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

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

FTO genotype is associated with phenotypic variability of body mass index

There is evidence across several species for genetic control of phenotypic variation of complex traits1, 2, 3, 4, such that the variance among phenotypes is genotype dependent. Understanding genetic control of variability is important in evolutionary biology, agricultural selection programmes and human medicine, yet for complex traits, no individual genetic variants associated with variance, as opposed to the mean, have been identified. Here we perform a meta-analysis of genome-wide association studies of phenotypic variation using ~170,000 samples on height and body mass index (BMI) in human populations. We report evidence that the single nucleotide polymorphism (SNP) rs7202116 at the FTO gene locus, which is known to be associated with obesity (as measured by mean BMI for each rs7202116 genotype)5, 6, 7, is also associated with phenotypic variability. We show that the results are not due to scale effects or other artefacts, and find no other experiment-wise significant evidence for effects on variability, either at loci other than FTO for BMI or at any locus for height. The difference in variance for BMI among individuals with opposite homozygous genotypes at the FTO locus is approximately 7%, corresponding to a difference of ~0.5 kilograms in the standard deviation of weight. Our results indicate that genetic variants can be discovered that are associated with variability, and that between-person variability in obesity can partly be explained by the genotype at the FTO locus. The results are consistent with reported FTO by environment interactions for BMI8, possibly mediated by DNA methylation9, 10. Our BMI results for other SNPs and our height results for all SNPs suggest that most genetic variants, including those that influence mean height or mean BMI, are not associated with phenotypic variance, or that their effects on variability are too small to detect even with samples sizes greater than 100,000.

Ludwig Levy (far left) with Essen color guard marching for a regional gymnastics competition (Gau-Turnfest); Leer, Germany.

Ludwig Levy, Peter W. and Willy Beherends, behind them: Wilma Bo?hammer, Kaethe Krueger, Tomma Thomsen and E?

Adult-type hypolactasia: Genotype-phenotype correlation

Adult-type hypolactasia (primary lactose malabsorption, lactase non-persistence) is the most common enzyme deficiency worldwide, and manifests with symptoms of lactose intolerance such as abdominal pain, gas formation and diarrhea. In humans with adult-type hypolactasia, lactase activity is high at birth, but declines during childhood to about one-tenth of the activity at birth. In 2002, a one base polymorphism C/T-13910, located 14 kilobases from the starting codon of the lactase-phlorizin hydrolase (LPH) gene was observed to be associated with the persistence of lactase activity. The T-13910 allele (C/T-13910 and T/T-13910 genotypes) associates with persistence of lactase activity throughout life, whereas the C/C-13910 genotype associates with adult-type hypolactasia. In this thesis work, the timing and mechanism of decline of lactase enzyme activity during development was studied using the C/T-13910 polymorphism as a molecular marker. We observed an excellent correlation between low lactase activity and the C/C-13910 genotype in all subjects > 12 years of age, irrespective their ethnicity. In children of African origin, the lactase activity declined somewhat earlier than among Finnish children. Furthermore, we observed an increasing imbalance in the relative lactase mRNA expression from the C-13910 and T-13910 alleles in Finnish children beginning from five years of age. The genetic test for adult-type hypolactasia showed a sensitivity of 93% and a specificity of 100% in the Finnish children and adolescents > 12 years of age. The relation of milk consumption and the milk-related abdominal complaints to the C/T-13910 genotypes associated with lactase persistence/non-persistence was studied by a questionnaire-based approach in > 2100 Finns. Both Finnish children and adults with the C/C-13910 genotype consumed significantly less dairy products compared to those with the C/T-13910 and T/T-13910 genotypes. Flatulence was the only of the abdominal symptoms of lactose intolerance that subjects with the C/C-13910 genotype reported significantly more often than those with the C/T-13910 and T/T-13910 genotypes. A minor proportion (<10%) of subjects with the C/C-13910 genotype, nevertheless, reported drinking milk without any symptoms afterwards. There was no association between cow's milk allergy starting as a newborn and adult-type hypolactasia. In an association study an increased risk of colorectal cancer was observed among those with molecular diagnosis of adult-type hypolactasia. It warrants further studies to clarify whether the increased risk observed in the Finnish population is associated with lactose or decreased intake of dairy products in these subjects.

