Genotypic variation and covariation in wheat seedling seminal root architecture and grain yield under field conditions.

KEY MESSAGE: Greater embryo size in a large and carefully phenotyped mapping population was genetically associated with a greater number of longer seminal roots to increase grain yield in droughted field environments. Breeding modification of root architecture is challenging in field environments owing to genetic and phenotypic complexity, and poor repeatability with root sampling. Seeds from a large mapping population varying in embryo size were harvested from a common glasshouse and standardised to a common size before assessing in rolled germination paper at 12 and 20 °C for seedling growth. Differences in genotype means were large and heritabilities high (h2 = 0.55-0.93) indicating strong and repeatable genotypic differences for most root traits. Seminal roots 1 to 3 were produced on all seedlings, whereas growth of seminal roots 4, 5 and 6 was associated with differences in embryo size. Increases in seminal root number from 4 to 6 per plant were strongly, genetically correlated with increases in total seminal length (rg = 0.84, < 0.01). Multivariate analysis confirmed initiation and growth of seminal roots 1, 2 and 3, and of roots 4, 5 and 6 behaved as genetically independent (rPg = 0.15 ns) cohorts. Tails representing extremes in seedling root length and number were associated with significant differences in grain yield of up to 35% in droughted field environments but were not different in irrigated environments. Increases in grain yield were linked to greater lengths of seminal roots 4, 5 and 6 and were largely independent of plant height or development. This is the first report on the genetic relationship of seedling root architecture and embryo size, and potential in selection of seminal root size for accessing deep-soil moisture in droughted environments.

"Rolled-upness": phenotyping leaf rolling in cereals using computer vision and functional data analysis approaches.

BACKGROUND: The flag leaf of a wheat (Triticum aestivum L.) plant rolls up into a cylinder in response to drought conditions and then unrolls when leaf water relations improve. This is a desirable trait for extending leaf area duration and improving grain size particularly under drought. But how do we quantify this phenotype so that different varieties of wheat or different treatments can be compared objectively since this phenotype can easily be confounded with inter-genotypic differences in root-water uptake and/or transpiration at the leaf level if using traditional methods? RESULTS: We present a new method to objectively test a range of lines/varieties/treatments for their propensity of leaves to roll. We have designed a repeatable protocol and defined an objective measure of leaf curvature called "rolled-upness" which minimises confounding factors in the assessment of leaf rolling in grass species. We induced leaf rolling by immersing leaf strips in an osmoticum of known osmotic pressure. Using micro-photographs of individual leaf cross-sections at equilibrium in the osmoticum, two approaches were used to quantify leaf rolling. The first was to use some properties of the convex hull of the leaf cross-section. The second was to use cubic smoothing splines to approximate the transverse leaf shape mathematically and then use a statistic derived from the splines for comparison. Both approaches resulted in objective measurements that could differentiate clearly between breeding lines and varieties contrasting genetically in their propensity for leaf rolling under water stress. The spline approach distinguished between upward and downward curvature and allowed detailed properties of the rolling to be examined, such as the position on the strip where maximum curvature occurs. CONCLUSIONS: A method applying smoothing splines to skeletonised images of transverse wheat leaf sections enabled objective measurements of inter-genotypic variation for hydronastic leaf rolling in wheat. Mean-curvature of the leaf cross-section was the measure selected to discriminate between genotypes, as it was straightforward to calculate and easily construed. The method has broad applicability and provides an avenue to genetically dissect the trait in cereals.

Of growing importance: combining greater early vigour and transpiration efficiency for wheat in variable rainfed environments.

