Choosing plant cultivars based on the probability of outperforming a check

Summary A major consideration in most plant breeding programs is the development of cultivars that have high probabilities of outperforming the check cultivar in a broad range of environments. Methods are presented for estimating and testing hypotheses regarding these probabilities, which are termed reliabilities. Reliabilities are shown to be directly related to several commonly used stability parameters. Data from international maize yield trials are used to illustrate and evaluate the repeatability of the approach. Results indicate that reliabilities can be useful aids to plant breeders since they (1) are easy to understand and compute, (2) are indices that weigh the importance of the difference in performance relative to stability, and (3) are potentially useful as genetic parameters since they are generally repeatable across randomly sampled sets of environments.Contribution from the Agricultural Research Division, University of Nebraska, Lincoln, Neb., Paper no. 9653     

Classifying genotypic data from plant breeding trials: a preliminary investigation using repeated checks

Summary Several subjective choices must be made when classifying genotypes based on data from plant breeding trials. One choice involves the method used to weight the contribution each environment makes to the classification. A second involves the use of either genotype-means for each environment or genotypevalues for each block, i.e., considering each block to be a different environment. Another involves whether environments (or blocks) in which genotypes are nonsignificantly different should be included or excluded from such classifications. An alternative to the use of raw or standardized data, is proposed in which each environment is weighted by a discrimination index (DI) that is based on the concept of repeatability. In this study the effect of three weighting methods (raw, standardized and DI), the choice of using environments or blocks, and the choice of including or excluding environments or blocks in which genotypic effects were not significant, were considered in factorial combination to give 12 options. A data set comprised of five check cultivars each repeated six times in each of three blocks at six environments was used. The effect of these options on the ability of a hierarchical clustering technique to correctly classify the repeats into five groups, each consisting of all the six repeats of a particular check cultivar, was investigated. It was found that the DI weighting method generally led to better recovery of the known structure. Using block data rather than environmental data also improved structure recovery for each of the three weighting methods. The exclusive use of environments in which genotypic effects were significant decreased structure recovery while the contrary generally occurred for blocks. The best structure recovery was obtained from the DI weighting applied to blocks (whether genotypes were significant or not).     

Mixing ability analysis of wheat cultivar mixtures under diseased and nondiseased conditions

Summary Mixing ability analyses, adapted from combining ability analyses used in plant breeding, were performed on yield and stripe rust (Puccinia striiformis) severity data for two-way mixtures among either four or five club wheat (Triticum aesitivum) cultivars grown in five environments. Initially, two statistics were calculated for each trait: general mixing ability (GMA), the average performance of a cultivar over all of the mixtures, and specific mixing ability (SMA), the deviation of a mixture from the estimated performance of the pair based on its average performance in mixtures. General mixing ability was further divided into two components: genotype performing ability (GPA), the innate ability of a cultivar to yield and resist disease in pure stand, and true general mixing ability (TGMA), the average ability of a cultivar to influence yield and disease when mixed with other cultivars. Significant mean squares for genotypes, GMA, SMA, and TGMA were found for all of the traits in most environments. Examination of TGMA and SMA revealed cultivars and cultivar combinations that were statistically better mixers than the others. Some of the significant effects were probably due to the use of cultivars that differed in height and stripe rust resistance, but for other combinations there was no apparent explanation for enhanced mixing ability.Paper No. 9132 of the Oregon Agricultural Experiment Station. Supported in part by USDA Grants 88-34106-3631 and 88-37151-3662     

A preference assay for quantifying symbiont choice in fungus-growing ants (Attini, Formicidae)

We describe a bioassay for the quantification of cultivar preference (symbiont choice) of fungus-growing ants. The bioassay simultaneously presents mycelium of multiple pure cultivar genotypes to worker ants in a cafeteria-style test arena, and preferred versus non-preferred cultivar genotypes can then be identified based on the ants’ quantifiable behavioral tendencies to convert any of the offered mycelium into a fungus garden. Under natural conditions, fungus-growing ants are likely to express such cultivar preferences when mutant cultivars arise in a garden, or when colonies acquire a novel cultivar from a neighboring colony to replace their resident cultivar. We show that workers from different nests of the fungus-growing ant Cyphomyrmex costatus exhibit repeatable preferences vis-à-vis specific cultivar genotypes. The identified preferred and rejected cultivars can then be used in a performance assay to test whether the ants prefer cultivar genotypes that are superior in enhancing colony fitness (measured, for example, as garden productivity or colony growth), as predicted by symbiont-choice theory. Received 24 February 2006; revised 23 June 2006; accepted 26 June 2006.     

