Determining environmental covariates which explain genotype environment interaction in winter wheat through probe genotypes and biadditive factorial regression

Genotype-environment interaction has been analyzed in a winter-wheat breeding network using bi-additive factorial regression models. This family of models generalizes both factorial regression and biadditive (or AMMI) models; it fits especially well when abundant external information is available on genotypes and/or environments. Our approach, focused on environmental characterization, was performed with two kinds of covariates: (1) deviations of yield components measured on four probe genotypes and (2) usual indicators of yield-limiting factors. The first step was based on the analysis of a crop diagnosis on four probe genotypes. Difference of kernel number to a threshold number (DKN) and reduction of thousand-kernel weight from a potential value (RTKW) were used to characterize the grain-number formation and the grain-filling periods, respectively. Grain yield was analyzed according to a biadditive factorial regression model using eight environmental covariates (DKN and RTKW measured on each of four probe genotypes). In the second step, the usual indicators of yield-limiting factors were too numerous for the analysis of grain yield. Thus a selection of a subset of environmental covariates was performed on the analysis of DKN and RTKW for the four probe genotypes. Biadditive factorial regression models involved environmental covariates related to each deviation and included environmental main effect, sum of water deficits, an indicator of nitrogen stress, sum of daily radiation, high temperature, pressure of powdery mildew and lodging. The correlations of each environmental covariate to the synthetic variates helped to discard those poorly involved in interaction (with | correlation | <0.3). The grain yield of 12 genotypes was interpreted with the retained covariates using biadditive factorial regression. The models explained about 75% of the interaction sums of squares. In addition, the biadditive factorial regression biplot gave relevant information about the interaction of the genotypes (interaction pattern and sensitivities to environmental covariates) with respect to the environmental covariates and proved to be interesting for such an approach. Received: 8 March 1999 / Accepted: 29 July 1999     

A comparison of results obtained with two methods for assessing yield stability

Summary A major objective of the CIMMYT Maize Program is to develop open-pollinated varieties of maize (Zea mays L.) that are well adapted to a wide range of environments. To achieve this breeding goal, it is essential that the program use a stability technique that will identify high-yielding, stable genotypes accurately in international trials conducted under different environmental conditions. The objective of this study was to compare a spatial method with a modified conventional regression analysis method to determine the yield stability of 27 CIMMYT maize varieties evaluated at 37 locations. The methods also were compared on the basis of their consistency in assessing the stability of varieties when certain locations were omitted, and when subsets of varieties were analyzed. The varieties found to be stable by the spatial method with all sites included in the analysis were also stable (1) when the lowest and highest yielding sites were excluded from the analyses, and (2) when the varieties were considered, along with others, as a subset of the original group of materials. Stability parameters determined by regression analysis, however, varied for some varieties when (1) extreme sites were excluded, and (2) a subset of entries was considered in isolation. Because the spatial method was more consistent in identifying high-yielding stable varieties, it was considered the more useful of the two methods.     

Effect of genome combinations on stability of yield and yield components in wheats and triticales

Summary The data on number of grains/spike, 100 grain weight and grain yield/plant in eighteen genotypes of four genome combinations (AABB- 4 genotypes, AABBDD- 6 genotypes, AABBRR- 5 genotypes and AABBDDRR- 3 genotypes) were recorded for eight environments created by combining two dates of sowing, two fertilizer regimes and two spacings. Two stability parameters-regression coefficient (b) and deviation from regression (S_d ²) were computed. Joint regression analyses revealed that the genotypes differed significantly for these characters. A significant variation due to environments was also found. A comparative study of performance of genotypes belonging to four genome combinations revealed that the genes for stability are not uniformly distributed in these genome combinations. Stability may largely depend on gene combination rather than on genome combination.     

Exploitation of yield stability in barley

Key message

Analyses of registration trials of winter barley suggested that yield and yield stability can be enhanced by developing hybrid instead of line varieties.