Increasing climate variability, particularly variability in the timing and amount of soil water, means that breeding wheat (Triticum aestivum L.) varieties with stable high grain yields is increasingly more challenging. Changing environmental conditions in water-limited rainfed environments will alter genotype ranking to reduce confidence in the identification of consistently higher yielding performers. Greater early vigour (EV) and transpiration efficiency (TE) are two physiological traits that have demonstrated benefits as breeding targets for efficient water-use in Mediterranean in-season water and monsoonal stored water environments, respectively. This Perspective discusses the hypothesis that combining higher TE and greater EV will broaden the adaptation and increase grain yields for wheats grown across most rainfed environments. We examine the physiology underpinning adaptation with greater EV and higher TE, as well as the challenges and potential benefits of deploying these traits in combination. We then discuss how these two traits interact with different environments and, in particular, the different wheat-growing regions of Australia. We conclude that the combination of these two traits is genetically and physiologically feasible, as well theoretically beneficial to average yield in most rainfed environments. Hence, we suggest a strategy for reliably managing the complex genetics underpinning EV and TE when phenotyping and selecting both traits in commercial wheat breeding programs.

Recurrent selection for wider seedling leaves increases early biomass and leaf area in wheat (Triticum aestivum L.).

The breeding of wheat with greater early vigour has potential to increase water- and nutrient-use efficiency, as well as to improve weed competitiveness to raise crop yields profitably. Given that wheat is inherently conservative in its early growth, a sustained breeding effort was initiated to increase genetically seedling leaf area in developing novel high vigour germplasm. A recurrent selection programme was initiated by intercrossing a genetically diverse set of 28 vigorous wheat lines identified globally. These were intercrossed at random and S1:2 progeny with the largest leaf 1 and 2 widths were intermated to develop new populations for assessment of early growth. This procedure was repeated for up to 60 segregating families per cycle across six cycles over 15 years. Thirty random S1:2 progeny were retained from each cycle and seed-increased together to produce seed for early vigour assessment in multiple sowings. The most vigorous wheat seedlings were identified in later cycles, with some lines producing more than double the leaf area and biomass of elite commercial wheat varieties. Phenotypic selection for greater leaf width was associated with a realized significant (P<0.01) linear increase per seedling of 0.41 mm per cycle (+7.1%) for mean leaf width, and correlated linear increases in total leaf area and biomass of 4.48 cm(2) per cycle (+10.3%) and 10.8 mg per cycle (+5.3%), respectively. Genetic gains in widths of leaves 2 (+8.4%) and 3 (+11.5%) were significantly (P<0.01) greater than for leaf 1 (+5.3%). Selection for greater leaf width was associated with linear increases in coleoptile tiller leaf area, small curvilinear increases in leaf 1 length, and reductions in numbers of leaves and mainstem tillers. Genetic variances were large and heritabilities high for leaf width and total leaf area in each cycle, but reduced linearly in size with selection across cycles. Coupling diverse germplasm with a simple, inexpensive, and repeatable selection process has confirmed the value of recurrent selection in developing uniquely vigorous wheat germplasm for use as parents in commercial breeding.

Protective effects of glycoursodeoxycholic acid in Barrett's esophagus cells.

Barrett's esophagus (BE) is a premalignant condition associated with the development of esophageal adenocarcinoma (EAC). Previous studies have implicated hydrophobic bile acids and gastric acid in BE and EAC pathogenesis. In this study, we tested the hypothesis that DNA damage, cytotoxicity and oxidative stress induced by bile acids and gastric acid can be attenuated by the cytoprotective, hydrophilic bile acid glycoursodeoxycholic acid (GUDCA). Non-dysplastic BE cells were exposed for 10 min to pH 4 and/or bile acid cocktail or to pH 4 and a modified cocktail consisting of a mixture of bile acids and GUDCA. DNA damage was evaluated by the comet assay; cell viability and proliferation were measured by trypan blue staining and the MTS assay; reactive oxygen species (ROS) were measured using hydroethidium staining; oxidative DNA/RNA damage was detected by immunostaining with antibody against 8-OH-dG; thiol levels were measured by 5-chloromethylfluorescein diacetate (CMFDA) staining; and the expression of antioxidant proteins was evaluated by western blotting. DNA damage and oxidative stress were significantly increased, while thiol levels were decreased in BE cells treated with pH 4 and bile acid cocktail compared with cells treated with pH 4 alone or untreated cells. Bile acids and low pH also significantly decreased cell proliferation. Expression of the antioxidant enzymes, MnSOD and CuZnSOD, was elevated in the cells treated with bile acids and low pH. When GUDCA was included in the medium, all these effects of pH 4 and bile acids were markedly reduced. In conclusion, treatment of BE cells with acidified medium and a bile acid cocktail at physiologically relevant concentrations induces DNA damage, cytotoxicity, and ROS. The cytoprotective bile acid, GUDCA, inhibits these deleterious effects by inhibiting oxidative stress.

