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

New tools derived from advances in molecular biology have not been widely adopted in plant breeding because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. We explore whether a crop growth and development modelling framework can link phenotype complexity to underlying genetic systems in a way that strengthens molecular breeding strategies. We use gene-to-phenotype simulation studies on sorghum to consider the value to marker-assisted selection of intrinsically stable QTLs that might be generated by physiological dissection of complex traits. The consequences on grain yield of genetic variation in four key adaptive traits – phenology, osmotic adjustment, transpiration efficiency, and staygreen – were simulated for a diverse set of environments by placing the known extent of genetic variation in the context of the physiological determinants framework of a crop growth and development model. It was assumed that the three to five genes associated with each trait, had two alleles per locus acting in an additive manner. The effects on average simulated yield, generated by differing combinations of positive alleles for the traits incorporated, varied with environment type. 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 with 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. We simulated a marker-assisted selection (MAS) breeding strategy based on the analyses of gene effects. When marker scores were allocated based on the contribution of gene effects to yield in a single environment, there was a wide divergence in rate of yield gain over all environments with breeding cycle depending on the environment chosen for the QTL analysis. It was suggested that knowledge resulting from trait physiology and modelling would overcome this dependency by identifying stable QTLs. The improved predictive power would increase the utility of the QTLs in MAS. 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 QTLs.

A review of the use of the basic cation saturation ratio and the "ideal" soil

The use of 'balanced' Ca, Mg, and K ratios, as prescribed by the basic cation saturation ratio (BCSR) concept, is still used by some private soil-testing laboratories for the interpretation of soil analytical data. This review aims to examine the suitability of the BCSR concept as a method for the interpretation of soil analytical data. According to the BCSR concept, maximum plant growth will be achieved only when the soil’s exchangeable Ca, Mg, and K concentrations are approximately 65 % Ca, 10 % Mg, and 5 % K (termed the ‘ideal soil’). This ‘ideal soil’ was originally proposed by Firman Bear and co-workers in New Jersey (USA) during the 1940s as a method of reducing luxury K uptake by alfalfa (Medicago sativa L.). At about the same time, William Albrecht, working in Missouri (USA), concluded through his own investigations that plants require a soil with a high Ca saturation for optimal growth. Whilst it now appears that several of Albrecht’s experiments were fundamentally flawed, the BCSR (‘balanced soil’) concept has been widely promoted, suggesting that the prescribed cationic ratios provide optimum chemical, physical, and biological soil properties. Our examination of data from numerous studies (particularly those of Albrecht and Bear, themselves) would suggest that, within the ranges commonly found in soils, the chemical, physical, and biological fertility of a soil is generally not influenced by the ratios of Ca, Mg, and K. The data do not support the claims of the BCSR, and continued promotion of the BCSR will result in the inefficient use of resources in agriculture and horticulture.

Alleviation of dormancy in annual ryegrass (Lolium rigidum) seeds by hydration and after-ripening

The effect of hydration (priming) treatment on dormancy release in annual ryegrass seeds from two populations was investigated. Hydration duration, number, and timing with respect to after-ripening were compared in an experiment involving 15 treatment regimens for 12 wk. Seeds were hydrated at 100% relative humidity for 0, 2, or 10 d at Weeks 1, 6, or 12 of after-ripening. Dormancy status was assessed after each hydration treatment by measuring seed germination at 12-hourly alternating 25/15 C (light/dark) periods using seeds directly from the hydration treatment and seeds subjected to 4 d postpriming desiccation. Seeds exposed to one or more hydration events during the 12 wk were less dormant than seeds that remained dry throughout after-ripening. The longer hydration of 10 d promoted greater dormancy loss than either a 2-d hydration or no hydration. For the seed lot that was most dormant at the start of the experiment, two or three rather than one hydration event or a hydration event earlier rather than later during after-ripening promoted greater dormancy release. These effects were not significant for the less-dormant seed lot. For both seed lots, the effect of a single hydration for 2 d at Week 1 or 6 of after-ripening was not manifested until the test at Week 12 of the experiment, suggesting that the hydration events alter the rate of dormancy release during subsequent after-ripening. A hydrothermal priming time model, usually used for modeling the effect of priming on germination rate of nondormant seeds, was successfully applied to dormancy release resulting from the hydration treatments.