Stability of Sweet Potato Cultivars to Alternaria Leaf and Stem Blight Disease

Alternaria leaf petiole and stem blight is an economically important disease of sweet potato ( Ipomoea batatus L.) in tropical and sub-tropical environments. Published research on cultivar resistance to the sweet potato disease is limited. To evaluate cultivar reaction and stability to the disease, multi-location and replicated experiments were established in 12 environments in Uganda. Disease severity (area under disease progress curves – AUDPC), and cultivar root yield were also assessed. Significant differences (P < 0.001) in AUDPC were detected among cultivars. Mean AUDPC ranged from 46.3 (Araka Red) to 78.4 (New Kawogo) across locations and seasons and the genotypes Araka Red and Tanzania had the lowest disease values. The location and season effects accounted for 67.1% and 7.5% of the total variance of AUDPC recorded among cultivars. The ranking of cultivars based on predicted AUDPC from Additive Main Effect and Multiplicative Interactive model (AMMI) showed that the NASPOT 1, the susceptible check, and New Kawogo were most susceptible to the disease in 11 of the 12 environments. Low and stable disease was consistently recorded and predicted on NASPOT 3 and the landrace cultivars Tanzania, Dimbuca, and Araka Red across environments. These results suggest that landrace cultivars had relative stability to the disease and wide adaptation across environments. These results suggest that AMMI statistical model and other multivariate techniques can be utilized for prediction of Alternaria disease stability in these locations.     

Assessment of a method for cultivar selection based on regional trial data

Summary In this study a method for analyzing regional trial data is investigated for its effectiveness in cultivar selection. The method is a synthesis of three procedures: (1) regression analysis for genotype × environment (GE) interaction, and subsequent cluster analysis for grouping cultivars for similarity of response; (2) superiority measure analysis of cultivar performance based on the distance mean square between the test cultivar and the maximum response; (3) type 4 stability analysis for three-way classification data (cultivar × location × year), to measure a cultivar's stability. Each of these three procedures is aimed at different aspects of the selection problem: the first obtains an overview of the types of cultivar response; the second measures a cultivar's general adaptability within the region; the third assesses a cultivar's ability to withstand unpredictable variation, namely that caused by year effects. Four sets of published data, each originally analyzed by a univariate or a multivariate approach, were used as examples. The results suggest that the present method provides direct and useful information for selection purposes. The superiority measure, which is the core of the method, can be used even if the data do not fit the linear model for GE interaction. Plotting the data with a fixed standard represented by the maximum response provides a simple visual tool for identifying environments where a cultivar performs well.Contribution No. C-035 from Research Program Service, Research Branch, Agriculture Canada, Ottawa, Ontario, K1A 0C6     

Behavioural responses of the seven‐spot ladybird Coccinella septempunctata to plant headspace chemicals collected from four crop Brassicas and Arabidopsis thaliana,infested with Myzus persicae

1 Insects using olfactory stimuli to forage for prey/hosts are proposed to encounter a ‘reliability–detectability problem’, where the usability of a stimulus depends on its reliability as an indicator of herbivore presence and its detectability. 2 We investigated this theory using the responses of female seven‐spot ladybirds Coccinella septempunctata (Coleoptera: Coccinellidae) to plant headspace chemicals collected from the peach‐potato aphid Myzus persicae and four commercially available Brassica cultivars; Brassica rapa L. cultivar ‘turnip purple top’, Brassica juncea L. cultivar ‘red giant mustard’, Brassica napus L. cultivar ‘Apex’, Brassica napus L. cultivar ‘Courage’ and Arabidopsis thaliana. For each cultivar/species, responses to plants that were undamaged, previously infested by M. persicae and infested with M. persicae, were investigated using dual‐choice Petri dish bioassays and circular arenas. 3 There was no evidence that ladybirds responded to headspace chemicals from aphids alone. Ladybirds significantly preferred headspace chemicals from B. napus cv. Apex that were undamaged compared with those from plants infested with aphids. For the other four species/cultivars, there was a consistent trend of the predators being recorded more often in the half of the Petri dish containing plant headspace chemicals from previously damaged and infested plants compared with those from undamaged ones. Furthermore, the mean distance ladybirds walked to reach aphid‐infested A. thaliana was significantly shorter than to reach undamaged plants. These results suggest that aphid‐induced plant chemicals could act as an arrestment or possibly an attractant stimulus to C. septempunctata. However, it is also possible that C. septempunctata could have been responding to aphid products, such as honeydew, transferred to the previously damaged and infested plants. 4 The results provide evidence to support the ‘reliability–detectability’ theory and suggest that the effectiveness of C. septempunctata as a natural enemy of aphids may be strongly affected by which species and cultivar of Brassica are being grown.     