Abstract

Yield stability is central to cope with the expected increased frequency of extreme weather conditions. The objectives of our study were to (1) examine the dimensioning of field trials needed to precisely portray yield stability of individual winter barley (Hordeum vulgare L.) genotypes, (2) compare grain yield performance and yield stability of two-rowed lines with those of six-rowed lines and hybrids, and (3) investigate the association of various agronomic traits with yield stability. Static and dynamic yield stability as well as grain yield performance was determined in five series of 3-year registration trials of winter barley in Germany. Each series included 4 or 5 six-rowed hybrids, 40–46 six-rowed inbred lines, as well as 42–49 two-rowed inbred lines. The genotypes were evaluated in 10–45 environments, i.e. year-by-location combinations. We found that precise assessment of yield stability of individual genotypes requires phenotyping in at least 40 test environments. Therefore, selection for yield stability is not usually feasible since the required number of test environments exceeds the common capacity of barley breeding programs. Also, indirect improvement of yield stability by means of agronomic traits seemed not possible since there was no constant association of any agronomic trait with yield stability. We found that compared with line varieties, hybrids showed on average higher grain yield performance combined with high dynamic yield stability. In conclusion, breeding hybrid instead of line varieties may be a promising way to develop high yielding and yield stable varieties.     

Genetic analyses using GGE model and a mixed linear model approach,and stability analyses using AMMI bi-plot for late-maturity alpha-amylase activity in bread wheat genotypes

Low falling number and discounting grain when it is downgraded in class are the consequences of excessive late-maturity α-amylase activity (LMAA) in bread wheat (Triticum aestivum L.). Grain expressing high LMAA produces poorer quality bread products. To effectively breed for low LMAA, it is necessary to understand what genes control it and how they are expressed, particularly when genotypes are grown in different environments. In this study, an International Collection (IC) of 18 spring wheat genotypes and another set of 15 spring wheat cultivars adapted to South Dakota (SD), USA were assessed to characterize the genetic component of LMAA over 5 and 13 environments, respectively. The data were analysed using a GGE model with a mixed linear model approach and stability analysis was presented using an AMMI bi-plot on R software. All estimated variance components and their proportions to the total phenotypic variance were highly significant for both sets of genotypes, which were validated by the AMMI model analysis. Broad-sense heritability for LMAA was higher in SD adapted cultivars (53%) compared to that in IC (49%). Significant genetic effects and stability analyses showed some genotypes, e.g. ‘Lancer’, ‘Chester’ and ‘LoSprout’ from IC, and ‘Alsen’, ‘Traverse’ and ‘Forefront’ from SD cultivars could be used as parents to develop new cultivars expressing low levels of LMAA. Stability analysis using an AMMI bi-plot revealed that ‘Chester’, ‘Lancer’ and ‘Advance’ were the most stable across environments, while in contrast, ‘Kinsman’, ‘Lerma52’ and ‘Traverse’ exhibited the lowest stability for LMAA across environments.     

Relationships Between Kendall's Coefficient of Concordance and a Nonparametric Measure of Phenotypic Stability with Implications for the Consistency in Rankings as Affected by Variance Components

For a two-way classification with rows (= genotypes) and columns (= environments) relationships between Kendall's coefficient of concordance W and a nonparametric measure of phenotypic stability S (= variance among the ranks over the environments) are presented. This provides an analogy between Wricke's ecovalence and the sum of squares of genotype-environment interactions on the parametric side and S and Kendall's W on the nonparametric side: S is a genotype's contribution to the discordance (1 — W) in the data set, while Wricke's ecovalence is a genotype's contribution to the genotype-environment interaction sum of squares. Genotype x environment interactions may lead, but must not necessarily lead to non-identical rank orders of the genotypes in different environments (crossover versus noncrossover interactions). When does interaction become rank interaction? The similarity of the rank orders (measured by W) can be approximately expressed by the ratio of the genotypic variance and sum of genotypic variance plus residual variance. For the consistency of rankings this relation leads to an approximate test of significance which is based on variance components. Finally, a numerical example is given using grain yield data of 20 genotypes (varieties) of winter wheat in 10 environments (locations) from German registration trials.     