Evaluation of synergistic interactions between the Colorado potato beetle (Coleoptera : Chrysomelidae) pathogen Beauveria bassiana and the insecticides, imidacloprid, and cyromazine

Laboratory studies investigated the interaction between the fungal entomopathogen Beauveria bassiana (Balsamo) Vuillemin and sublethal doses of the insecticides imidacloprid and cyromazine when applied to larvae of the Colorado potato beetle, Leptinotarsa decemlinenta (Say). When second instars were fed potato leaf discs treated with sublethal doses of imidacloprid and a range of doses of B. bassiana, a synergistic action was demonstrated. Similar results were observed when larvae were sprayed directly with B. bassiana conidia and immediately fed leaf discs treated with imidacloprid. No synergistic interaction was detected when larvae were fed leaf discs treated with sublethal doses of imidacloprid 24 h after application of R. bassiana conidia to larvae. However, a synergistic interaction was detected when larvae were fed leaf discs treated with imidacloprid and sprayed with B, bassiana conidia 24 h later. Although sublethal doses of both imidacloprid and the triazine insect growth regulator (IGR) cyromazine prolonged the duration of the second instar, only imidacloprid interacted with B. bassiana to produce a synergistic response in larval mortality. In leaf consumption studies, the highest dose of B, bassiana tested promoted feeding in inoculated second instars. Feeding was inhibited when larvae were fed foliage treated with sublethal doses of imidacloprid and significantly reduced when fed foliage treated with a sublethal dose of cyromazine. Starvation of larvae for 24 h immediately after B. bassiana treatment produced a similar result to the combined treatment of B. bassiana and imidacloprid and increased the level of mycosis when compared with B. bassiana controls. Imidacloprid treatment affected neither the rate of germination of B. bassiana conidia on the insect cuticle nor the rate at which conidia were removed from the integument after application. The statistical analysis used to detect synergism and the possible role of starvation-induced stress factors underlying the observed synergistic interactions are discussed.

Development of a mungbean (Vigna radiata) RFLP linkage map and its comparison with lablab (Lablab purpureus) revelas a high level of colinearity between the two genomes

A genetic linkage map of mungbean (Vigna radiata, 2n = 2x = 22) consisting of 255 RFLP loci was developed using a recombinant inbred population of 80 individuals. The population was derived from an intersubspecific cross between the cultivated mungbean variety 'Berken' and a wild mungbean genotype 'ACC 41' (V radiata subsp. sublobata). The total length of the map, which comprised 13 linkage groups, spanned 737.9 cM with an average distance between markers of 3.0 cM and a maximum distance between linked markers of 15.4 cM. The mungbean map was compared to a previously published map of lablab (Lablab purpureus, 2n = 2x = 24) using a common set of 65 RFLP probes. In contrast to some other comparative mapping studies among members of the Fabaceae, where a high level of chromosomal rearrangement has been observed, marker order between mungbean and lablab was found to be highly conserved. However, the two genomes have apparently accumulated a large number of duplications/deletions after they diverged.

Mechanisms and diversity of resistance to sorghum midge, Stenodiplosis sorghicola in Sorghum bicolor

Sorghum midge, Stenodiplosis sorghicola (Coquillett) is the most important pest of grain sorghum worldwide, and plant resistance is an important component for the control of this pest. To identify sorghum genotypes with diverse mechanisms of resistance to sorghum midge, we studied oviposition, larval survival, and midge damage in 27 sorghum midge-resistant genotypes, and a susceptible check under greenhouse conditions. Observations were also recorded on floral characteristics and compensation in grain mass. Of the 28 sorghum genotypes tested, 19 showed high levels of antixenosis to oviposition as a component of resistance, and had

Low temperature induced spikelet sterility in rice. II. Effects of panicle and root temperatures

Low temperatures impose restrictions on rice (Oryza sativa L.) production at high latitudes. This study is related to low temperature damage that can arise mid-season during the panicle development phase. The objective of this study was to determine whether low temperature experienced by the root, panicle, or foliage is responsible for increased spikelet sterility. In temperature-controlled glasshouse experiments, water depth, and water and air temperatures, were changed independently to investigate the effects of low temperature in the root, panicle, and foliage during microspore development on spikelet sterility. The total number of pollen and number of engorged pollen grains per anther, and the number of intercepted and germinated pollen grains per stigma, were measured. Spikelet sterility was then analysed in relation to the total number of pollen grains per spikelet and the efficiency with which these pollen grains became engorged, were intercepted by the stigma, germinated, and were involved in fertilisation. There was a significant combined effect of average minimum panicle and root temperatures on spikelet sterility that accounted for 86% of the variation in spikelet sterility. Total number of pollen grains per anther was reduced by low panicle temperature, but not by low root temperature. Whereas engorgement efficiency ( the percentage of pollen grains that were engorged) was determined by both root and panicle temperature, germination efficiency (the percentage of germinated pollen grains relative to the number of engorged pollen grains intercepted by the stigma) was determined only by root temperature. Interception efficiency (i.e. percentage of engorged pollen grains intercepted by the stigma), however, was not affected by either root or panicle temperature. Engorgement efficiency was the dominant factor explaining the variation in spikelet sterility. It is concluded that both panicle and root temperature affect spikelet sterility in rice when the plant encounters low temperatures during the microspore development stage.

