Measurement and management of genotype-environment interaction (GxE) for the improvement of rainfed lowland rice yield in Cambodia

The magnitude and nature of genotype-by-environment interactions (G×E) for grain yield (GY) and days to flower (DTF) in Cambodia were examined using a random population of 34 genotypes taken from the Cambodian rice improvement program. These genotypes were evaluated in multi-environment trials (MET) conducted across three years (2000 to 2002) and eight locations in the rainfed lowlands. The G×E interaction was partitioned into components attributed to genotype-by-location (G×L), genotype-by-year (G×Y) and genotype-by-location-by-year (G×L×Y) interactions. The G×L×Y interaction was the largest component of variance for GY. The G×L interaction was also significant and comparable in size to the genotypic component (G). The G×Y interaction was small and non significant. A major factor contributing to the large G×L×Y interactions for GY was the genotypic variation for DTF in combination with environmental variation for the timing and intensity of drought. Some of the interactions for GY associated with timing of plant development and exposure to drought were repeatable across the environments enabling the identification of three-target populations of environments (TPE) for consideration in the breeding program. Four genotypes were selected for wide adaptation in the rainfed lowlands in Cambodia.

Effect of environment and genotype on bread-making quality of spring-sown spring wheat cultivars in China

Improvement of end-use quality in bread wheat depends on a thorough understanding of current wheat quality and the influences of genotype (G), environment (E), and genotype by environment interaction (G x E) on quality traits. Thirty-nine spring-sown spring wheat (SSSW) cultivars and advanced lines from China were grown in four agro-ecological zones comprising seven locations during the 1998 and 1999 cropping seasons. Data on 12 major bread-making quality traits were used to investigate the effect of G, E, and G x E on these traits. Wide range variability for protein quantity and quality, starch quality parameters and milling quality in Chinese SSSW was observed. Genotype and environment were found to significantly influence all quality parameters as major effects. Kernel hardness, flour yield, Zeleny sedimentation value and mixograph properties were mainly influenced by the genetic variance components, while thousand kernel weight, test weight, and falling number were mostly influenced by the environmental variance components. Genotype, environment, and their interaction had important effects on test weight, mixing development time and RVA parameters. Cultivars originating from Zone VI (northeast) generally expressed high kernel hardness, good starch quality, but poor milling and medium to weak mixograph performance; those from Zone VII (north) medium to good gluten and starch quality, but low milling quality; those from Zone VIII (central northwest) medium milling and starch quality, and medium to strong mixograph performance; those from Zone IX (western/southwestern Qinghai-Tibetan Plateau) medium milling quality, but poor gluten strength and starch parameters; and those from Zone X (northwest) high milling quality, strong mixograph properties, but low protein content. Samples from Harbin are characterized by good gluten and starch quality, but medium to poor milling quality; those from Hongxinglong by strong mixograph properties, medium to high milling quality, but medium to poor starch quality and medium to low protein content; those from Hohhot by good gluten but poor milling quality; those from Linhe by weak gluten quality, medium to poor milling quality; those from Lanzhou by poor bread-making and starch quality; those from Yongning by acceptable bread-making and starch quality and good milling quality; and those from Urumqi by good milling quality, medium gluten quality and good starch pasting parameters. Our findings suggest that Chinese SSSW quality could be greatly enhanced through genetic improvement for targeted well-characterized production environments.

Mixed model formulations for multi-environment trials

When studying genotype X environment interaction in multi-environment trials, plant breeders and geneticists often consider one of the effects, environments or genotypes, to be fixed and the other to be random. However, there are two main formulations for variance component estimation for the mixed model situation, referred to as the unconstrained-parameters (UP) and constrained-parameters (CP) formulations. These formulations give different estimates of genetic correlation and heritability as well as different tests of significance for the random effects factor. The definition of main effects and interactions and the consequences of such definitions should be clearly understood, and the selected formulation should be consistent for both fixed and random effects. A discussion of the practical outcomes of using the two formulations in the analysis of balanced data from multi-environment trials is presented. It is recommended that the CP formulation be used because of the meaning of its parameters and the corresponding variance components. When managed (fixed) environments are considered, users will have more confidence in prediction for them but will not be overconfident in prediction in the target (random) environments. Genetic gain (predicted response to selection in the target environments from the managed environments) is independent of formulation.