A thermodynamic comparison of HPr proteins from extremophilic organisms

A thermodynamic stability study of five histidine-containing phosphocarrier protein (HPr) homologues derived from organisms inhabiting diverse environments is described. These HPr homologues are from Bacillus subtilis (Bs), Streptococcus thermophilus (St), Bacillus staerothermophilus (Bst), Bacillus halodurans (Bh), and Oceanobacillus iheyensis (Oi). Analyses of solvent and thermal denaturation experiments provide the cardinal thermodynamic parameters, like deltaG, deltaH, deltaS, T(m), and deltaC(p), that characterize the conformational stability for each homologue. The homologue from Bacillus staerothermophilus (BstHPr) was established as the most thermostable homologue and also the homologue with highest deltaG at all temperatures. A good correlation between habitat temperature of the organism and thermal stability of the protein is also seen. Stability curves (deltaG vs T) for every homologue are also reported; these reveal very similar deltaC(p) and temperature of maximum stability (T(S)) values for all HPr homologues. Stability curves show that the higher thermal stability of some homologues is not a result of change in curvature of the curve or a shift to higher temperature, but rather a displacement of the stability curves to higher deltaG values. Stability curves also allowed estimation of deltaG at habitat temperature of the organisms, and we find good agreement between homologues. Electrostatic contributions to stability of each homologue were investigated by measuring stability as a function of varying pH and NaCl concentration, and our results suggest that most HPr homologues share similar electrostatic contributions to stability.     

基因与环境互作对云南保山烤烟主要潜香型物质的影响

为研究云南保山烤烟不同品种潜香型物质在不同环境条件下的稳定性问题,将云南保山3个烤烟常栽品种(K326、Y87、Y99)种植在3个海拔的2种土壤上,应用AMMI模型对烤烟主要潜香型物质进行基因型(G)、环境(E)和基因型与环境(G×E)互作分析.结果表明： 基因型、环境及其互作对烤烟叶黄素含量、β-胡萝卜素含量、绿原酸含量的影响均达到显著水平;芸香苷含量主要受基因型影响.烤烟主要潜香型物质含量及其稳定性受G×E互作影响显著,叶黄素含量、β-胡萝卜素含量、绿原酸含量随海拔的增加而显著增加,其稳定性也不同程度得到加强;K326适种在中低海拔区,Y87、Y99适种在中高海拔区.
     

Analysing yield stability of maize genotypes using a spatial model

Summary The yield stability of some CIMMYT tropical maize (Zea mays L.) populations of early and intermediate maturity, measured by the performance of varieties derived from them, was determined. Results of the stability analyses, conducted over international environments from 1980 to 1983, indicated that selections from Mezcla Amarilla exhibited good stability in high yielding sites. Varieties derived from Antigua-Republica Dominicana tended to be more stable in unfavourable environments, whereas selections from Blanco Cristalino-1 and Blanco Dentado-2 were stable in both low and high production sites. The combination of enviromental factors in the specific test locations, namely Poza Rica (Mexico), Tocumen (Panama), Islamabad (Pakistan), and Ferkessedougou (Ivory Coast), allowed selection of varieties that are very stable in other regions of the world. The varieties formed on the basis of multilocational data do not seem to be any more stable than those formed using data from a single location.     

Implication of correlations among some common stability statistics — a Monte Carlo simulations

Stability analysis of multilocation trials is often based on a mixed two-way model. Two stability measures in frequent use are the environmental variance (S _i ² )and the ecovalence (W _i). Under the two-way model the rank orders of the expected values of these two statistics are identical for a given set of genotypes. By contrast, empirical rank correlations among these measures are consistently low. This suggests that the two-way mixed model may not be appropriate for describing real data. To check this hypothesis, a Monte Carlo simulation was conducted. It revealed that the low empirical rank correlation amongS _i ² and W _i is most likely due to sampling errors. It is concluded that the observed low rank correlation does not invalidate the two-way model. The paper also discusses tests for homogeneity of S _i ² as well as implications of the two-way model for the classification of stability statistics.     