Quantitative trait loci for carbon isotope discrimination are repeatable across environments and wheat mapping populations.

Wheat productivity is commonly limited by a lack of water essential for growth. Carbon isotope discrimination (Delta), through its negative relationship with transpiration efficiency, has been used in selection of higher wheat yields in breeding for rainfed environments. The potential also exists for selection of increased Delta for improved adaptation to irrigated and high rainfall environments. Selection efficiency of Delta would be enhanced with a better understanding of its genetic control. Three wheat mapping populations (Cranbrook/Halberd, Sunco/Tasman and CD87/Katepwa) containing between 161 and 190 F(1)-derived, doubled-haploid progeny were phenotyped for Delta and agronomic traits in 3-5 well-watered environments. The range for Delta was large among progeny (c. 1.2-2.3 per thousand), contributing to moderate-to-high single environment (h (2) = 0.37-0.91) and line-mean (0.63-0.86) heritabilities. Transgressive segregation was large and genetic control complex with between 9 and 13 Delta quantitative trait loci (QTL) identified in each cross. The Delta QTL effects were commonly small, accounting for a modest 1-10% of the total additive genetic variance, while a number of chromosomal regions appeared in two or more populations (e.g. 1BL, 2BS, 3BS, 4AS, 4BS, 5AS, 7AS and 7BS). Some of the Delta genomic regions were associated with variation in heading date (e.g. 2DS, 4AS and 7AL) and/or plant height (e.g. 1BL, 4BS and 4DS) to confound genotypic associations between Delta and grain yield. As a group, high Delta progeny were significantly (P < 0.10-0.01) taller and flowered earlier but produced more biomass and grain yield in favorable environments. After removing the effect of height and heading date, strong genotypic correlations were observed for Delta and both yield and biomass across populations (r (g) = 0.29-0.57, P < 0.05) as might be expected for the favorable experimental conditions. Thus selection for Delta appears beneficial in increasing grain yield and biomass in favorable environments. However, care must be taken to avoid confounding genotypic differences in Delta with stature and development time when selecting for improved biomass and yield especially in environments experiencing terminal droughts. Polygenic control and small size of individual QTL for Delta may reduce the potential for QTL in marker-assisted selection for improved yield of wheat.

Genetic variation in tolerance to the osmotic stress componentof salinity stress in durum wheat.

Salinity affects plant growth by the osmotic stress of the salt around the roots as well as by toxicity caused by excessive accumulation of salt in leaves. The aim of this study was to determine whether there is significant genetic variation in tolerance to osmotic stress that can be useful in improving the salinity tolerance of crop plants. Durum wheat is a salt-sensitive crop whose yield is reduced by moderately saline soils. Genetic variation in tolerance to osmotic stress in durum wheat was examined in 50 international durum varieties and landraces by measuring the response of stomatal conductance to salt stress before salts built up in the leaf. Stomatal conductance is a sensitive indicator of the osmotic stress because it is reduced immediately with the onset of salinity, and is the initial and most profound cause of a decline in CO2 assimilation rate. Genetic differences of 2-3-fold were found in the magnitude of the response of stomatal conductance to salt-induced osmotic stress. Higher stomatal conductance in salt related to higher CO2 assimilation rate. There was a positive relationship between stomatal conductance and relative growth rate in salt. This study shows the potential for new genetic gains in salt tolerance in durum wheat.

