Crop diagnosis and probe genotypes for interpreting genotype environment interaction in winter wheat trials

Genotype*environment interaction has been analyzed with 12 genotypes and four probe genotypes in French wheat trials. An integrated approach was developed which combined crop diagnosis with the analysis of interaction by factorial regression. Crop diagnosis was helpful to characterize the environments and to select environmental variables. Such an approach succeeded in providing an agronomic explanation of genotype*environment interaction and in defining the responses or parameters for each genotype and each environment. Earliness at heading, susceptibility to powdery mildew and susceptibility to lodging were the three major genotypic covariates. Interaction could also be related to environment features, measured indirectly by the behavior of the four probe genotypes during the formation of yield, what we called the outputs of a simplified crop diagnosis, or described directly by indicators of yield-limiting factors. Two important crop diagnosis covariates were analyzed in order to characterize interaction during the formation of yield: the reduction in kernel number, which described the time-period until flowering, and the reduction in thousand kernel weight, which corresponded to the period after flowering. These variates were estimated for each probe genotype and allowed us to compare the behavior of the 12 genotypes to that of the probe genotypes. Both periods of the formation of yield contributed to the interaction, and ’Camp-Rémy’ was the probe of particular interest for the comparisons. When true environmental variates were used, factorial regression revealed that water deficits during the formation of grain number and level of nitrogen were predominant. Such an integrated approach could be exploited when varieties are tested in a network where numerous and diverse yield-limiting factors may occur. Received: 3 August 1998 / Accepted: 16 March 1999     

The presentation of treatment responses from block experiments after analysis of variance of transformed data

In pearl millet, severe water deficit during the period of panicle development delays flowering. The flowering response of both main shoot and tillers to water stress during panicle development was investigated using four hybrids. Panicle initiation of all tillers occurred in the three early genotypes despite water stress. In the late genotype, however, panicle initiation of tillers occurred only after the release of stress. The delay in flowering due to water stress was more pronounced in the tillers than in the main shoot. However, the proportion of tillers producing an inflorescence was increased by water stress. Grain yield losses on the main shoot by water stress were compensated by an increase in tiller grain yields. Delay in flowering and buffering by tillers provide an important adaptive mechanism to overcome a period of drought stress prior to flowering.     

Choosing probe genotypes for the analysis of genotype-environment interaction in winter wheat trials

Genotype-environment interaction was analyzed in French multi-environment wheat (Triticum aestivum L.) trials using probe genotypes and bi-additive factorial regression. Probe genotypes are specific genotypes in which the comparisons of yield components to reference values describe the most-important environmental factors that limited grain yield. The time-period until flowering was described by the deviation of kernel number from a threshold number while the grain-filling period was described by the reduction of thousand-kernel weight from a potential value. The aim of this paper was to determine the convenient number and the characteristics of probe genotypes to include in wheat breeding trials. Two sets of genotypes were used to model genotype-environment interaction: set 1 with 12 varieties tested in 18 environments and set 2 with ten lines tested in 14 environments. Set 2 was used for validation. Seven probe genotypes described the environments by providing environmental covariates, namely differences in yield components, for further analysis of interaction in set 1 and set 2. Interaction was modelled with bi-additive factorial regressions including differences in yield components. Several rounds of models were fitted to determine the optimal number of probe genotypes (i.e. environmental covariates) to introduce. From the seven probe genotypes, all the possible combinations including one to seven genotypes were studied. Significance of the combinations was tested with critical values obtained from simulations through 1,000 random permutations. Taking into account the information available on the probe genotypes, one would think that two, three or four probe genotypes would be sufficient, otherwise the number should reach four or five genotypes. In all cases, these numbers will provide models more-parsimonious than the classical AMMI model. The important information to be known on the probe genotypes prior their first multilocation experiment is: interaction pattern, earliness, and differences in yield component. Tested for the first time, a quadruplet is better than a triplet because the probability of choosing complementary genotypes increases with their number.     

Integration of statistical and physiological analyses of adaptation of near-isogenic barley lines

Seven near-isogenic barley lines, differing for three independent mutant genes, were grown in 15 environments in Spain. Genotype x environment interaction (G x E) for grain yield was examined with the Additive Main Effects and Multiplicative interaction (AMMI) model. The results of this statistical analysis of multilocation yield-data were compared with a morpho-physiological characterization of the lines at two sites (Molina-Cano et al. 1990). The first two principal component axes from the AMMI analysis were strongly associated with the morpho-physiological characters. The independent but parallel discrimination among genotypes reflects genetic differences and highlights the power of the AMMI analysis as a tool to investigate G x E. Characters which appear to be positively associated with yield in the germplasm under study could be identified for some environments.     