Dynamic gait stability index based on plantar pressures and fuzzy logic

Stability during locomotion, or dynamic stability, is critical to ensure safe locomotion and a high quality of life. A dynamic stability measure should be easily applied in a clinical setting and must provide a quantitative index that can be used for comparisons over a range of tasks and environments. Plantar foot pressure data acquired by shoe-insole sensors have potential to provide such a measure. To generate a quantitative dynamic gait stability index, six gait parameters were extracted from a commercial plantar pressure measurement system (F-Scan): anterior–posterior (A/P) center of force (CoF) motion, medial–lateral (M/L) CoF motion, maximum lateral position, cell triggering, stride time (ST), and double support time (DST). A fuzzy logic controller combined these six parameters and generated the index. To validate the stability index, 15 healthy subjects performed four tasks intended to induce increasing levels of instability. Fifty-seven gait parameter combinations were assessed to determine the most effective index. A combination of A/P motion, M/L motion, maximum lateral position, and cell triggering parameters was the most consistently effective index across all subjects. However, small changes in ST and DST for able-bodied subjects may have reduced the effectiveness of these measures in the index calculation. The index combining all six parameters should be investigated further with populations with disabilities or pathological gait.     

Linear and non-linear regression analysis of genotype X environment interactions in pearl millet

Summary Regression analysis was computed on the grain yield of 15 single cross F₁ hybrids of pearl millet (Pennisetum typhoides (Burm.) S. & H.) evaluated in 20 environments at 19 sites in India to assess the nature of genotype X environment interactions. Linear, quadratic, cubic, twoand three-intersecting straight line models were examined for fit. The interactions of six hybrids viz. MH 110, MH 113, MH 114, MH 115, MH 120 and MBH 110 were explained by the linear regression model. The response of the remaining nine hybrids was largely non-linear. The two and three-intersecting straight line models fit better than the quadratic and cubic models and explained non-linearity of response. The two-intersecting straight line models fit for 6 hybrids MH 106, MH 107, MH 112, MH 116, MH 117 and BJ 104. The response of MH 109 was best explained by a three-intersecting straight line model, but there still existed a significant remainder variation. The truncation of environmental range by assuming moving division points was more efficient than the fixed division points for the segmental regression models. The stability of hybrid varieties on the best fitting model has been discussed.     

Breeding progress,variation, and correlation of grain and quality traits in winter rye hybrid and population varieties and national on-farm progress in Germany over 26 years

Key message

Grain yield of hybrid varieties and population varieties in official German variety trials increased by 23.3 and 18.1%, respectively, over the last 26 years. On-farm gain in grain yield (18.9%) was comparable to that of population varieties in variety trials, yet at a level considerably lower than in variety trials. Rye quality is subject to large year-to-year fluctuation. Increase in grain yield and decline of protein concentration did not negatively influence quality traits.

Abstract

Performance progress of grain and quality traits of 78 winter rye varieties tested in official German trials to assess the value for cultivation and use (VCU) were evaluated during 1989 and 2014. We dissected progress into a genetic and a non-genetic component for hybrid and population varieties by applying mixed models, including regression components to model trends. VCU trial results were compared with grain yield and quality data from a national harvest survey (on-farm data). Yield gain for hybrid varieties was 23.3% (18.9 dt ha^?1) and for population varieties 18.1% (13.0 dt ha^?1) relative to 1989. On-farm yield progress of 18.9% (8.7 dt ha^?1) was considerably lagging behind VCU trials, and mean yield levels were substantially lower than in field trials. Most of the yield progress was generated by genetic improvement. For hybrid varieties, ear density was the determining yield component, whereas for population varieties, it was thousand grain mass. Results for VCU trials showed no statistically significant gains or losses in rye quality traits. For on-farm data, we found a positive but non-significant gain in falling number and amylogram viscosity and temperature. Variation of grain and quality traits was strongly influenced by environments, whereas genotypic variation was less than 19% of total variation. Grain yield was strongly negatively associated with protein concentration, yet was weakly to moderately positively associated with quality traits. In general, our results from VCU trials and on-farm data indicated that increasing grain yield and decreasing protein concentration did not negatively affect rye quality traits.