Nutrient content of whole cottonseed.

The objective of this study was to determine if the nutrient and gossypol contents and in vitro digestibility of 3 types of genetically modified whole cottonseed differed from traditional whole cottonseed. Samples of seed from traditional (no genetic modifications) and genetically modified varieties of cotton grown in 1999 and 2000 were analyzed. Genetic modifications included the insertion of genes to protect cotton from insect pests (Bt), and damage from glyphosate herbicides (RR), and from both (Bt/RR). Year effects were significant for in vitro dry matter (DM) digestibility, gossypol, DM, crude protein (CP), fat, neutral detergent fiber (NDF), acid detergent fiber (ADF), and ash. Higher rainfall resulted in higher CP, fat, and ash and lower NDF and gossypol. There were no differences among seed types for ground or whole seed digestibility, DM, CP, fat, NDF, ADF, ash, lignin, net energy for lactation, amino acids, total fatty acids, or seed index. Overall, the nutrient content and digestibility of varieties of genetically modified seed were similar to that of varieties of traditional whole cottonseed.

Breeding for high water-use efficiency.

There is a pressing need to improve the water-use efficiency of rain-fed and irrigated crop production. Breeding crop varieties with higher water-use efficiency is seen as providing part of the solution. Three key processes can be exploited in breeding for high water-use efficiency: (i) moving more of the available water through the crop rather than it being wasted as evaporation from the soil surface or drainage beyond the root zone or being left behind in the root zone at harvest; (ii) acquiring more carbon (biomass) in exchange for the water transpired by the crop, i.e. improving crop transpiration efficiency; (iii) partitioning more of the achieved biomass into the harvested product. The relative importance of any one of these processes will vary depending on how water availability varies during the crop cycle. However, these three processes are not independent. Targeting specific traits to improve one process may have detrimental effects on the other two, but there may also be positive interactions. Progress in breeding for improved water-use efficiency of rain-fed wheat is reviewed to illustrate the nature of some of these interactions and to highlight opportunities that may be exploited in other crops as well as potential pitfalls. For C3 species, measuring carbon isotope discrimination provides a powerful means of improving water-use efficiency of leaf gas exchange, but experience has shown that improvements in leaf-level water-use efficiency may not always translate into higher crop water-use efficiency or yield. In fact, the reverse has frequently been observed. Reasons for this are explored in some detail. Crop simulation modelling can be used to assess the likely impact on water-use efficiency and yield of changing the expression of traits of interest. Results of such simulations indicate that greater progress may be achieved by pyramiding traits so that potential negative effects of individual traits are neutralized. DNA-based selection techniques may assist in such a strategy.

Breeding Opportunities for Increasing the Efficiency of Water Use and Crop Yield in Temperate Cereals.

Genetic advances in grain yield under rainfed conditions have been achieved by empirical breeding methods. Progress is slowed, however, by large genotype x season and genotype x location interactions arising from unpredictable rainfall, which is a feature of dry environments. A good understanding of factors limiting and/or regulating yield now provides us with an opportunity to identify and then select for physiological and morphological traits that increase the efficiency of water use and yield under rainfed conditions. The incorporation of these traits into breeders' populations should broaden their genetic base. It also may lead to faster selection methods and selection for the traits may result in correlated gains in yield. Here, we undertake a review of factors that limit yield in rainfed environments and discuss genetic opportunities and genetic progress in overcoming them. The examples given are for wheat (Triticum aestivum L.), but the principles apply to all cereal crops grown in dry environments.

Improving Intrinsic Water-Use Efficiency and Crop Yield.

