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.

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.

Simulating the effects of dominance and epistasis on selection response in the CIMMYT wheat breeding program using QuCim

Plant breeders use many different breeding methods to develop superior cultivars. However, it is difficult, cumbersome, and expensive to evaluate the performance of a breeding method or to compare the efficiencies of different breeding methods within an ongoing breeding program. To facilitate comparisons, we developed a QU-GENE module called QuCim that can simulate a large number of breeding strategies for self-pollinated species. The wheat breeding strategy Selected Bulk used by CIMMYT's wheat breeding program was defined in QuCim as an example of how this is done. This selection method was simulated in QuCim to investigate the effects of deviations from the additive genetic model, in the form of dominance and epistasis, on selection outcomes. The simulation results indicate that the partial dominance model does not greatly influence genetic advance compared with the pure additive model. Genetic advance in genetic systems with overdominance and epistasis are slower than when gene effects are purely additive or partially dominant. The additive gene effect is an appropriate indicator of the change in gene frequency following selection when epistasis is absent. In the absence of epistasis, the additive variance decreases rapidly with selection. However, after several cycles of selection it remains relatively fixed when epistasis is present. The variance from partial dominance is relatively small and therefore hard to detect by the covariance among half sibs and the covariance among full sibs. The dominance variance from the overdominance model can be identified successfully, but it does not change significantly, which confirms that overdominance cannot be utilized by an inbred breeding program. QuCim is an effective tool to compare selection strategies and to validate some theories in quantitative genetics.

Genetic variation for carbon isotope discrimination in sunflower: Association with transpiration efficiency and evidence for cytoplasmic inheritance

Plants accumulate isotopes of carbon at different rates because of discrimination against C-13 relative to C-12. In plants that fix carbon by the C-3 pathway, the amount of discrimination correlates negatively with transpiration efficiency (TE) where TE is the amount of dry matter accumulated per unit water transpired. Therefore, carbon isotope discrimination (Delta) has become a useful tool for selecting genotypes with improved TE and performance in dry environments. Surveys of 161 sunflower (Helianthus spp.) genotypes of diverse origin revealed a large and unprecedented range of genetic variation for Delta (19.5-23.8parts per thousand). A strong negative genetic correlation (r(g)) between TE and Delta (r(g) = -0.87, P < 0.001) was observed in glasshouse studies. Gas exchange measurements of field grown plants indicated that Delta was strongly correlated with stomatal conductance to water vapor (g), (r(g) 0.64, P < 0.01), and the ratio of net assimilation rate (A) to g, (r(g) = 0.86, P < 0.001), an instantaneous measure of TE. Genotype CMSHA89MAX1 had the lowest TE (and highest Delta) of all genotypes tested in these studies and low yields in hybrid combination. Backcrossing studies showed that the TE of this genotype was due to an adverse effect of the MAX1 cytoplasm, which was inherited from the diploid perennial H. maximiliani Schrader. Overall, these studies suggested that there is an excellent opportunity for breeders to develop sunflower germplasm with improved TE. This can be achieved, in part, by avoiding cytoplasms such as the MAX1 cytoplasm.

Estimating percolation and lateral water flow on sloping land in rainfed lowland rice ecosystem

Quantifying water losses in paddy fields assists estimation of water availability in rainfed lowland rice ecosystem. Little information is available on water balance in different toposequence positions of sloped rainfed lowland. Therefore, the aim of this work was to quantify percolation and the lateral water flow with special reference to the toposequential variation. Data used for the analysis was collected in Laos and northeast Thailand. Percolation and water tables were measured on a daily basis using a steel cylindrical tube with a lid and perforated PVC tubes, respectively. Percolation rate was determined using linear regression analysis of cumulative percolation. Assuming that the total amount of evaporation and transpiration was equivalent to potential evapotranspiration, the lateral water flow was estimated using the water balance equation. Separate perched water and groundwater tables were observed in paddy fields on coarse-textured soils. The percolation rate varied between 0 and 3 mm/day across locations, and the maximum water loss by lateral movement was more than 20 mm/day. Our results are in agreement with the previously reported findings, and the methodology of estimating water balance components appears reasonably acceptable. With regard to the toposequential variation, the higher the position in the topoesquence, the greater potential for water loss because of higher percolation and lateral flow rates.

Global adaptation of spring bread and durum wheat lines near-isogenic for major reduced height genes

