The accuracy of varietal selection using factor analytic models for multi-environment plant breeding trials

Modeling of cultivar x trial effects for multienvironment trials (METs) within a mixed model framework is now common practice in many plant breeding programs. The factor analytic (FA) model is a parsimonious form used to approximate the fully unstructured form of the genetic variance-covariance matrix in the model for MET data. In this study, we demonstrate that the FA model is generally the model of best fit across a range of data sets taken from early generation trials in a breeding program. In addition, we demonstrate the superiority of the FA model in achieving the most common aim of METs, namely the selection of superior genotypes. Selection is achieved using best linear unbiased predictions (BLUPs) of cultivar effects at each environment, considered either individually or as a weighted average across environments. In practice, empirical BLUPs (E-BLUPs) of cultivar effects must be used instead of BLUPs since variance parameters in the model must be estimated rather than assumed known. While the optimal properties of minimum mean squared error of prediction (MSEP) and maximum correlation between true and predicted effects possessed by BLUPs do not hold for E-BLUPs, a simulation study shows that E-BLUPs perform well in terms of MSEP.

Buffel grass in Queensland's semi-arid woodlands: response to local and landscape scale variables, and relationship with grass, forb and reptile species.

Buffel grass [Pennisetum ciliare (L.) Link] has been widely introduced in the Australian rangelands as a consequence of its value for productive grazing, but tends to competitively establish in non-target areas such as remnant vegetation. In this study, we examined the influence landscape-scale and local-scale variables had upon the distribution of buffel grass in remnant poplar box (Eucalyptus populnea F. Muell.) dominant woodland fragments in the Brigalow Bioregion, Queensland. Buffel grass and variables thought to influence its distribution in the region were measured at 60 sites, which were selected based on the amount of native woodland retained in the landscape and patch size. An information-theoretic modelling approach and hierarchical partitioning revealed that the most influential variable was the percent of retained vegetation within a 1-km spatial extent. From this, we identified a critical threshold of similar to 30% retained vegetation in the landscape, above which the model predicted buffel grass was not likely to occur in a woodland fragment. Other explanatory variables in the model were site based, and included litter cover and long-term rainfall. Given the paucity of information on the effect of buffel grass upon biodiversity values, we undertook exploratory analyses to determine whether buffel grass cover influenced the distribution of grass, forb and reptile species. We detected some trends; hierarchical partitioning revealed that buffel grass cover was the most important explanatory variable describing habitat preferences of four reptile species. However, establishing causal links - particularly between native grass and forb species and buffel grass - was problematic owing to possible confounding with grazing pressure. We conclude with a set of management recommendations aimed at reducing the spread of buffel grass into remnant woodlands.

The effect of row configuration on yield reliability in grain sorghum: II. Modelling the effects of row configuration

In recent years many sorghum producers in the more marginal (<600 mm annual rainfall) cropping areas of Qld and northern NSW have utilised skip row configurations in an attempt to improve yield reliability and reduce sorghum production risk. But will this work in the long run? What are the trade-offs between productivity and risk of crop failure? This paper describes a modelling and simulation approach to study the long-term effects of skip row configurations. Detailed measurements of light interception and water extraction from sorghum crops grown in solid, single and double skip row configurations were collected from three on-farm participatory research trials established in southern Qld and northern NSW. These measurements resulted in changes to the model that accounted for the elliptical water uptake pattern below the crop row and reduced total light interception associated with the leaf area reduction of the skip configuration. Following validation of the model, long-term simulation runs using historical weather data were used to determine the value of skip row sorghum production as a means of maintaining yield reliability in the dryland cropping regions of southern Qld and northern NSW.

Reproductive Performance of Caprine Feral Does Mated to Boer or Feral Bucks in Semi-Arid Queensland

A strong world demand and current firm prices for goat meat provides opportunities for some wool/beef production enterprises in western Queensland to increase farm viability through diversification. In particular, there is rising interest in the use of Boer goats to improve productive performance of the Australian feral goat. Pastoral graziers have noted the high prolificacy of feral goats grazed in semi-arid areas, but there is no information on the breeding ability of feral does mated to Boer bucks. Animal production for a consuming world : proceedings of 9th Congress of the Asian-Australasian Association of Animal Production Societies [AAAP] and 23rd Biennial Conference of the Australian Society of Animal Production [ASAP] and 17th Annual Symposium of the University of Sydney, Dairy Research Foundation, [DRF]. 2-7 July 2000, Sydney, Australia.