Environment characterization as an aid to wheat improvement: interpreting genotype-environment interactions by modelling water-deficit patterns in North-Eastern Australia

Genotype-environment interactions (GEI) limit genetic gain for complex traits such as tolerance to drought. Characterization of the crop environment is an important step in understanding GEI. A modelling approach is proposed here to characterize broadly (large geographic area, long-term period) and locally (field experiment) drought-related environmental stresses, which enables breeders to analyse their experimental trials with regard to the broad population of environments that they target. Water-deficit patterns experienced by wheat crops were determined for drought-prone north-eastern Australia, using the APSIM crop model to account for the interactions of crops with their environment (e.g. feedback of plant growth on water depletion). Simulations based on more than 100 years of historical climate data were conducted for representative locations, soils, and management systems, for a check cultivar, Hartog. The three main environment types identified differed in their patterns of simulated water stress around flowering and during grain-filling. Over the entire region, the terminal drought-stress pattern was most common (50% of production environments) followed by a flowering stress (24%), although the frequencies of occurrence of the three types varied greatly across regions, years, and management. This environment classification was applied to 16 trials relevant to late stages testing of a breeding programme. The incorporation of the independently-determined environment types in a statistical analysis assisted interpretation of the GEI for yield among the 18 representative genotypes by reducing the relative effect of GEI compared with genotypic variance, and helped to identify opportunities to improve breeding and germplasm-testing strategies for this region.     

A mixed-model quantitative trait loci (QTL) analysis for multiple-environment trial data using environmental covariables for QTL-by-environment interactions, with an example in maize

Complex quantitative traits of plants as measured on collections of genotypes across multiple environments are the outcome of processes that depend in intricate ways on genotype and environment simultaneously. For a better understanding of the genetic architecture of such traits as observed across environments, genotype-by-environment interaction should be modeled with statistical models that use explicit information on genotypes and environments. The modeling approach we propose explains genotype-by-environment interaction by differential quantitative trait locus (QTL) expression in relation to environmental variables. We analyzed grain yield and grain moisture for an experimental data set composed of 976 F(5) maize testcross progenies evaluated across 12 environments in the U.S. corn belt during 1994 and 1995. The strategy we used was based on mixed models and started with a phenotypic analysis of multi-environment data, modeling genotype-by-environment interactions and associated genetic correlations between environments, while taking into account intraenvironmental error structures. The phenotypic mixed models were then extended to QTL models via the incorporation of marker information as genotypic covariables. A majority of the detected QTL showed significant QTL-by-environment interactions (QEI). The QEI were further analyzed by including environmental covariates into the mixed model. Most QEI could be understood as differential QTL expression conditional on longitude or year, both consequences of temperature differences during critical stages of the growth.     

Evaluation of breeding strategies for drought tolerance in potato by means of crop growth simulation

Breeding strategies for drought tolerance in potato were evaluated by means of a crop growth model, in which seasonal courses of crop dry matter accumulation and soil moisture availability were simulated in dependence of plant characteristics and weather and soil data.Several plant characteristics substantially influenced the simulated instantaneous water consumption of the genotype. However, effects of genotypic differences on final tuber yield were much smaller because of the close relationship between transpiration and growth. Hence, a lower water consumption not only saved water for later use, but was also at the expense of the actual growth rate. Selection for low-transpiration types, at unchanged water use efficiency, would result in lower yields under optimum conditions.Short periods of drought, in general, reduced tuber yield of late genotypes less than that of early genotypes. Late genotypes had a surplus of leaf area for full light interception giving a lower impact of leaf area reduction. Late drought affected early genotypes less because of escape.The simulation results emphasized the complexity of selection for drought tranrance caused by the many plant processes involved, the contrast between instantaneous and cumulative reactions and the strong genotype × environment interaction for drought tolerance.     