     

Performance of hybrid poplar clones in short rotation coppice in Mediterranean environments: analysis of genotypic stability

Improving production in short rotation coppice (SRC) plantations requires, among other elements, a proper understanding of clonal performance. Genotypic stability over a range of environments is a factor of concern for breeding and recommendation purposes. Most common stability measures can be embedded in a mixed‐model framework accounting for interaction and heterocedasticity in genotype‐by‐environment tables. Data from nine hybrid poplars of different taxonomic background were tested in four Mediterranean sites under three agronomic practices (control, herbicide application, and supplementary fertilization) for total biomass (TB), stem biomass (SB), and branch biomass (BB) at the end of the first rotation. Stability models (stability variance, Finlay–Wilkinson and Eberhart–Russell) were compared, also allowing for the definition of groups of genotypes with distinct taxonomic backgrounds and a priori different variabilities. Results showed that genotype‐by‐environment (GE) interactions were associated with factors inherent to evaluation sites rather than to the agronomic practices tested. Depending on biomass fraction, regression models provided appropriate stability measures. Highly reactive clones to improving environmental conditions (e.g., ‘AF2’) tended to show the largest mean TB. However, this was not always the case, as clone ‘Monviso’ showed both intermediate reactivity (i.e., stable sensu Eberhart–Russell) and enhanced overall performance. The taxonomic group was relevant for explaining stability patterns for SB. The stability assessment for BB indicated different patterns in biomass allocation. Present findings point to the feasibility of either exploiting specific adaptation (in which case hybrid type may play a relevant role) or searching for broadly adapted, stable material exhibiting good performance in Mediterranean conditions.     

Environmental stability and heritability estimates for grain yield and test weight in triticale

Hexaploid triticale has many advantages over both parental species for both grain and forage production in certain environments. Additional information on environmental stability and heritability would be desirable to develop appropriate selection strategies in the production of superior widely-adapted cultivars. The grain yield of 22 diverse genotypes grown at four ecologically-distinct geographical locations [Quincy, FL, USA (approximate geographical coordinates (AGC) = 30 degreesN 84 degreesW, approximate elevation (AE) = 58 m), Plains, GA, USA (AGC = 32 degreesN 84 degreesW, AE = 76 m), Bozeman, MT USA (AGC = 45 degreesN 111 degreesW, AE = 1458 m), and Aberdeen, ID, USA (AGC = 42 degreesN 112 degreesW, AE = 1360 m)] was measured in two years with winter and spring planting dates only at Bozeman and Aberdeen. Test weight (grain weight in a given volume) was determined for two years at Bozeman and Aberdeen at both planting dates and one year at Quincy. Stability analyses indicated that significant (P < 0.01) variation in means, regression coefficients, and deviation mean squares of the genotypes were present for both characters. Realized heritability (h2) estimates were as follows: grain yield ranged from -0.02 to 0.80 with a mean of 0.57; test weight ranged from 0.63 to 1.05 with a mean of 0.93. The results indicated that substantial genetic variation is present and selection for widely-adapted cultivars would be effective for both characters especially test weight.     

A method of estimating varietal stability for data of long-term trials

Summary A method is proposed to analyze the stability of cultivars in long-term varietal trials. The method involves the following steps: (i) regress a standard variety on environmental means; (ii) regress varieties under test on the standard variety; (iii) transform, through a procedure of reparameterization, the regression computed for each variety under test on the standard variety into the regression of the variety on environmental means. Although this method is proposed to analyze data sets from complex designs, it may also possess some advantages over conventional procedures for simpler designs.     