Analysis of line x environment interactions for yield in navy beans. 2. Pattern analysis of lines and environment within years

Seven years of multi-environment yield trials of navy bean (Phaseolus vulgaris L.) grown in Queensland were examined. As is common with plant breeding evaluation trials, test entries and locations varied between years. Grain yield data were analysed for each year using cluster and ordination analyses (pattern analyses). These methods facilitate descriptions of genotype performance across environments and the discrimination among genotypes provided by the environments. The observed trends for genotypic yield performance across environments were partly consistent with agronomic and disease reactions at specific environments and also partly explainable by breeding and selection history. In some cases, similarities in discrimination among environments were related to geographic proximity, in others management practices, and in others similarities occurred between geographically widely separated environments which differed in management practices. One location was identified as having atypical line discrimination. The analysis indicated that the number of test locations was below requirements for adequate representation of line x environment interaction. The pattern analyses methods used were an effective aid in describing the patterns in data for each year and illustrated the variations in adaptive patterns from year to year. The study has implications for assessing the number and location of test sites for plant breeding multi-environment trials, and for the understanding of genetic traits contributing to line x environment interactions.

Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems

New tools derived from advances in molecular biology have not been widely adopted in plant breeding for complex traits because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. In this study, we explored whether physiological dissection and integrative modelling of complex traits could link phenotype complexity to underlying genetic systems in a way that enhanced the power of molecular breeding strategies. A crop and breeding system simulation study on sorghum, which involved variation in 4 key adaptive traits-phenology, osmotic adjustment, transpiration efficiency, stay-green-and a broad range of production environments in north-eastern Australia, was used. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages assuming gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies in the data. Based on the analyses of gene effects, a range of marker-assisted selection breeding strategies was simulated. It was shown that the inclusion of knowledge resulting from trait physiology and modelling generated an enhanced rate of yield advance over cycles of selection. This occurred because the knowledge associated with component trait physiology and extrapolation to the target population of environments by modelling removed confounding effects associated with environment and gene context dependencies for the markers used. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate genetic regions.

Milling quality and protein properties of autumn-sown Chinese wheats evaluated through multi-location trials

Eight milling quality and protein properties of autumn-sown Chinese wheats were investigated using 59 cultivars and advanced lines grown in 14 locations in China from 1995 to 1998. Wide ranges of variability for all traits were observed across genotypes and locations. Genotype, location, year, and their interactions all significantly influenced most of the quality parameters. Kernel hardness, Zeleny sedimentation value, and mixograph development time were predominantly influenced by the effects of genotype. Genotype, location and genotype x location interaction were all important sources of variation for thousand kernel weight, test weight, protein content, and falling number, whereas genotype x location interaction had the largest effect on flour yield. Most of the genotypes were characterized by weak gluten strength with Zeleny sedimentation values less than 40 ml and mixograph development time shorter than 3 min. Eight groups of genotypes were recognized based on the average quality performance, grain hardness and gluten strength were the two parameters that determined the grouping, with contributions from protein content. Genotypes such as Zhongyou 16 and Annong 8903 displayed good milling quality, high grain hardness, protein content and strong gluten strength with high sedimentation value and long mixograph development time. Genotypes such as Lumai 15 and Yumai 18 were characterized by low grain hardness, protein content and weak gluten strength. Genotypes such as Yannong 15 and Chuanmai 24 were characterized by strong gluten strength with high sedimentation value and long mixograph development time, but low grain hardness and protein content lower than 12.3%. Genotypes such as Jingdong 6 and Xi'an 8 had weak gluten strength, but with high grain hardness and protein content higher than 12.2%. Five groups of locations were identified, and protein content and gluten strength were the two parameters that determined the grouping. Beijing, Shijiazhuang, Nanyang, Zhumadian and Nanjing produced wheats with medium to strong gluten strength and medium protein content, although there was still a large variation for most of the traits investigated between the locations. Wheat produced in Yantai was characterized by strong gluten strength, but with low protein content. Jinan, Anyang and Linfen locations produced wheats with medium to weak gluten strength and medium to high protein content. Wheats produced in Yangling, Zhenzhou, and Chengdu were characterized by weak gluten strength with medium to low protein content, whereas wheats produced in Xuzhou and Wuhan were characterized by weak gluten strength with low protein content. Industrial grain quality could be substantially improved through integrating knowledge of geographic genotype distribution with key location variables that affected end-use quality.

