated with Azospirillum brasiliense. Genotype 96 had the highest values of the characteristics used to calculate the GISI, along with the stability between environments.

scholarly journals Application of GGE biplot graphs in multi-environment trials on selection of forest trees

2016 ◽  
Vol 58 (4) ◽  
pp. 228-239 ◽  
Author(s):  
Krzysztof Ukalski ◽  
Marcin Klisz
Keyword(s):  
Fixed Effects ◽  
Principal Component ◽  
Tree Height ◽  
European Beech ◽  
Real Data ◽  
Environment Interaction ◽  
Forest Trees ◽  
Gge Biplot ◽  
Genotype Environment Interaction ◽  
Selection Of

Abstract In the studies on selection and population genetics of forest trees that include the analysis of genotype × environment interaction (GE), the use of biplot graphs is relatively rare. This article describes the models and analytic methods useful in the biplot graphs, which enable the analyses of mega-environments, selection of the testing environment, as well as the evaluation of genotype stability. The main method presented in the paper is the GGE biplot method (G - genotype effect, GE -genotype × environment interaction effect). At the same time, other methods have also been referred to, such as, SVD (singular value decomposition), PCA (principal component analysis), linear-bilinear SREG model (sites regression), linear-bilinear GREG model (genotypes regression) and AMMI (additive main effects multiplicative interaction). The potential of biplot method is presented based on the data on growth height of 20 European beech genotypes (Fagus sylvatica L.), generated from real data concerning selection trials and carried out in 5 different environments. The combined ANOVA was performed using fixed- -effects, as well as mixed-effects models, and significant interaction GE was shown. The GGE biplot graphs were constructed using PCA. The first principal component (GGE1) explained 54%, and the second (GGE2) explained more than 23% of the total variation. The similarity between environments was evaluated by means of the AEC method, which allowed us to determine one mega-environment that comprised of 4 environments. None of the tested environments represented the ideal one for trial on genotype selection. The GGE biplot graphs enabled: (a) the detection of a stable genotype in terms of tree height (high and low), (b) the genotype evaluation by ranking with respect to the height and genotype stability, (c) determination of an ideal genotype, (d) the comparison of genotypes in 2 chosen environments.

scholarly journals Delineation of Genotype × Environment Interaction for Identification of Stable Genotypes to Grain Yield in Mungbean

2020 ◽  
Vol 2 ◽  
Author(s):  
Santhi Madhavan Samyuktha ◽  
Devarajan Malarvizhi ◽  
Adhimoolam Karthikeyan ◽  
Manickam Dhasarathan ◽  
Arumugam Thanga Hemavathy ◽  
...  
Keyword(s):  
Grain Yield ◽  
Tamil Nadu ◽  
Stability Index ◽  
Environment Interaction ◽  
Gge Biplot ◽  
Genotype Environment Interaction ◽  
South Indian ◽  
Indian State ◽  
Wide Adaptation ◽  
High Yields

In the present study, fifty-two mungbean (Vigna radiata) genotypes were evaluated for seven morphological traits at three different environments in South Indian state Tamil Nadu, namely Virinjipuram (E1), Eachangkottai (E2), and Bhavanisagar (E3) during Kharif 2017, 2018, and 2019, respectively. The data collected were subjected to variability and correlation analyses, followed by stability analysis using additive main effects and multiplicative interaction (AMMI) model, genotype and genotype × environment interaction effects (GGE) biplot. Variablility was observed among the genotypes for the following traits viz., plant height, days to fifty per cent flowering, number of pods per plant, pod length, number of seeds per pod, hundred seed weight and grain yield. Correlation analysis showed that the trait number of pods per plant was significantly associated with grain yield. The G × E was smaller than the genetic variation of grain yield as it portrayed the maximum contribution of genotypic effects (61.07%). GGE biplot showed E3 as a highly discriminating and representative environment. It also identified environment-specific genotypes viz., EC 396111 for E1, EC 396125 for E2 and EC 396101 for E3 environments. The genotypes with minimum genotype stability index (GSI) viz., V2802BG (7), HG 22 (13), and EC 396098 (13) were observed with wide adaptation and high yields across all the three environments. In summary, we identified stable genotypes adapted across environments for grain yield. These genotypes can be used as parent/pre-breeding materials in future mungbean breeding programs.

Evaluation of sugarcane genotypes with respect to sucrose yield across three crop cycles using GGE biplot analysis

2021 ◽  
pp. 1-13
Author(s):  
Aliya Momotaz ◽  
Per H. McCord ◽  
R. Wayne Davidson ◽  
Duli Zhao ◽  
Miguel Baltazar ◽  
...  
Keyword(s):  
Block Design ◽  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
Gge Biplot ◽  
Genotype By Environment ◽  
Biplot Analysis ◽  
Genotype Environment Interaction ◽  
Area 5 ◽  
Randomized Complete Block Design ◽  
Main Effects

Summary The experiment was carried out in three crop cycles as plant cane, first ratoon, and second ratoon at five locations on Florida muck soils (histosols) to evaluate the genotypes, test locations, and identify the superior and stable sugarcane genotypes. There were 13 sugarcane genotypes along with three commercial cultivars as checks included in this study. Five locations were considered as environments to analyze genotype-by-environment interaction (GEI) in 13 genotypes in three crop cycles. The sugarcane genotypes were planted in a randomized complete block design with six replications at each location. Performance was measured by the traits of sucrose yield tons per hectare (SY) and commercial recoverable sugar (CRS) in kilograms of sugar per ton of cane. The data were subjected to genotype main effects and genotype × environment interaction (GGE) analyses. The results showed significant effects for genotype (G), locations (E), and G × E (genotype × environment interaction) with respect to both traits. The GGE biplot analysis showed that the sugarcane genotype CP 12-1417 was high yielding and stable in terms of sucrose yield. The most discriminating and non-representative locations were Knight Farm (KN) for both SY and CRS. For sucrose yield only, the most discriminating and non-representative locations were Knight Farm (KN), Duda and Sons, Inc. USSC, Area 5 (A5), and Okeelanta (OK).

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