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

We derive a quantile-adjusted conditional maximum likelihood estimator for the dispersion parameter of the negative binomial distribution and compare its performance, in terms of bias, to various other methods. Our estimation scheme outperforms all other methods in very small samples, typical of those from serial analysis of gene expression studies, the motivating data for this study. The impact of dispersion estimation on hypothesis testing is studied. We derive an "exact" test that outperforms the standard approximate asymptotic tests.     

MEASURING NATURAL SELECTION ON PHENOTYPIC PLASTICITY

To understand natural selection we need to integrate its measure across environments. We present a method for measuring phenotypic selection that combines the potential for both environmental variation and phenotypic plasticity. The method uses path analysis and a measure of selection that is analogous to selection on breeding values. For individuals growing in alternative environments, paths are created that represent potential changes in the environment. The probabilities for these changes are then multiplied by the path coefficients to calculate selection coefficients. Selection on plasticity is measured as the difference in selection within each environment. We illustrate these methods using data on selection in an experimental population of Arabidopsis thaliana. Individuals from 36 families were grown in one of four environments, a factorial combination of shaded/open and early/late shading. For final height of the inflorescence, there was positive selection in both the open and shaded environments and negative selection on plasticity of height. For bolting time, there was also positive selection in both environments, but no selection on plasticity. We show how to use this information to examine how selection would change with changes in environmental frequencies and their transition probabilities. These methods can be expanded to encompass continuous traits and continuous environments as well as other complexities of natural selection.     

Estimation of capture probabilities using generalized estimating equations and mixed effects approaches

Modeling individual heterogeneity in capture probabilities has been one of the most challenging tasks in capture–recapture studies. Heterogeneity in capture probabilities can be modeled as a function of individual covariates, but correlation structure among capture occasions should be taking into account. A proposed generalized estimating equations (GEE) and generalized linear mixed modeling (GLMM) approaches can be used to estimate capture probabilities and population size for capture–recapture closed population models. An example is used for an illustrative application and for comparison with currently used methodology. A simulation study is also conducted to show the performance of the estimation procedures. Our simulation results show that the proposed quasi‐likelihood based on GEE approach provides lower SE than partial likelihood based on either generalized linear models (GLM) or GLMM approaches for estimating population size in a closed capture–recapture experiment. Estimator performance is good if a large proportion of individuals are captured. For cases where only a small proportion of individuals are captured, the estimates become unstable, but the GEE approach outperforms the other methods.     

Genotypic variations in activities of phospho<Emphasis Type="Italic">enol</Emphasis>pyruvate carboxylase and correlations with leaf photosynthetic characteristics and crop productivity of cassava grown in low-land seasonally-dry tropics

Field trials with a large group of cassava germplasm were conducted at the seasonally-dry and hot environments in southwest Colombia to investigate photosynthetic characteristics and production under drought conditions. Measurement of net photosynthetic rate (P _N), photosynthetic nitrogen use efficiency (PNUE), mesophyll conductance to CO₂ diffusion (g _m), and phosphoenolpyruvate carboxylase (PEPC) activity of upper canopy leaves were made in the field. All photosynthetic characteristics were significantly correlated with final dry root yield (Yield). Correlations among the photosynthetic traits were also significant. PEPC activity was highly significantly correlated with P _N and PNUE, indicating the importance of the enzyme in cassava photosynthesis and productivity. Among a small selected group from the preliminary trial for yield performance, the second year Yield was highly significantly correlated with P _N measured on the first year crop. Thus variations in the measured photosynthetic traits are genetically controlled and underpin variations in yield. One short-stemmed cultivar M Col 2215 was selected for high root dry matter content, high harvest index, and tolerance to drought. It was tested under the semi-arid conditions of the west coast of Ecuador; participating farmers evaluated cultivar performance. This cultivar was adopted by farmers and officially released in 1992 under the name Portoviejo 650.     