Improving drought tolerance in rainfed lowland rice: An example from Thailand

A large portion of the world's poor farm in rainfed systems where the water supply is unpredictable and droughts are common. In Thailand there are approximately 6.2 million ha of rain fed lowland rice, which account for 67% of the country's total rice-growing area. This rice system is often characterised by too much and too little water in the same season. Farmers' estimates of their annual losses to drought are as high as 45% in the upper parts of the toposequence. In contrast to irrigated rice systems, gains from crop improvement of rainfed rice have been modest, in part because there has been little effort to breed and select for drought tolerance for the target rainfed environments. The crop improvement strategy being used in Thailand considers three mechanisms that influence yield in the drought prone targets: yield potential as an important mechanism for mild drought (where yield loss is less than 50%), drought escape (appropriate phenology) and drought tolerance traits of leaf water potential, sterility, flower delay and drought response index for more severe drought conditions. Genotypes are exposed to managed drought environments for selection of drought tolerant genotypes. A marker assisted selection (MAS) scheme has been developed and applied for selection of progenies in the backcrossing program. The plant breeding program uses rapid generation advance techniques that enable early yield testing in the target population of environments (TPE) through inter-station (multi-location yield testing) and on-farm trials. A farmer participatory approach has been used to identify the TPE for the breeding program. Four terrace paddy levels have been identified, upper (drought), middle (drought prone to favorable) and lower (flooded). This paper reports the change in the breeding program for the drought prone tainted lowland rice environments of North and Northeast Thailand by incorporating our knowledge on adaptation and on response of rice to drought. (c) 2005 Elsevier B.V. All rights reserved.

Management of plant invasions mediated by frugivore interactions

1. Some of the most damaging invasive plants are dispersed by frugivores and this is an area of emerging importance in weed management. It highlights the need for practical information on how frugivores affect weed population dynamics and spread, how frugivore populations are affected by weeds and what management recommendations are available. 2. Fruit traits influence frugivore choice. Fruit size, the presence of an inedible peel, defensive chemistry, crop size and phenology may all be useful traits for consideration in screening and eradication programmes. By considering the effect of these traits on the probability, quality and quantity of seed dispersal, it may be possible to rank invasive species by their desirability to frugivores. Fruit traits can also be manipulated with biocontrol agents. 3. Functional groups of frugivores can be assembled according to broad species groupings, and further refined according to size, gape size, pre- and post-ingestion processing techniques and movement patterns, to predict dispersal and establishment patterns for plant introductions. 4. Landscape fragmentation can increase frugivore dispersal of invasives, as many invasive plants and dispersers readily use disturbed matrix environments and fragment edges. Dispersal to particular landscape features, such as perches and edges, can be manipulated to function as seed sinks if control measures are concentrated in these areas. 5.Where invasive plants comprise part of the diet of native frugivores, there may be a conservation conflict between control of the invasive and maintaining populations of the native frugivore, especially where other threats such as habitat destruction have reduced populations of native fruit species. 6. Synthesis and applications. Development of functional groups of frugivore-dispersed invasive plants and dispersers will enable us to develop predictions for novel dispersal interactions at both population and community scales. Increasingly sophisticated mechanistic seed dispersal models combined with spatially explicit simulations show much promise for providing weed managers with the information they need to develop strategies for surveying, eradicating and managing plant invasions. Possible conservation conflicts mean that understanding the nature of the invasive plant-frugivore interaction is essential for determining appropriate management.