Time to flowering of temperate pulses in vivo and generation turnover in vivo–in vitro of narrow-leaf lupin accelerated by low red to far-red ratio and high intensity in the far-red region

Understanding the role light quality plays on floral initiation is key to a range of pre-breeding tools, such as accelerated single-seed-descent. We have elucidated the effect of light quality on early flowering onset in cool-season grain legumes and developed predictive models for time to flowering under the optimised light conditions. Early and late flowering genotypes of pea, chickpea, faba bean, lentil and lupin were grown in controlled environments under different light spectra (blue and far red-enriched LED lights and metal halide). All species and genotypes showed a positive response to a decreasing red to far-red ratio (R:FR). In general, ratios above 3.5 resulted in the longest time to flowering. In environments with R:FR below 3.5, light with the highest intensity in the FR region was the most inductive. We demonstrate the importance of considering both relative (R:FR) and absolute (FR photons) light values for flower induction in grain legumes. Greater response to light spectra was observed in the later flowering genotypes, enabling a drastic compression of time to flowering between phenologically diverse genotypes. A novel protocol for robust in vitro germination of immature seeds was developed for lupin, a species known for its recalcitrance to in vitro manipulation. We show how combining this protocol with growth under conditions optimized for early flowering drastically speeds generation turnover. The improved understanding of the effect of light on flowering regulation and the development of robust in vitro culture protocols will assist the development and exploitation of biotechnological tools for legume breeding.     

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.     

Sustainable production of crops and pastures under drought in a Mediterranean environment

Mediterranean environments are characterised by cool wet winters and hot dry summers. While native vegetation in Mediterranean-climatic zones usually comprises a mixture of perennial and annual plants, agricultural development in the Mediterranean-climatic region of Australia has led to the clearing of the perennial vegetation and its replacement with annual crops and pastures. In the Mediterranean environments of southern Australia this has led to secondary (dryland) salinisation. In order to slow land degradation, perennial trees and pasture species are being reintroduced to increase the productivity of the saline areas. The annual crops and pastures that form the backbone of dryland farming systems in the Mediterranean-climatic zone of Australia are grown during the cool wet winter months on incoming rainfall and mature during spring and early summer as temperatures and rates of evaporation rise and rainfall decreases. Thus, crop and pasture growth is usually curtailed by terminal drought. Where available, supplementary irrigation in spring can lead to significant increases in yield and water use efficiency. In order to sustain production of annual crops in Mediterranean environments, both agronomic and genetic options have been employed. An analysis of the yield increases of wheat in Mediterranean-climatic regions shows that there has generally been an increase in the yields over the past decades, albeit at a lower rate than in more temperate regions. Approximately half of this increase can be attributed to agronomic improvements and half to genetic improvements. The agronomic improvements that have been utilised to sustain the increased yields include earlier planting to more closely match crop growth to rainfall distribution, use of fertilisers to increase early growth, minimum tillage to enable earlier planting and increase plant transpiration at the expense of soil evaporation, rotations to reduce weed control and disease incidence, and use of herbicides, insecticides and fungicides to reduce losses from weeds, insects and disease. Genetic improvements include changing the phenological development to better match the rainfall, increased early vigour, deeper rooting, osmotic adjustment, increased transpiration efficiency and improved assimilate storage and remobilisation. Mediterranean environments that are subjected annually to terminal drought can be both environmentally and economically sustainable, but to maximise plant water use efficiency while maintaining crop productivity requires an understanding of the interaction between genotypes, environment and management.     

Correlation of endogenous free polyamine levels with root nodule senescence in different genotypes in Vigna mungo L

Endogenous free polyamines, nitrogenase (EC 1.1.8.6.1, acetylene reduction), and leghaemoglobin (pyridine-hemochrome assay) levels were compared among five genotypes of developing Vigna root nodules grown under field conditions. Nitrogenase activity and leghaemoglobin level attained a peak at the flowering stage and gradually declined thereafter. Individual and total polyamine also followed the same pattern. Ranking on the basis of legume yield and other morphometric attributes was PDU-2 > UH-28 > UH-82 > T-9 > Sardhomash. Except spermine, the levels of putrescine, spermidine, and total polyamine showed significant differences (p<0.05) amongst the genotypes, particularly from flowering to mid-pod development stage. Genotype, development stage, and their interaction between the two had significant (p<0.01) effects on individual as well as total polyamines. Moreover, significant high linear correlations were found between total free polyamine and putrescine with conventional nodule senescence marker like nitrogenase (R2 = 0.94 and R2 = 0.92, respectively). Putrescine had an overall positive correlation with high legume yield. The results strongly suggest a relationship between polyamine and nodule senescence. Endogenous free polyamine and putrescine may be considered as genotypic markers for nodule senescence in field grown V. mungo. It is suggested that the flowering stage is more suitable for selection.     