Survival and Growth of Damara, Dorper, Dorset, Rambouillet, South African Meat Merino First Cross Lambs in Semi Arid Queensland

The recent introduction to Australia of superior sheep meat breeds from South Africa provides a basis for improving the quality and amount of sheep meat grown in Queensland’s semi arid area. Alternatively suitable breeds from existing Australian stocks of dual purpose and traditional terminal meat sheep may bring the desired attributes required by the market place. There has been no critical assessment of sheep meat breeds suitably adapted to the rangeland environment of western Queensland. Animal production for a consuming world : proceedings of 9th Congress of the Asian-Australasian Association of Animal Production Societies [AAAP] and 23rd Biennial Conference of the Australian Society of Animal Production [ASAP] and 17th Annual Symposium of the University of Sydney, Dairy Research Foundation, [DRF]. 2-7 July 2000, Sydney, Australia.

Adaptability of Damara, Dorper and Traditional Meat Sheep Breeds in Semi-Arid Queensland

Reproductive rate is a major contributing factor to the profitability of a sheep meat enterprise. Low reproduction rate is a feature of sheep husbandry in semi-arid Queensland. High ambient temperatures are implicated in poor fertility (Moule 1970) where variation in response can be due to breed and to animals within a breed (Hopkins and Stephenson 1978). Breeds recently imported from South Africa were selected in arid environments and may be better adapted to pastoral conditions of northern Australia than traditional breeds. Animal production for a consuming world : proceedings of 9th Congress of the Asian-Australasian Association of Animal Production Societies [AAAP] and 23rd Biennial Conference of the Australian Society of Animal Production [ASAP] and 17th Annual Symposium of the University of Sydney, Dairy Research Foundation, [DRF]. 2-7 July 2000, Sydney, Australia. This study will investigate (a) the thermoregulatory ability of Damara, Dorper, Poll Dorset, Rambouillet, South African Meat Merino and Queensland medium wool Merino rams prior to joinings in the autumn and spring of 1999, 2000 and 2001 and (b) the association between thermoregulatory parameters (rectal temperature and respiration rate) and ewe fertility. Results for the initial autumn joining are reported in this paper.

Modelling Mortality and Reproduction Rates for Management of Sheep Flocks in Northern Australia

By quantifying the effects of climatic variability in the sheep grazing lands of north western and western Queensland, the key biological rates of mortality and reproduction can be predicted for sheep. These rates are essential components of a decision support package which can prove a useful management tool for producers, especially if they can easily obtain the necessary predictors. When the sub-models of the GRAZPLAN ruminant biology process model were re-parameterised from Queensland data along with an empirical equation predicting the probability of ewes mating added, the process model predicted the probability of pregnancy well (86% variation explained). Predicting mortality from GRAZPLAN was less successful but an empirical equation based on relative condition of the animal (a measure based on liveweight), pregnancy status and age explained 78% of the variation in mortalities. A crucial predictor in these models was liveweight which is not often recorded on producer properties. Empirical models based on climatic and pasture conditions estimated from the pasture production model GRASP, predicted marking and mortality rates for Mitchell grass (Astrebla sp.) pastures (81% and 63% of the variation explained). These prediction equations were tested against independent data from producer properties and the model successfully validated for Mitchell grass communities.

Modelling discard ogives from Irish demersal fisheries

Annual discard ogives were estimated using generalized additive models (GAMs) for four demersal fish species: whiting, haddock, megrim, and plaice. The analysis was based on data collected on board commercial vessels and at Irish fishing ports from 1995 to 2003. For all species the most important factors influencing annual discard ogives were fleet (combination of gear, fishing ground, and targeted species), mean length of the catch and year, and, for megrim, also minimum landing size. The length at which fish are discarded has increased since 2000 for haddock, whiting, and plaice. In contrast, discarded length has decreased for megrim, accompanying a reduction in minimum landing size in 2000.