Seed viability and dormancy mechanisms of Leucopogon melaleucoides Cunn. ex DC. (Epacridaceae)

Leucopogon melaleucoides, a flowering shrub, is desired by floricultural markets but is difficult to propagate. Seed viability was tested and dormancy mechanisms were studied to develop a commercial propagation system. Although around 56% of seed were viable, germination was completely inhibited unless the endocarp was removed. After-ripened seed (8 months after collection) germinated faster than fresh seed (2 days after collection), but germination occurred over a prolonged period (155 days). Germination of after-ripened seed was promoted with GA(3) or a commercial smoke product containing unknown plant growth regulators. All viable seed treated with GA(3) at 1000 mg L-1 had germinated after 24 days. The results suggest that both a physical and physiological dormancy mechanism occur for this species, with removal of the endocarp and pretreatment with 1000 mg L-1 GA(3) promoting complete germination of viable seed.

On systems thinking, systems biology and the in Silico Plant

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

Potential yield and water-use effficiency benefits in sorghum from limited maximum transpiration rate

Limitations on maximum transpiration rates, which are commonly observed as midday stomatal closure, have been observed even under well-watered conditions. Such limitations may be caused by restricted hydraulic conductance in the plant or by limited supply of water to the plant from uptake by the roots. This behaviour would have the consequences of limiting photosynthetic rate, increasing transpiration efficiency, and conserving soil water. A key question is whether the conservation of water will be rewarded by sustained growth during seed fill and increased grain yield. This simulation analysis was undertaken to examine consequences on sorghum yield over several years when maximum transpiration rate was imposed in a model. Yields were simulated at four locations in the sorghum-growing area of Australia for 115 seasons at each location. Mean yield was increased slightly ( 5 - 7%) by setting maximum transpiration rate at 0.4 mm h(-1). However, the yield increase was mainly in the dry, low-yielding years in which growers may be more economically vulnerable. In years with yield less than similar to 450 g m(-2), the maximum transpiration rate trait resulted in yield increases of 9 - 13%. At higher yield levels, decreased yields were simulated. The yield responses to restricted maximum transpiration rate were associated with an increase in efficiency of water use. This arose because transpiration was reduced at times of the day when atmospheric demand was greatest. Depending on the risk attitude of growers, incorporation of a maximum transpiration rate trait in sorghum cultivars could be desirable to increase yields in dry years and improve water use efficiency and crop yield stability.

Modelling, nitrogen dynamics in sugarcane systems: Recent advances and applications

Substantial amounts of nitrogen (N) fertiliser are necessary for commercial sugarcane production because of the large biomass produced by sugarcane crops. Since this fertiliser is a substantial input cost and has implications if N is lost to the environment, there are pressing needs to optimise the supply of N to the crops' requirements. The complexity of the N cycle and the strong influence of climate, through its moderation of N transformation processes in the soil and its impact on N uptake by crops, make simulation-based approaches to this N management problem attractive. In this paper we describe the processes to be captured in modelling soil and plant N dynamics in sugarcane systems, and review the capability for modelling these processes. We then illustrate insights gained into improved management of N through simulation-based studies for the issues of crop residue management, irrigation management and greenhouse gas emissions. We conclude by identifying processes not currently represented in the models used for simulating N cycling in sugarcane production systems, and illustrate ways in which these can be partially overcome in the short term. (c) 2005 Elsevier B.V. All rights reserved.

Synthesis, crystal structure and herbicidal activity of mimics of intermediates of the KARI reaction

Two mimics of the intermediate in the reaction catalyzed by ketol-acid reductoisomerase (KARI) were synthesized. Their structures were established on the basis of elemental analyses, IR, H-1 NMR and GC/mass detector. The crystal structure of compound 2 was found to be a substituted dioxane, formed by the condensation of two molecules. The two compounds showed some herbicidal activity on the basis of tests using rape root and barnyard grass growth inhibition. However, the herbicidal effect was weaker in greenhouse tests. (c) 2004 Society of Chemical Industry.

Effects of litter and fine root composition on their decomposition in a Rhodic Paleustalf under different land uses

Plant litter and fine roots are important in maintaining soil organic carbon (C) levels as well as for nutrient cycling. The decomposition of surface-placed litter and fine roots of wheat ( Triticum aestivum ), lucerne ( Medicago sativa ), buffel grass ( Cenchrus ciliaris ), and mulga ( Acacia aneura ), placed at 10-cm and 30-cm depths, was studied in the field in a Rhodic Paleustalf. After 2 years, = 60% of mulga roots and twigs remained undecomposed. The rate of decomposition varied from 4.2 year -1 for wheat roots to 0.22 year -1 for mulga twigs, which was significantly correlated with the lignin concentration of both tops and roots. Aryl+O-aryl C concentration, as measured by 13 C nuclear magnetic resonance spectroscopy, was also significantly correlated with the decomposition parameters, although with a lower R 2 value than the lignin concentration. Thus, lignin concentration provides a good predictor of litter and fine root decomposition in the field.