A conservative pattern of water use, rather than deep or profuse rooting, is critical for the terminal drought tolerance of chickpea

Chickpea is mostly grown on stored soil moisture, and deep/profuse rooting has been hypothesized for almost three decades to be critical for improving chickpea tolerance to terminal drought. However, temporal patterns of water use that leave water available for reproduction and grain filling could be equally critical. Therefore, variation in water use pattern and root depth/density were measured, and their relationships to yield tested under fully irrigated and terminal drought stress, using lysimeters that provided soil volumes equivalent to field conditions. Twenty chickpea genotypes having similar plant phenology but contrasting for a field-derived terminal drought-tolerance index based on yield were used. The pattern of water extraction clearly discriminated tolerant and sensitive genotypes. Tolerant genotypes had a lower water uptake and a lower index of stomatal conductance at the vegetative stage than sensitive ones, while tolerant genotypes extracted more water than sensitive genotypes after flowering. The magnitude of the variation in root growth components (depth, length density, RLD, dry weight, RDW) did not distinguish tolerant from sensitive genotypes. The seed yield was not significantly correlated with the root length density (RLD) in any soil layers, whereas seed yield was both negatively related to water uptake between 23-38 DAS, and positively related to water uptake between 48-61 DAS. Under these conditions of terminal drought, the most critical component of tolerance in chickpea was the conservative use of water early in the cropping cycle, explained partly by a lower canopy conductance, which resulted in more water available in the soil profile during reproduction leading to higher reproductive success.     

The effect of day length, vernalization and DNA demethylation on the flowering time in Arabidopsis thaliana

We studied the effect of three factors on the induction of flowering in Arabidopsis thaliana , i.e. vernalization, day length and DNA demethylation. Seven natural late flowering genotypes and 13 late flowering mutants were used in the experiments. The effect of the vernalization and the short day (SD) was uniform in all genotypes used, resulting in shortening (vernalization) or extension of the period before the appearance of the first flower primordia. On the other hand, the effect of the demethylating agent (5-azacytidine [5-azaC]) was not uniform in the genotypes used. In all natural late genotypes (except Lu-1 ), the shortening of the flowering time (FT) after 5-azaC treatment was observed. On the contrary, only five mutants – dl , pm , M63 , M73 and fca-1 – showed a shortening of the FT, while in the majority of the late flowering mutants, no significant response (earlier flowering) was found. The different response to the vernalization and demethylation treatment in late flowering mutants shows the possibility of two different pathways leading to the flowering, both of which are regulated by DNA demethylation. The different response of natural and induced late flowering genotypes after 5-azaC treatment shows that genes that play a role in flower development are of a different nature.     

甘蔗品种主要性状的基因型与环境及其互作效应分析

用AMMI模型双标图对国家第六轮甘蔗品种区域试验5个试点的12个甘蔗品种试验数据进行分析,研究甘蔗区试中不同品种的产量稳定性问题。结果表明,参试品种的6个产量性状在品种间和地点间差异显著,品种与地点的互作效应差异显著;FN30、YG16蔗茎产量和含糖量高,稳定性强,属于高产、稳产性较好的品种。AMMI模型很好地解释了甘蔗品种产量性状的基因型效应、环境效应和GE互作效应。     

Developmental behavior of gene expression for brown rice thickness under different environments

The dynamic changes of genetic effects, including main effects, and genotype x environment (GE) interaction effects on brown rice thickness (BRT) across environments were investigated by using the developmental genetic models. Seven cytoplasmic male sterile lines of indica rice (Oryza sativa L.) as females and five restoring lines as males were used in a factorial design to produce grains of F(1)s and F(2)s in two environments (years) for developmental genetic analysis. The results indicate that genetic effects, especially GE interaction effects of triploid endosperm genes, cytoplasm genes, and diploid maternal plant genes were important to the performance of BRT at various filling stages of rice. The BRT was genetically controlled by the net genetic effects of genes expressed at the early and late filling stages (1-7 days and 15-21 days after flowering, respectively). The differences in net genetic effects under different environments for endosperm, cytoplasm, and maternal plant genes were found, and the net GE interaction effects were more important to BRT at the early filling and mature stages of rice. Some net genetic effects, especially for net cytoplasm effects spasmodically expressed, were detected among filling stages. Higher additive and cytoplasm main effects, along with their interaction effects, were found, which would be useful for selection for BRT in breeding programs. The predicated genetic effects at different filling stages show that the parents of V20 and Xieqingzao were better than others for improving BRT of progenies.     