Modelling Leaf Production and Crop Development in Maize (Zea mays L.) After Tassel Initiation Under Diverse Conditions of Temperature and Photoperiod

Prediction of the initiation, appearance and emergence of leaves is critically important to the success of simulation models of crop canopy development and some aspects of crop ontogeny. Data on leaf number and crop ontogeny were collected on five cultivars of maize differing widely in maturity and genetic background grown under natural and extended photoperiods, and planted on seven sowing dates from October 1993 to March 1994 at Gatton, South-east Queensland. The same temperature coefficients were established for crop ontogeny before silking, and the rates of leaf initiation, leaf tip appearance and full leaf expansion, the base, optimum and maximum temperatures for each being 8, 34 and 40 degrees C. After silking, the base temperature for ontogeny was 0 degrees C, but the optimum and maximum temperatures remained unchanged. The rates of leaf initiation, appearance of leaf tips and full leaf expansion varied in a relatively narrow range across sowing times and photoperiod treatments, with average values of 0.040 leaves (degrees Cd)-1, 0.021 leaves (degrees Cd)-1, and 0.019 leaves (degrees Cd)-1, respectively. The relationships developed in this study provided satisfactory predictions of leaf number and crop ontogeny (tassel initiation to silking, emergence to silking and silking to physiological maturity) when assessed using independent data from Gatton (South eastern Queensland), Katherine and Douglas Daly (Northern Territory), Walkamin (North Queensland) and Kununurra (Western Australia).

Short-term responses of leaf growth rate to water deficit scale up to whole-plant and crop levels: An integrated modelling approach in maize.

Physiological and genetic studies of leaf growth often focus on short-term responses, leaving a gap to whole-plant models that predict biomass accumulation, transpiration and yield at crop scale. To bridge this gap, we developed a model that combines an existing model of leaf 6 expansion in response to short-term environmental variations with a model coordinating the development of all leaves of a plant. The latter was based on: (1) rates of leaf initiation, appearance and end of elongation measured in field experiments; and (2) the hypothesis of an independence of the growth between leaves. The resulting whole-plant leaf model was integrated into the generic crop model APSIM which provided dynamic feedback of environmental conditions to the leaf model and allowed simulation of crop growth at canopy level. The model was tested in 12 field situations with contrasting temperature, evaporative demand and soil water status. In observed and simulated data, high evaporative demand reduced leaf area at the whole-plant level, and short water deficits affected only leaves developing during the stress, either visible or still hidden in the whorl. The model adequately simulated whole-plant profiles of leaf area with a single set of parameters that applied to the same hybrid in all experiments. It was also suitable to predict biomass accumulation and yield of a similar hybrid grown in different conditions. This model extends to field conditions existing knowledge of the environmental controls of leaf elongation, and can be used to simulate how their genetic controls flow through to yield.

Effect of fragmentation, habitat loss and within-patch habitat characteristics on ant assemblages in semi-arid woodlands of eastern Australia.

The reliability of ants as bioindicators of ecosystem condition is dependent on the consistency of their response to localised habitat characteristics, which may be modified by larger-scale effects of habitat fragmentation and loss. We assessed the relative contribution of habitat fragmentation, habitat loss and within-patch habitat characteristics in determining ant assemblages in semi-arid woodland in Queensland, Australia. Species and functional group abundance were recorded using pitfall traps across 20 woodland patches in landscapes that exhibited a range of fragmentation states. Of fragmentation measures, changes in patch area and patch edge contrast exerted the greatest influence on species assemblages, after accounting for differences in habitat loss. However, 35% of fragmentation effects on species were confounded by the effects of habitat characteristics and habitat loss. Within-patch habitat characteristics explained more than twice the amount of species variation attributable to fragmentation and four times the variation explained by habitat loss. The study indicates that within-patch habitat characteristics are the predominant drivers of ant composition. We suggest that caution should be exercised in interpreting the independent effects of habitat fragmentation and loss on ant assemblages without jointly considering localised habitat attributes and associated joint effects.

Amelioration of soil compaction can take 5 years on a Vertisol under no till in the semi-arid subtropics

Heavy wheel traffic causes soil compaction, which adversely affects crop production and may persist for several years. We applied known compaction forces to entire plots annually for 5 years, and then determined the duration of the adverse effects on the properties of a Vertisol and the performance of crops under no-till dryland cropping with residue retention. For up to 5 years after a final treatment with a 10 Mg axle load on wet soil, soil shear strength at 70-100 mm and cone index at 180-360 mm were significantly (P < 0.05) higher than in a control treatment, and soil water storage and grain yield were lower. We conclude that compaction effects persisted because (1) there were insufficient wet-dry cycles to swell and shrink the entire compacted layer, (2) soil loosening by tillage was absent and (3) there were fewer earthworms in the compacted soil. Compaction of dry soil with 6 Mg had little effect at any time, indicating that by using wheel traffic only when the soil is dry, problems can be avoided. Unfortunately such a restriction is not always possible because sowing, tillage and harvest operations often need to be done when the soil is wet. A more generally applicable solution, which also ensures timely operations, is the permanent separation of wheel zones and crop zones in the field--the practice known as controlled traffic farming. Where a compacted layer already exists, even on a clay soil, management options to hasten repair should be considered, e.g. tillage, deep ripping, sowing a ley pasture or sowing crop species more effective at repairing compacted soil.