Greater yield per unit rainfall is one of the most important challenges in dryland agriculture. Improving intrinsic water-use efficiency (W(T)), the ratio of CO(2) assimilation rate to transpiration rate at the stomata, may be one means of achieving this goal. Carbon isotope discrimination (Delta(13)C) is recognized as a reliable surrogate for W(T) and there have now been numerous studies which have examined the relationship between crop yield and W(T) (measured as Delta(13)C). These studies have shown the relationship between yield and W(T) to be highly variable. The impact on crop yield of genotypic variation in W(T) will depend on three factors: (i) the impact of variation in W(T) on crop growth rate, (ii) the impact of variation in W(T) on the rate of crop water use, and (iii) how growth and water use interact over the crop's duration to produce grain yield. The relative importance of these three factors will differ depending on the crop species being grown and the nature of the cropping environment. Here we consider these interactions using (i) the results of field trials with bread wheat (Triticum aestivum L.), durum wheat (T. turgidum L.), and barley (Hordeum vulgare L.) that have examined the association between yield and Delta(13)C and (ii) computer simulations with the SIMTAG wheat crop growth model. We present details of progress in breeding to improve W(T) and yield of wheat for Australian environments where crop growth is strongly dependent on subsoil moisture stored from out-of-season rains and assess other opportunities to improve crop yield using W(T).

Effect of salinity on water relations and growth of wheat genotypes with contrasting sodium uptake.

Four wheat genotypes with contrasting degrees of Na+ exclusion were selected to see if low Na+ uptake had an adverse effect on water relations or growth rates during exposure to saline conditions. Plants were grown in supported hydroponics with and without 150 mM NaCl, and sampled for measurements of water relations, biomass, stomatal conductance, and ion accumulation. After 4 weeks exposure to salt, biomass was reduced in all genotypes to a similar extent (about 50%), with the effect of salinity on relative growth rate confined largely to the first week. There was little difference between genotypes in the effect of salinity on water relations, as indicated by their relative water content and estimated turgor. Osmotic adjustment occurred in all genotypes, with one of the low-Na+ genotypes having the greatest adjustment. In the low-Na+ genotypes, osmotic adjustment depended on higher K+ and high organic solute accumulation. Stomatal conductance of all genotypes was reduced by saline conditions, but the reduction was greater in the low-Na+ genotypes. These genotypes also showed a larger fall in the value of carbon isotope discrimination measured in expanding leaves, indicating a greater transpiration efficiency when exposed to saline conditions. Chlorophyll fluorescence measurements failed to indicate damage to photochemical pathways in either high- or low-Na+ genotypes. These data indicate that selecting lines with low Na+ accumulation for the purpose of improving salt tolerance is unlikely to introduce limitations for osmotic adjustment.

On combinatorial DNA word design.

We consider the problem of designing DNA codes, namely sets of equi-length words over the alphabet [A, C, G, T] that satisfy certain combinatorial constraints. This problem is motivated by the task of reliably storing and retrieving information in synthetic DNA strands for use in DNA computing or as molecular bar codes in chemical libraries. The primary constraints that we consider, defined with respect to a parameter d, are as follows: for every pair of words w, x in a code, there are at least d mismatches between w and x if w not equal x and also between the reverse of w and the Watson-Crick complement of x. Extending classical results from coding theory, we present several upper and lower bounds on the maximum size of such DNA codes and give methods for constructing such codes. An additional constraint that is relevant to the design of DNA codes is that the free energies and enthalpies of the code words, and thus the melting temperatures, be similar. We describe dynamic programming algorithms that can (a) calculate the total number of words of length n whose free energy value, as approximated by a formula of Breslauer et al. (1986) falls in a given range, and (b) output a random such word. These algorithms are intended for use in heuristic algorithms for constructing DNA codes.

DNA computing on surfaces.