Responses of cow pea (Vigna unguiculata) varieties and their hybrids to variation in day and night temperature regimes

The effects of each of four contrasting combinations of two day (30, 26°C) and two night (24, 19°C) temperatures were studied on four cowpea varieties and their F₁ hybrids. Early vegetative development was enhanced by the higher day, higher night temperature and flowering occurred first in plants receiving this treatment. The hybrids showed marked heterosis for leaf area but not for time to flowering. The ten genotypes studied showed correlated responses to increases in night temperature and differed in the degree of their response. The extent of the response (or stability) of varieties was often determined by the character values in the environment with the highest yield and heterotic hybrids were the least stable. Grain yield was highest in the lower day temperature environments but there was variation between genotypes in whether this occurred at the lower or higher night temperature. The pattern of responses shown by hybrids agreed with those of their parents indicating that stability was an inherited character. The results confirmed and extended those in earlier studies and emphasised the importance of a greater understanding of the nature of responses to the environment in selecting new varieties.     

Interpersonal Similarity between Body Movements in Face-To-Face Communication in Daily Life

Individuals are embedded in social networks in which they communicate with others in their daily lives. Because smooth face-to-face communication is the key to maintaining these networks, measuring the smoothness of such communication is an important issue. One indicator of smoothness is the similarity of the body movements of the two individuals concerned. A typical example noted in experimental environments is the interpersonal synchronization of body movements such as nods and gestures during smooth face-to-face communication. It should therefore be possible to estimate quantitatively the smoothness of face-to-face communication in social networks through measurement of the synchronization of body movements. However, this is difficult because social networks, which differ from disciplined experimental environments, are open environments for the face-to-face communication between two individuals. In such open environments, their body movements become complicated by various external factors and may follow unstable and nonuniform patterns. Nevertheless, we consider there to be some interaction during face-to-face communication that leads to the interpersonal synchronization of body movements, which can be seen through the interpersonal similarity of body movements. The present study aims to clarify such interaction in terms of body movements during daily face-to-face communication in real organizations of more than 100 people. We analyzed data on the frequency of body movement for each individual during face-to-face communication, as measured by a wearable sensor, and evaluated the degree of interpersonal similarity of body movements between two individuals as their frequency difference. Furthermore, we generated uncorrelated data by resampling the data gathered and compared these two data sets statistically to distinguish the effects of actual face-to-face communication from those of the activities accompanying the communication. Our results confirm an interpersonal similarity of body movements between two individuals in face-to-face communication, for all the organizations studied, and suggest that some body interaction is behind this similarity.     

Association of functional markers with flowering time in lentil

In the present study, a diverse panel of 96 accessions of lentil germplasm was used to study flowering time over environments and to identify simple sequence repeat markers associated with flowering time through association mapping. The study showed high broad sense heritability estimate (h ² bs=0.93) for flowering time in lentil. Screening of 534 SSR markers resulted in an identification of 75 SSR polymorphic markers (13.9%) across studied genotypes. These markers amplified 266 loci and generated 697 alleles ranging from two to 16 alleles per locus. Model-based cluster analysis used for the determination of population structure resulted in the identification of two distinct subpopulations. Distribution of flowering time was ranged from 40 to 70 days in subpopulation I and from 54 to 69 days in subpopulation II and did not skew either late or early flowering time within a subpopulation. No admixture was observed within the subpopulations. Use of the most accepted maximum likelihood model (P3D mixed linear model with optimum compression) of MTA analysis showed significant association of 26 SSR markers with flowering time at <0.05 probability. The percent of phenotypic explained by each associated marker with flowering time ranged from 2.1 to 21.8% and identified QTLs for flowering time explaining high phenotypic variation across the environments (10.7-21.8%) or in a particular environment (10.2-21.4%). In the present study, 13 EST-SSR showed significant association with flowering time and explained large phenotypic variation (2.3-21.8%) compared to genomic SSR markers (2.1-10.2%). Hence, these markers can be used as functional markers in the lentil breeding program to develop short duration cultivars.