The effect of major dwarfing genes, Rht-B1 and Rht-D1, in bread (Triticum aestivum L.) and durum (Triticum turgidum L. var. durum) wheats varies with environment. Six reduced-height near-isogenic spring wheat lines, included in the International Adaptation Trial (IAT), were grown in 81 trials around the world. Of the 56 IAT trials yielding > 3 Mg ha(-1), the mean yield of semidwarfs was significantly greater than tails in 54% of trials; in the 27 trials yielding < 3 Mg ha-1, semidwarfs were superior in only 24%. Sixteen pairs of semidwarf-tall near-isolines were grown in six managed drought environment trials (DETs) in northwestern Mexico. In these trials, semidwarfs outyielded talls in all but the most droughted environment (2.5 Mg ha(-1)). The effect of the height alleles varied with genetic background and environment. For both yield and height, variance components for allele and environment by allele interaction were larger than those for genetic background and genetic background by environment. Pattern analysis showed that tall and semidwarf lines had similar adaptation to stressed environments (< 2.8 Mg ha(-1), low rainfall), while semidwarfs yielded more in less stressed environments (> 4.3 Mg ha(-1), high rainfall). The best adapted near-isogenic pair had a Kauz background, where the tall was only 16% taller than the dwarf. In the Kauz-derived pair, the semidwarf outyielded the tall in only 13% of trials with no differences in low yielding trials. This supports the idea that '' short talls '' may be useful in marginal environments (yield < 3 Mg ha(-1)).

Timing, magnitude, and location of initial soluble aluminum injuries to mungbean roots

Despite a century's knowledge that soluble aluminum (Al) is associated with acid soils and poor plant growth, it is still uncertain how Al exerts its deleterious effects. Hypotheses include reactions of Al with components of the cell wall, plasmalemma, or cytoplasm of cells close to the root tip, thereby reducing cell expansion and root growth. Digital microscopy was used to determine the initial injuries of soluble Al to mungbean (Vigna radiata L.) roots. Roots of young seedlings were marked with activated carbon particles and grown in 1 mm CaCl2 solution at pH 6 for ca. 100 min (control period), and AlCl3 solution was added to ensure a final concentration of 50 muM Al (pH 4). Further studies were conducted on the effects of pH 4 with and without 50 muM Al. Four distinct, but possibly related, initial detrimental effects of soluble Al were noted. First, there was a 56-75% reduction in the root elongation rate, first evident 18-52 min after the addition of Al, root elongation continuing at a decreased rate for ca. 20 It. Decreasing solution pH from 6 to 4 increased the root elongation rate 4-fold after 5 min, which decreased to close to the original rate after 130 min. The addition of Al during the period of rapid growth at pH 4 reduced the root elongation rate by 71% 14 min after the addition of Al. The activated carbon marks on the roots showed that, during the control period, the zone of maximum root growth occurred at 2,200-5,100 mum from the root tip (i.e. the cell elongation zone). It was there that Al first exerted its detrimental effect and low pH increased root elongation. Second, soluble Al prevented the progress of cells from the transition to the elongation phase, resulting in a considerable reduction of root growth over the longer term. The third type of soluble Al injury occurred after exposure for ca. 4 h to 50 mum Al when a kink developed at 2,370 mum from the root tip. Fourth, ruptures of the root epidermal and cortical cells at 1,900-2,300 mum from the tip occurred greater than or equal to4.3 h after exposure to soluble Al. The timing and location of Al injuries support the contention that Al initially reduces cell elongation, thus decreasing root growth and causing damage to epidermal and cortical cells.

A simple regional-scale model for forecasting sorghum yield across North-Eastern Australia

Sorghum is the main dryland summer crop in NE Australia and a number of agricultural businesses would benefit from an ability to forecast production likelihood at regional scale. In this study we sought to develop a simple agro-climatic modelling approach for predicting shire (statistical local area) sorghum yield. Actual shire yield data, available for the period 1983-1997 from the Australian Bureau of Statistics, were used to train the model. Shire yield was related to a water stress index (SI) that was derived from the agro-climatic model. The model involved a simple fallow and crop water balance that was driven by climate data available at recording stations within each shire. Parameters defining the soil water holding capacity, maximum number of sowings (MXNS) in any year, planting rainfall requirement, and critical period for stress during the crop cycle were optimised as part of the model fitting procedure. Cross-validated correlations (CVR) ranged from 0.5 to 0.9 at shire scale. When aggregated to regional and national scales, 78-84% of the annual variation in sorghum yield was explained. The model was used to examine trends in sorghum productivity and the approach to using it in an operational forecasting system was outlined. (c) 2005 Elsevier B.V. All rights reserved.

Molecular Breeding for Rainfed Lowland Rice in the Mekong Region

In the past 20 years, the rice-breeding program in Thailand had little success in developing new cultivars to replace Kao Dawk Mali 105 (KDML105) and Kao Khor 6 (RD6) for the tainted lowland rice environments. The main reason for the poor adoption of new cultivars by farmers is the susceptibility to diseases and unacceptable grain qualities. The conventional breeding program also takes at least 15 years from initial crossing to the release of new cultivars. A new breeding strategy can be established to shorten the period for cultivar improvement by using marker-assisted selection (MAS), rapid generations advance (RGA), and early generation testing in multi-locations for grain yield and qualities. Four generation of MAS backcross breeding were conducted to transfer genes and QTL for bacterial blight resistance (BLB), submergence tolerance (SUB), brown plant hopper resistance (BPH) and blast resistance (BL) into KDML105. Selected backcross lines, introgressed with target gene/QTL, were tolerant to SUB and resistant to BLB, BPH and BL. The agronomic performance and grain quality of these lines were as good as or better than KDML105.