DNA computing was proposed as a means of solving a class of intractable computational problems in which the computing time can grow exponentially with problem size (the 'NP-complete' or non-deterministic polynomial time complete problems). The principle of the technique has been demonstrated experimentally for a simple example of the hamiltonian path problem (in this case, finding an airline flight path between several cities, such that each city is visited only once). DNA computational approaches to the solution of other problems have also been investigated. One technique involves the immobilization and manipulation of combinatorial mixtures of DNA on a support. A set of DNA molecules encoding all candidate solutions to the computational problem of interest is synthesized and attached to the surface. Successive cycles of hybridization operations and exonuclease digestion are used to identify and eliminate those members of the set that are not solutions. Upon completion of all the multistep cycles, the solution to the computational problem is identified using a polymerase chain reaction to amplify the remaining molecules, which are then hybridized to an addressed array. The advantages of this approach are its scalability and potential to be automated (the use of solid-phase formats simplifies the complex repetitive chemical processes, as has been demonstrated in DNA and protein synthesis). Here we report the use of this method to solve a NP-complete problem. We consider a small example of the satisfiability problem (SAT), in which the values of a set of boolean variables satisfying certain logical constraints are determined.

Progress toward demonstration of a surface based DNA computation: a one word approach to solve a model satisfiability problem.

A multi-base encoding strategy is used in a one word approach to surface-based DNA computation. In this designed DNA model system, a set of 16 oligonucleotides, each a 16mer, is used with the format 5'-FFFFvvvvvvvvFFFF-3' in which 4-8 bits of data are stored in eight central variable ('v') base locations, and the remaining fixed ('F') base locations are used as a word label. The detailed implementations are reported here. In order to achieve perfect discrimination between each oligonucleotide, the efficiency and specificity of hybridization discrimination of the set of 16 oligonucleotides were examined by carrying out the hybridization of each individual fluorescently tagged complement to an array of 16 addressed immobilized oligonucleotides. A series of preliminary hybridization experiments are presented and further studies about hybridization, enzymatic destruction, read out and demonstrations of a SAT problem are forthcoming.

Surface-based DNA computing operations: DESTROY and READOUT.

DNA computing on surfaces is where complex combinatorial mixtures of DNA molecules are immobilized on a substrate and subsets are tagged and enzymatically modified (DESTROY) in repeated cycles of the DNA computation. A restriction enzyme has been chosen for the surface DESTROY operation. For the READOUT operation, both cycle sequencing and PCR amplification followed by addressed array hybridization were studied to determine the DNA sequences after the computations.

A surface-based approach to DNA computation.

A scalable approach to DNA-based computations is described. Complex combinatorial mixtures of DNA molecules encoding all possible answers to a computational problem are synthesized and attached to the surface of a solid support. This set of molecules is queried in successive MARK (hybridization) and DESTROY (enzymatic digestion) operations. Determination of the sequence of the DNA molecules remaining on the surface after completion of these operations yields the answer to the computational problem. Experimental demonstrations of aspects of the strategy are presented.

Demonstration of a word design strategy for DNA computing on surfaces.

A strategy for DNA computing on surfaces using linked sets of 'DNA words' that are short oligonucleotides (16mers) is proposed. The 16mer words have the format 5'-FFFFvvvvvvvvFFFF-3' in which 4-8 bits of data are stored in 8 variable ('v') base locations, and the remaining fixed ('F') base locations are used as a word label. Using a template and map strategy, a set of 108 8mers each of which possesses at least a 4 base mismatch with the complements to all the other members of the set (4bm complements) are identified for use as a variable base sequence set. In addition, sets of 4 and 12 word labels of the form ABCD....DCBA that are respectively 8bm and 6bm complements with each other are identified. The 16mers are chosen to have a G/C content of 50% in order to make the thermodynamic stability of the perfectly matched hybridized DNA duplexes similar; a simple pairwise additive method is used to estimate the perfect match and mismatch hybridization thermodynamics. A series of preliminary experiments are presented that use small arrays of 16mers attached to chemically modified gold surfaces and fluorescently labeled complements to study the hybridization adsorption and enzymatic manipulation of the oligonucleotides.

Family dynamics.

This case study submitted as a case commentary for the RACGP examination presents the importance of opportunistic inquiries about the health of a mother presenting with a sick or injured child. It revealed significant psychosocial problems that could be helped with basic caring, support and counselling.