Predicting Additive and Non-additive Genetic Effects from Trials Where Traits Are Affected by Interplot Competition

There are two key types of selection in a plant breeding program, namely selection of hybrids for potential commercial use and the selection of parents for use in future breeding. Oakey et al. (in Theoretical and Applied Genetics 113, 809-819, 2006) showed how both of these aims could be achieved using pedigree information in a mixed model analysis in order to partition genetic effects into additive and non-additive effects. Their approach was developed for field trial data subject to spatial variation. In this paper we extend the approach for data from trials subject to interplot competition. We show how the approach may be used to obtain predictions of pure stand additive and non-additive effects. We develop the methodology in the context of a single field trial using an example from an Australian sorghum breeding program.

The importance of modelling heterogeneity in complex disease: application to NIMH Schizophrenia Genetics Initiative data

As for other complex diseases, linkage analyses of schizophrenia (SZ) have produced evidence for numerous chromosomal regions, with inconsistent results reported across studies. The presence of locus heterogeneity appears likely and may reduce the power of linkage analyses if homogeneity is assumed. In addition, when multiple heterogeneous datasets are pooled, inter-sample variation in the proportion of linked families (alpha) may diminish the power of the pooled sample to detect susceptibility loci, in spite of the larger sample size obtained. We compare the significance of linkage findings obtained using allele-sharing LOD scores (LOD(exp))-which assume homogeneity-and heterogeneity LOD scores (HLOD) in European American and African American NIMH SZ families. We also pool these two samples and evaluate the relative power of the LOD(exp) and two different heterogeneity statistics. One of these (HLOD-P) estimates the heterogeneity parameter alpha only in aggregate data, while the second (HLOD-S) determines alpha separately for each sample. In separate and combined data, we show consistently improved performance of HLOD scores over LOD(exp). Notably, genome-wide significant evidence for linkage is obtained at chromosome 10p in the European American sample using a recessive HLOD score. When the two samples are combined, linkage at the 10p locus also achieves genome-wide significance under HLOD-S, but not HLOD-P. Using HLOD-S, improved evidence for linkage was also obtained for a previously reported region on chromosome 15q. In linkage analyses of complex disease, power may be maximised by routinely modelling locus heterogeneity within individual datasets, even when multiple datasets are combined to form larger samples.

Comparative analysis of Tritrichomonas foetus (Riedmuller, 1928) cat genotype, T. foetus (Riedmuller, 1928) cattle genotype and Tritrichomonas suis (Davaine, 1875) at 10 DNA loci

The parasitic protists in the genus Tritrichomonas cause significant disease in domestic cattle and cats. To assess the genetic diversity of feline and bovine isolates of Tritrichomonas foetus (Riedmuller, 1928) Wenrich and Emmerson, 1933, we used 10 different genetic regions, namely the protein coding genes of cysteine proteases 1,2 and 4-9 (CP1, 2, 4-9) involved in the pathogenesis of the disease caused by the parasite. The cytosolic malate dehydrogenase 1 (MDH1) and internal transcribed spacer region 2 of the rDNA unit (ITS2) were included as additional markers. The gene sequences were compared with those of Tritrichomonas suis (Davaine. 1875) Morgan and Hawkins, 1948 and Tritrichomonas mobilensis Culberson et al., 1986. The study revealed 100% identity for all 10 genes among all feline isolates (=T. foetus cat genotype), 100% identity among all bovine isolates (=T. foetus cattle genotype) and a genetic distinctness of 1% between the cat and cattle genotypes of T. foetus. The cattle genotype of T. foetus was 100% identical to T. suis at nine loci (CP1, 2,4-8, ITS2, MDH1). At CP9, three out of four T. suis isolates were identical to the T. foetus cattle genotype, while the T. suis isolate SUI-H3B sequence contained a single unique nucleotide substitution. Tritrichomonas mobilensis was 0.4% and 0.7% distinct from the cat and cattle genotypes of T. foetus, respectively. The genetic differences resulted in amino acid changes in the CP genes, most pronouncedly in CP2, potentially providing a platform for elucidation of genotype-specific host-pathogen interactions of T. foetus. On the basis of this data we judge T. suis and T. foetus to be subjective synonyms. For the first time, on objective nomenclatural grounds, the authority of T. suis is given to Davaine, 1875, rather than the commonly cited Gruby and Delafond, 1843. To maintain prevailing usage of T. foetus, we are suppressing the senior synomym T. suis Davaine, 1875 according to Article 23.9, because it has never been used as a valid name after 1899 and T. foetus is widely discussed as the cause of bovine trichomonosis. Thus bovine, feline and porcine isolates should all be given the name T. foetus. This promotes the stability of T. foetus for the veterinary and economically significant venereal parasite causing bovine trichomonosis. (C) 2012 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Classifying genotype by environment interactions for targeted germplasm deployment with a focus on Eucalyptus