Modelling the potential spread of Solenopsis invicta Buren (Hymenoptera: Formicidae) (red imported fire ant) in Australia

Quantifying the potential spread and density of an invading organism enables decision-makers to determine the most appropriate response to incursions. We present two linked models that estimate the spread of Solenopsis invicta Buren (red imported fire ant) in Australia based on limited data gathered after its discovery in Brisbane in 2001. A stochastic cellular automaton determines spread within a location (100 km by 100 km) and this is coupled with a model that simulates human-mediated movement of S. invicta to new locations. In the absence of any control measures, the models predict that S. invicta could cover 763 000–4 066 000 km2 by the year 2035 and be found at 200 separate locations around Australia by 2017–2027, depending on the rate of spread. These estimated rates of expansion (assuming no control efforts were in place) are higher than those experienced in the USA in the 1940s during the early invasion phases in that country. Active control efforts and quarantine controls in the USA (including a concerted eradication attempt in the 1960s) may have slowed spread. Further, milder winters, the presence of the polygynous social form, increased trade and human mobility in Australia in 2000s compared with the USA in 1940s could contribute to faster range expansion.

Modelling climatic risks of aflatoxin contamination in maize

Aflatoxins are highly carcinogenic mycotoxins produced by two fungi, Aspergillus flavus and A. parasiticus, under specific moisture and temperature conditions before harvest and/or during storage of a wide range of crops including maize. Modelling of interactions between host plant and environment during the season can enable quantification of preharvest aflatoxin risk and its potential management. A model was developed to quantify climatic risks of aflatoxin contamination in maize using principles previously used for peanuts. The model outputs an aflatoxin risk index in response to seasonal temperature and soil moisture during the maize grain filling period using the APSIM's maize module. The model performed well in simulating climatic risk of aflatoxin contamination in maize as indicated by a significant R2 (P ≤ 0.01) between aflatoxin risk index and the measured aflatoxin B1 in crop samples, which was 0.69 for a range of rainfed Australian locations and 0.62 when irrigated locations were also included in the analysis. The model was further applied to determine probabilities of exceeding a given aflatoxin risk in four non-irrigated maize growing locations of Queensland using 106 years of historical climatic data. Locations with both dry and hot climates had a much higher probability of higher aflatoxin risk compared with locations having either dry or hot conditions alone. Scenario analysis suggested that under non-irrigated conditions the risk of aflatoxin contamination could be minimised by adjusting sowing time or selecting an appropriate hybrid to better match the grain filling period to coincide with lower temperature and water stress conditions.

Architectural modelling of maize under water stress

Two field experiments using maize (Pioneer 31H50) and three watering regimes [(i) irrigated for the whole crop cycle, until anthesis, (ii) not at all (experiment 1) and (iii) fully irrigated and rain grown for the whole crop cycle (experiment 2)] were conducted at Gatton, Australia, during the 2003-04 season. Data on crop ontogeny, leaf, sheath and internode lengths and leaf width, and senescence were collected at 1- to 3-day intervals. A glasshouse experiment during 2003 quantified the responses of leaf shape and leaf presentation to various levels of water stress. Data from experiment 1 were used to modify and parameterise an architectural model of maize (ADEL-Maize) to incorporate the impact of water stress on maize canopy characteristics. The modified model produced accurate fitted values for experiment 1 for final leaf area and plant height, but values during development for leaf area were lower than observed data. Crop duration was reasonably well fitted and differences between the fully irrigated and rain-grown crops were accurately predicted. Final representations of maize crop canopies were realistic. Possible explanations for low values of leaf area are provided. The model requires further development using data from the glasshouse study and before being validated using data from experiment 2 and other independent data. It will then be used to extend functionality in architectural models of maize. With further research and development, the model should be particularly useful in examining the response of maize production to water stress including improved prediction of total biomass and grain yield. This will facilitate improved simulation of plant growth and development processes allowing investigation of genotype by environment interactions under conditions of suboptimal water supply.