Genotype × environment interaction analysis of North American shrub willow yield trials confirms superior performance of triploid hybrids

Development of dedicated bioenergy crop production systems will require accurate yield estimates, which will be important for determining many of the associated environmental and economic impacts of their production. Shrub willow (Salix spp) is being promoted in areas of the USA and Canada due to its adaption to cool climates and wide genetic diversity available for breeding improvement. Willow breeding in North America is in an early stage, and selection of elite genotypes for commercialization will require testing across broad geographic regions to gain an understanding of how shrub willow interacts with the environment. We analyzed a dataset of first‐rotation shrub willow yields of 16 genotypes across 10 trial environments in the USA and Canada for genotype‐by‐environment interactions using the additive main effects and multiplicative interactions (AMMI) model. Mean genotype yields ranged from 5.22 to 8.58 oven‐dry Mg ha^?1 yr^?1. Analysis of the main effect of genotype showed that one round of breeding improved yields by as much as 20% over check cultivars and that triploid hybrids, most notably Salix viminalis × S. miyabeana, exhibited superior yields. We also found important variability in genotypic response to environments, which suggests specific adaptability could be exploited among 16 genotypes for yield gains. Strong positive correlations were found between environment main effects and AMMI parameters and growing environment temperatures. These findings demonstrate yield improvements are possible in one generation and will be important for developing cultivar recommendations and for future breeding efforts.     

THERMAL PERCEPTIONS AND PREFERENCES IN INDOOR ENVIRONMENTS

Sensory analysis was applied to the study of thermal perception, in order to determine and characterize end‐users’ preferences concerning five indoor thermal environments generated by different heating systems. In this review, we developed a sensory profile method to describe and quantify the sensory characteristics of the thermal environments. A consumer test was also performed in order to investigate the hedonic judgment of 119 end users. The results show that trained assessors are able to describe and quantify sensory differences between the environments with high reliability. Consumers’ preferences are influenced by both their thermal sensations in the environments, as expressed by the sensory panel, and their personal opinions of the corresponding heating systems.     

The significance threshold for coherence when using the Welch's periodogram method: Effect of overlapping segments

A classical tool to identify coupling mechanisms between two biological signals is transfer function (TF) analysis, commonly estimated by the Welch's periodogram method. However, the reliability of TF estimation depends on the coherence function, an index of linear coupling in the frequency domain. Thus, a threshold value has to be determined before assuming a coupling between two signals at a given frequency.Koopmans (The spectral analysis of time series) proposed a theoretical expression in the case of non-overlapping segments. Overlapping segments, however, improves the estimation of TF.In the present study, a modification of the expression by Koopmans is proposed for taking into account the effect of the overlapping procedure, including the most common case of a 50% overlapping ratio. Simulation tests were done on non-coherent signals (using the Hanning window), and a Kolmogorov–Smirnov test was used to check for the adequacy with the proposed threshold formula. The results showed that for an overlapping ratio of 50%, no statistical difference could be found (P > 0.05), except when using less than seven segments.The method has been applied to the computation of the transfer function between systolic blood pressure and heart rate.     

Expected utility maximization and selection of stable plant cultivars

Summary In most plant breeding programs, selection of the best commercially suitable cultivars for a target group of environments is based on information obtained from evaluation trials cultivated in a sample of environments. Information on the performance of cultivars collected in a sample of environments can only be approximate and, consequently, selection of the best cultivar involves choosing among cultivars that respond uncertainly in many environments. The agronomic and/or economic value of a cultivar across environments may be considered the general or overall utility of the cultivar. Data from a sample of environments therefore provides only an estimate of any cultivar's overall utility, with the overall goal of selection among all cultivars being the maximization of the expected utility. Within this frame-work, expected utility maximization, an approach to decision making that has been well developed in the disciplines of economics and statistics, can assist the plant breeder in making such decisions. This research was initiated (1) to determine how expected utility maximization might be used to develop indices that are useful for selecting broadly adapted plant cultivars, and (2) to determine how the breeder's preferences might affect choice of the best cultivar. The data used in this research were from USDA Regional Soybean Tests. The results indicated that expected utility maximization, which explicitly incorporates into the selection rule the plant breeder's preferences regarding stability, can be a useful aid in the selection of stable plant cultivars.     

Genetic control of durable resistance to yellow rust (Puccinia striiformis) in the wheat cultivar Hybride de Bersée

The wheat cultivar Hybride de Bersee is described as possessing durable resistance to yellow rust. Some races of Puccinia striiformis can infect it at the seedling stage but not severely in the field. Using euploid and aneuploid stocks of Bersee it was shown that a large part of this resistance was controlled by chromosome 5BS-7BS, the effect being detectable in seedlings and at later growth stages. Measurements of spore production from infected seedlings showed that the line ditelosomic for the 5BS arm of the chromosome was more resistant than the line ditelosomic for the 7BS arm under environments favouring high spore production, but more susceptible under environments favouring low spore production. Thus both arms of the chromosome could contribute to resistance in appropriate environments. Chromosome 5BS-7BS did not carry the factors controlling the race-specific resistance to race 37 E132 of P. striiformis. The possibility of exploiting the resistance carried by chromosome 5BS-7BS in wheat breeding programmes is discussed.     