Pattern analysis on grain yield performance of Chinese and CIMMYT spring wheat cultivars sown in China and CIMMYT

Understanding the relationships among testing environments is essential for better targeting cultivars to production environments. To identify patterns of cultivar, environment, cultivar-by-environment interactions, and opportunities for indirect selection for grain yield, a set of 25 spring wheat cultivars from China and the International Maize and Wheat Improvement Center (CIMMYT) was evaluated in nine environments in China and four management environments at CIMMYT in Cd. Obregon, Mexico, during two wheat seasons. Genetic background and original environment were the main factors influencing grain yield performance of the cultivars. Baviacora M 92, Xinchun 2 and Xinchun 6 showed relatively more stable and higher grain yields, whereas highly photoperiod sensitive cultivars Xinkehan 9, Kefeng 6 and Longmai 19 proved consistently inferior across environments, except in Harbin and Keshan, the two high latitude environments. Longmai 26, also from high latitude environments in the northeastern Heilongjiang province, was however probably not as photoperiodicly sensitive as other cultivars; from that region, and produced much higher grain yield and expressed a broader adaptation. None of the environments reported major diseases. Pattern analyses revealed that photoperiod response and planting option on beds were the two main factors underlying the observed interactions for grain yield. The production environment of planting on the flat in Mexico grouped together with Huhhot and Urumqi in both wheat seasons, indicating an indirect response to selection for grain yield in this CIMMYT managed environment could benefit the two Chinese environments. Both the environment of planting on the flat with Chinese Hejin and Yongning, and the three CIMMYT enviromnents planting on raised beds with Chinese Yongning grouped together only in one season, showing that repeatability may not be stable in this case.

Pattern analysis on protein properties of Chinese and CIMMYT spring wheat cultivars sown in China and CIMMYT

Improvement of processing quality is a very important objective for Chinese wheat breeding programs. Twenty-five CIMMYT and Chinese spring wheat cultivars were grown at four managed conditions by CIMMYT in Cd. Obregon, Sonora, Mexico and in nine environments in China, over two successive wheat seasons from 2000 to 2002. These trials were used to identify patterns of cultivar, environment and cultivar x environment interactions, and to determine opportunities for indirect selection for protein content and the protein-quality related parameter, SDS sedimentation (SDSS) value. The cultivar Inqalab 91 showed low levels of interaction with environments in the 2000-01 crop cycle for protein content, and expressed intermediate levels for both protein content and SDSS value, across most of the environments in both years. Longmai 26 had consistently high protein content and SDSS value across environments in both years, indicating that it is possible to breed cultivars expressing high yields with good protein properties. Cluster analyses revealed that cultivars grouped differently for protein content and SDSS value. Besides photoperiod, water availability appeared to influence the ranking of cultivars for protein content and SDSS value. Temperature and soil type may underlie the observed interactions for protein content, while temperature may also be a factor associated with interactions for SDSS value. The full irrigation managed environment in Mexico, with the cultivars sown on raised beds two months later than optimum and exposing them to late heat, clustered together with the Chinese environments Huhhot, Yongning, and Hejin in the 2000-01 season for SDSS value. This indicates that there is an opportunity to exploit indirect responses to selection in the CIMMYT management environments for SDSS value with relevance for China's spring wheat regions. However, there seemed little chance for positive indirect selection in CIMMYT's managed environments for China in regard to protein content, as environments clustered distinctly. Pattern analyses permitted a sensible and useful summary for this multi environment experiment, helping in understanding natural relationships and variations in cultivar performance among the various environment groups, and assisting in the structuring of environments.

The effects of density on the growth and survival of different families of juvenile Penaeus japonicus Bate

Variations in the growth and survival of six families of juvenile (initial mean weight = 4.16 g) Penaeus japonicus were examined at two densities (48 and 144 individuals m(-2)) in a controlled laboratory experiment. Survival was very high throughout the experiment (95.4%), but differed significantly between densities and rearing tanks. Family, sex and family x density interaction did not significantly affect survival. Mean specific growth rate (SGR) of the shrimp was 18% faster at the low density (1.93 +/- 0.05% day(-1)) than at high density (1.64 +/- 0.03% day(-1)). However, there was a small but significant interaction between family and density indicating that growth of the families was not consistent at both densities. The inconsistent growth of the families across the two densities resulted in a change in the relative performance (ranking) of families at each density. Sex, rearing tank and rearing cage also affected growth of the shrimp. Mean SGR of the females (1.79 +/- 0.03% day(-1)) was 5% faster than males (1.70 +/- 0.03% day(-1)) when averaged across both densities. Shrimp grew significantly faster in rearing tank 3 than rearing tank 1 or 2 at both densities. Results of the present study suggest that family x density interaction could affect the efficiency of selection for growth if shrimp stocks produced from shrimp breeding programs are to be grown across a wide range of densities. Crown Copyright (C) 2004 Published by Elsevier B.V. All rights reserved.