A novel methodology for describing genotype by environment interactions estimated from multi-environment field trials is described and an empirical example using an extensive trial network of eucalypts is presented. The network of experiments containing 65 eucalypts was established in 38 replicated field trials across the tropics and subtropics of eastern Australia, with a selection of well-tested species used to provide a more detailed examination of productivity differentials across environmental gradients. By focusing on changes in species’ productivity across environmental gradients, the results are applicable for all species established across the range of environments evaluated in the trial network and simultaneously classify species and environments so that results may be applied across the landscape. The methodology developed was able to explain most (93 %) of the variation in the selected species relative changes in productivity across the various environmental variables examined. Responses were primarily regulated by changes in variables related to water availability and secondarily by temperature related variables. Clustering and ordination can identify groups of species with similar physiological responses to environment and may also guide the parameterisation and calibration of process based models of plant growth. Ordination was particularly useful in the identification of species with distinct environmental response patterns that would be useful as probes for extracting more information from future trials.

Can competition with pasture be used to manipulate bellyache bush (Jatropha gossypiifolia L.) population biology?

Bellyache bush (Jatropha gossypiifolia L.) is an invasive weed that poses economic and environmental problems in northern Australia. Competition between pasture and bellyache bush was examined in North Queensland using combinations of five pasture treatments (uncut (control); cut as low, medium, and high pasture; and no pasture) and four bellyache bush densities (0, 2, 6 and 12plantsm(-2)) in a buffel grass (Cenchrus ciliaris L.) dominated pasture. The pasture treatments were applied approximately once per year but no treatments were applied directly to the bellyache bush plants. Measurements of bellyache bush flowering, seed formation, and mortality were undertaken over a 9-year period, along with monitoring the pasture basal cover and plant species diversity. Maximum flowering rates of bellyache bush occurred after 9 years (97%) in plots containing no pasture, with the lowest rates of 9% in uncut control plots. Earliest flowering (322 days after planting) and seed formation (411 days) also occurred in plots with no pasture compared with all other pasture treatments (range 1314-1393 days for seed formation to occur). No seeds were produced in uncut plots. At the end of 9 years, mortality rates of bellyache bush plants initially planted averaged 73% for treatments with some pasture compared with 55% under the no-pasture treatment. The percentage of herbaceous plant basal cover in uncut plots was increased 5-fold after 9 years, much greater than the average 2% increase recorded across the low, medium, and high pasture treatments. The number of herbaceous species in uncut plots remained largely unchanged, whereas there was an average reduction of 46% in the cut pasture treatments. Buffel grass remained the species with the greatest basal cover across all cut pasture treatments, followed by sabi grass (Urochloa mosambicensis (Hack.) Dandy) and then red Natal grass (Melinis repens (Willd.) Ziska). These results suggest that grazing strategies that maintain a healthy and competitive pasture layer may contribute to reducing the rate of spread of bellyache bush and complement traditional control techniques such as the use of herbicides.

Barley genotype expressing "stay-green"-like characteristics maintains starch quality of the grain during water stress condition

The identification of "stay-green" in sorghum and its positive correlation with yield increases has encouraged attempts to incorporate "stay-green"-like traits into the genomes of other commercially important cereal crops. However, knowledge on the effects of "stay-green" expression on grain quality under extreme physiological stress is limited. This study examines impacts of "stay-green"-like expression on starch biosynthesis in barley (Hordeum vulgare L.) grain under mild, severe, and acute water stress conditions induced at anthesis. The proportions of long amylopectin branches and amylose branches in the grain of Flagship (a cultivar without "stay-green"-like characteristics) were higher at low water stress, suggesting that water stress affects starch biosynthesis in grain, probably due to early termination of grain fill. The changes in long branches can affect starch properties, such as the rates of enzymatic degradation, and hence its nutritional value. By contrast, grain from the "stay-green"-like cultivar (ND24260) did not show variation in starch molecular structure under the different water stress levels. The results indicate that the cultivar with "stay-green"-like traits has a greater potential to maintain starch biosynthesis and quality in grain during drought conditions, making the "stay-green"-like traits potentially useful in ensuring food security. (C) 2013 Elsevier Ltd. All rights reserved.