Environmental osmolality influences sperm motility activation in an anuran amphibian

Evolutionary theory predicts that selection will favour sperm traits that maximize fertilization success in local fertilization environments. In externally fertilizing species, osmolality of the fertilization medium is known to play a critical role in activating sperm motility, but there remains limited evidence for adaptive responses to local osmotic environments. In this study, we used a split‐sample experimental design and computer‐assisted sperm analysis to (i) determine the optimal medium osmolality for sperm activation (% sperm motility and sperm velocity) in male common eastern froglets (Crinia signifera), (ii) test for among‐population variation in percentage sperm motility and sperm velocity at various activation‐medium osmolalities and (iii) test for among‐population covariation between sperm performance and environmental osmolality. Frogs were obtained from nine populations that differed in environmental osmolality, and sperm samples of males from different populations were subjected to a range of activation‐medium osmolalities. Percentage sperm motility was optimal between 10 and 50 mOsm kg^?1, and sperm velocity was optimal between 10 and 100 mOsm kg^?1, indicating that C. signifera has evolved sperm that can function across a broad range of osmolalities. As predicted, there was significant among‐population variation in sperm performance. Furthermore, there was a significant interaction between activation‐medium osmolality and environmental osmolality, indicating that frogs from populations with higher environmental osmolality produced sperm that performed better at higher osmolalities in vitro. This finding may reflect phenotypic plasticity in sperm functioning, or genetic divergence resulting from spatial variation in the strength of directional selection. Both of these explanations are consistent with evolutionary theory, providing some of the first empirical evidence that local osmotic environments can favour adaptive sperm motility responses in species that use an external mode of fertilization.     

State-vector models of the cell cycle 1. Parametrization and fits to labeled mitoses data

In this paper we study the Hahn model of the cell cycle from the point of view that a cell population's age distribution is more relevant to labeled mitoses data than is the distribution of its transit times.Closed-form relationships are derived between the transition probabilities of the Hahn model and the transit time of the mean of a cohort of labeled cells (with the variance of their transit time through mitosis). Constraints result which define the acceptable values for the number of ages in the state vector and the length of the time step (rarely does the dimension of the state vector equal the number of time steps in the generation time).A generalization to distinct probabilities for G₁, S and G₂M is presented, and the automatic fitting of fraction-labeled mitoses (FLM) data is described. The doubling time of the population is used to define the daughter factor, via the largest eigenvalue of the state transition matrix. The performance of the generalized Hahn model is compared to that of other commonly used fitting methods using two sets of FLM data from the literature. The synthesis of continuous labeling curves is discussed as an independent check of the parametrization. Based on the stable age distribution resulting from fits to experimental FLM data, it is shown that a nonlinear relationship exists between biological age and time.     

A comparison of inoculation methods for determining potato cultivar reaction to black leg

Two methods of inoculating tubers, one by dipping them in an aqueous suspension of Erwinia carotovora subsp. atroseptica, the other by inserting the end of a wooden toothpick charged with undiluted bacteria into the rose-end near a sprout, were compared over two years for their ability to produce black leg and for their effect on plant growth and yield on a number of cultivars chosen because of expected differences in susceptibility. Although both methods produced a similar rank order for cultivar reaction, the more consistent results were obtained using the toothpick method, clear differences in black leg incidence and yield being evident between the susceptible cultivars Ulster Sceptre and Maris Bard and the more resistant Pentland cultivars. As some cultivars appear more tolerant to black leg than others, yield may be as important a criterion as disease incidence when assessing overall cultivar performance. The inoculation of the base and middle of stems and the infiltration of the bacterium into tubers were also investigated as alternative methods for assessing cultivar susceptibility.     

Heritability of male attractiveness persists despite evidence for unreliable sexual signals in Drosophila simulans

Sexual signals can be used to attract mates, but to be honest indicators of signaller quality they need to convey information reliably. However, environmental variation and genotype‐by‐environment (G × E) interactions have the potential to compromise the reliability of sexual signals. Here, we test the reliability of cuticular hydrocarbons (CHCs) as signals of heritable aspects of male attractiveness in Drosophila simulans. We examined the heritability of male attractiveness and a measure of the difference between fathers' and sons' CHC profiles across dietary and temperature environments. Our results show that environmental heterogeneity disrupts the similarity of some components of father and son CHC profile. However, overall male attractiveness is heritable within and across environments, so that sire attractiveness is a good predictor of son attractiveness even with environmental heterogeneity. This suggests that although some male CHC signals are unreliable, attractive genotypes retain their attractiveness across environments on average.