Stability of performance of okra as influenced by planting date

Summary Fifteen selected okra genotypes, consisting of six from a pedigree breeding programme and nine established varieties as checks, were evaluated in five different environments for stability of performance. Performance was measured by pod yield per plant, number of days to flowering, final plant height, number of branches per plant, number of pods per plant and edible pod weight. A regression method and a genotype grouping technique were employed in the evaluation. The results showed significant genotype × environment interaction only with respect to number of days to flowering and number of branches per plant. Additive environmental effect was significant for all characters. Line UI 313 was considered stable with respect to pod yield per plant and edible pod weight. One line resulting from the pedigree breeding programme was also considered stable by the genotype-grouping technique.     

小麦品种蛋白质品质性状稳定性研究

用陕西省关中小麦品种区域试验所选用的12个小麦品种（品系）在12个试点的数据资料。分析了品种,环境及品种与环境互作（CEI）对籽粒硬度,蛋白质含量,沉淀值及湿面筋含量的影响。结果表明：基因型效应对所有品质参数均有显著影响,基因型与环境互作对沉淀值影响较大,而对籽粒硬度,蛋白质含量与湿面筋含量影响较小,环境效应对湿面筋含量和好粒硬度影响较大,而对蛋白质含量与沉淀值影响较小,蛋白质品质参数的回归系数（b值）表明,基因型对不同环境的反应存在着显著差异。对于籽粒硬度,蛋白质含量与湿面筋含量回归偏差显著的品种很少,这表明线性回归模式占了基因型变异的绝大部分,一些品种的沉淀值显著偏离了回归,上述结果表明,要改善小麦品种的蛋白质品质,也应重视环境对小麦蛋白质品质的影响。     

Genetic properties of four types of stability parameter

Summary The genetic properties of four types of stability parameter for individual genotypes were investigated using a set of diallel cross data (28 genotypes x four locations x 3 years). The specific parameters studied were: the variance of a genotype across environments (T1); the genotype x environment (GE) interaction effect for a genotype, squared and summed across all environments (T2); the residual mean square (MS) of deviations from the regression of a genotype on an environmental index (T3); and years within locations MS for a genotype, averaged over all locations (T4). Each stability statistic was fitted to the additive model, based on the assumption that if the stability parameter is heritable, stability of F₁ is most likely to be the average stability of its parents. The results showed that T1 and T4 were additive, but T2 and T3 were not. A study of the consistency of stability rankings between two seeding rates over the same set of environments showed a similar pattern. It appears that stability parameters of types 1 and 4 are heritable, and thus useful for selection, while those of types 2 and 3 are nonheritable, and thus not useful.Contribution No. R-029     

Stability of Adult‐plant Resistance to Septoria tritici blotch in 24 European Winter Wheat Varieties Across Nine Field Environments

Septoria tritici blotch (STB) is one of the most important leaf diseases in wheat worldwide. Objectives of this study were (i) to compare inoculation and natural infection; (ii) to evaluate the level of adult‐plant resistance to STB using four isolates; and (iii) to analyse environmental stability of 24 winter wheat (Triticum aestivum L.) varieties in inoculated vs. non‐inoculated field trials across 3 years including nine environments (location × year combinations). Field trials were sown in split‐plot design inoculated with four aggressive isolates of S. tritici plus one non‐inoculated variant as main factor and 24 wheat varieties as subfactor. Septoria tritici blotch severity was visually scored as percentage flag leaves covered with lesions bearing pycnidia. Overall STB rating ranged from 8% (Solitär) to 63% (Rubens) flag leaf area affected, resulting in significant (P < 0.01) genotypic variance. Variance of genotype × environment interaction amounted to approximately 50% of the genotypic variance. Genotype × isolate interaction variance was significant too (P < 0.01) but of minor importance. Therefore, environmental stability of varieties should be a major breeding goal. The varieties Solitär, History and Florett were most resistant and stable as revealed by a regression approach, and the susceptible varieties were generally unstable. Hence, STB resistance and stability are correlated (P < 0.01), but there were some exceptions (Tuareg, Ambition). Promising candidates for an environmentally stable, effective adult‐plant resistance have been identified.