Estimating an Aggregate Economic Genotype to Facilitate Breeding and Selection of Strawberry Genotypes in Southeast Queensland

The Queensland strawberry (Fragaria ×ananassa) breeding program in subtropical Australia aims to improve sustainable profitability for the producer. Selection must account for the relative economic importance of each trait and the genetic architecture underlying these traits in the breeding population. Our study used estimates of the influence of a trait on production costs and profitability to develop a profitability index (PI) and an economic weight (i.e., change in PI for a unit change in level of trait) for each trait. The economic weights were then combined with the breeding values for 12 plant and fruit traits on over 3000 genotypes that were represented in either the current breeding population or as progenitors in the pedigree of these individuals. The resulting linear combination (i.e., sum of economic weight × breeding value for all 12 traits) estimated the overall economic worth of each genotype as H, the aggregate economic genotype. H values were validated by comparisons among commercial cultivars and were also compared with the estimated gross margins. When the H value of ‘Festival’ was set as zero, the H values of genotypes in the pedigree ranged from –0.36 to +0.28. H was highly correlated (R2 = 0.77) with the year of selection (1945–98). The gross margins were highly linearly related (R2 > 0.98) to H values when the genotype was planted on less than 50% of available area, but the relationship was non-linear [quadratic with a maximum (R2 > 0.96)] when the planted area exceeded 50%. Additionally, with H values above zero, the variation in gross margin increased with increasing H values as the percentage of area planted to a genotype increased. High correlations among some traits allowed the omission of any one of three of the 12 traits with little or no effect on ranking (Spearman’s rank correlation 0.98 or greater). Thus, these traits may be dropped from the aggregate economic genotype, leading to either cost reductions in the breeding program or increased selection intensities for the same resources. H was efficient in identifying economically superior genotypes for breeding and deployment, but because of the non-linear relationship with gross margin, calculation of a gross margin for genotypes with high H is also necessary when cultivars are deployed across more than 50% of the available area.

Effects of weed control and fertilization at early establishment on tree nitrogen and water use in an exotic F1 hybrid pine of subtropical Australia

Purpose We investigated the effects of weed control and fertilization at early establishment on foliar stable carbon (δ13C) and nitrogen (N) isotope (δ15N) compositions, foliar N concentration, tree growth and biomass, relative weed cover and other physiological traits in a 2-year old F1 hybrid (Pinus elliottii var. elliottii (Engelm) × Pinus caribaea var. hondurensis (Barr. ex Golf.)) plantation grown on a yellow earth in southeast Queensland of subtropical Australia. Materials and methods Treatments included routine weed control, luxury weed control, intermediate weed control, mechanical weed control, nil weed control, and routine and luxury fertilization in a randomised complete block design. Initial soil nutrition and soil fertility parameters included (hot water extractable organic carbon (C) and total nitrogen (N), total C and N, C/N ratio, labile N pools (nitrate (NO3 −) and ammonium (NH4 +)), extractable potassium (K+)), soil δ15N and δ13C. Relative weed cover, foliar N concentrations, tree growth rate and physiological parameters including photosynthesis, stomatal conductance, photosynthetic nitrogen use efficiency, foliar δ15N and foliar δ13C were also measured at early establishment. Results and discussion Foliar N concentration at 1.25 years was significantly different amongst the weed control treatments and was negatively correlated to the relative weed cover at 1.1 years. Foliar N concentration was also positively correlated to foliar δ15N and foliar δ13C, tree height, height growth rates and tree biomass. Foliar δ15N was negatively correlated to the relative weed cover at 0.8 and 1.1 years. The physiological measurements indicated that luxury fertilization and increasing weed competition on these soils decreased leaf xylem pressure potential (Ψxpp) when compared to the other treatments. Conclusions These results indicate how increasing N resources and weed competition have implications for tree N and water use at establishment in F1 hybrid plantations of southeast Queensland, Australia. These results suggest the desirability of weed control, in the inter-planting row, in the first year to maximise site N and water resources available for seedling growth. It also showed the need to avoid over-fertilisation, which interfered with the balance between available N and water on these soils.

Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East

Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.

Optimizing genotype by environment by management to maximize opportunities for maize productivity in North Eastern Australia.

The major objective of this experiment was to identify optimum plant population densities for different maize maturity groups depending on the environments’ potential and identify situations that reduce risk of crop failures while maximizing opportunities for better yield when weather conditions are good.