Challenges to environmental toxicology and epidemiology: where do we stand and which way do we go?

Modern toxicology investigates a wide array of both old and new health hazards. Priority setting is needed to select agents for research from the plethora of exposure circumstances. The changing societies and a growing fraction of the aged have to be taken into consideration. A precise exposure assessment is of importance for risk estimation and regulation. Toxicology contributes to the exploration of pathomechanisms to specify the exposure metrics for risk estimation. Combined effects of co-existing agents are not yet sufficiently understood. Animal experiments allow a separate administration of agents which can not be disentangled by epidemiological means, but their value is limited for low exposure levels in many of today's settings. As an experimental science, toxicology has to keep pace with the rapidly growing knowledge about the language of the genome and the changing paradigms in cancer development. During the pioneer era of assembling a working draft of the human genome, toxicogenomics has been developed. Gene and pathway complexity have to be considered when investigating gene-environment interactions. For a best conduct of studies, modem toxicology needs a close liaison with many other disciplines like epidemiology and bioinformatics. (C) 2004 Elsevier Ireland Ltd. All rights reserved.

Rhizodeposits of Trifolium pratense and Lolium perenne: Their comparative effects on 2,4-D mineralization in two contrasting soils

Rhizosphere enhanced biodegradation of organic pollutants has been reported frequently and a stimulatory role for specific components of rhizodeposits postulated. As rhizodeposit composition is a function of plant species and soil type, we compared the effect of Lolium perenne and Trifolium pratense grown in two different soils (a sandy silt loam: pH 4, 2.8% OC, no previous 2,4-D exposure and a silt loam: pH 6.5, 4.3% OC, previous 2,4-D exposure) on the mineralization of the herbicide 2,4-D (2,4-dichlorophenoxyacetic acid). We investigated the relationship of mineralization kinetics to dehydrogenase activity, most probable number of 2,4-D degraders (MPN2,4-D) and 2,4-D degrader composition (using sequence analysis of the gene encoding alpha-ketoglutarate/2,4-D dioxygenase (tfdA)). There were significant (P < 0.01) plant-soil interaction effects on MPN2,4-D and 2,4-D mineralization kinetics (e.g. T pratense rhizodeposits enhanced the maximum mineralization rate by 30% in the acid sandy silt loam soil, but not in the neutral silt loam soil). Differences in mineralization kinetics could not be ascribed to 2,4-D degrader composition as both soils had tfdA sequences which clustered with tfdAs representative of two distinct classes of 2,4-D degrader: canonical R. eutropha JMP134-like and oligotrophic alpha-proteobacterial-like. Other explanations for the differential rhizodeposit effect between soils and plants (e.g. nutrient competition effects) are discussed. Our findings stress that complexity of soil-plant-microbe interactions in the rhizosphere make the occurrence and extent of rhizosphere-enhanced xenobiotic degradation difficult to predict.

A genetically informed study of the processes underlying the association between parental marital instability and offspring adjustment

Parental divorce is associated with problematic offspring adjustment, but the relation may be due to shared genetic or environmental factors. One way to test for these confounds is to study offspring of twins discordant for divorce. The current analyses used this design to separate the mechanisms responsible for the association between parental divorce, experienced either before or after the age of 16, and offspring well-being. The results were consistent with a causal role of divorce in earlier initiation of sexual intercourse and emotional difficulties, in addition to a greater probability of educational problems, depressed mood, and suicidal ideation. In contrast, the increased risk for cohabitation and earlier initiation of drug use was explained by selection factors, including genetic confounds.