Parameter estimation and sensitivity analysis of fat deposition models in beef steers using acslXtreme.

The Davis Growth Model (a dynamic steer growth model encompassing 4 fat deposition models) is currently being used by the phenotypic prediction program of the Cooperative Research Centre (CRC) for Beef Genetic Technologies to predict P8 fat (mm) in beef cattle to assist beef producers meet market specifications. The concepts of cellular hyperplasia and hypertrophy are integral components of the Davis Growth Model. The net synthesis of total body fat (kg) is calculated from the net energy available after accounting tor energy needs for maintenance and protein synthesis. Total body fat (kg) is then partitioned into 4 fat depots (intermuscular, intramuscular, subcutaneous, and visceral). This paper reports on the parameter estimation and sensitivity analysis of the DNA (deoxyribonucleic acid) logistic growth equations and the fat deposition first-order differential equations in the Davis Growth Model using acslXtreme (Hunstville, AL, USA, Xcellon). The DNA and fat deposition parameter coefficients were found to be important determinants of model function; the DNA parameter coefficients with days on feed >100 days and the fat deposition parameter coefficients for all days on feed. The generalized NL2SOL optimization algorithm had the fastest processing time and the minimum number of objective function evaluations when estimating the 4 fat deposition parameter coefficients with 2 observed values (initial and final fat). The subcutaneous fat parameter coefficient did indicate a metabolic difference for frame sizes. The results look promising and the prototype Davis Growth Model has the potential to assist the beef industry meet market specifications.

Effect of timing of a deficit-irrigation allocation on corn evapotranspiration, yield, water use efficiency and dry mass

Water regulations have decreased irrigation water supplies in Nebraska and some other areas of the USA Great Plains. When available water is not enough to meet crop water requirements during the entire growing cycle, it becomes critical to know the proper irrigation timing that would maximize yields and profits. This study evaluated the effect of timing of a deficit-irrigation allocation (150 mm) on crop evapotranspiration (ETc), yield, water use efficiency (WUE = yield/ETc), irrigation water use efficiency (IWUE = yield/irrigation), and dry mass (DM) of corn (Zea mays L.) irrigated with subsurface drip irrigation in the semiarid climate of North Platte, NE. During 2005 and 2006, a total of sixteen irrigation treatments (eight each year) were evaluated, which received different percentages of the water allocation during July, August, and September. During both years, all treatments resulted in no crop stress during the vegetative period and stress during the reproductive stages, which affected ETc, DM, yield, WUE and IWUE. Among treatments, ETc varied by 7.2 and 18.8%; yield by 17 and 33%; WUE by 12 and 22%, and IWUE by 18 and 33% in 2005 and 2006, respectively. Yield and WUE both increased linearly with ETc and with ETc/ETp (ETp = seasonal ETc with no water stress), and WUE increased linearly with yield. The yield response factor (ky) averaged 1.50 over the two seasons. Irrigation timing affected the DM of the plant, grain, and cob, but not that of the stover. It also affected the percent of DM partitioned to the grain (harvest index), which increased linearly with ETc and averaged 56.2% over the two seasons, but did not affect the percent allocated to the cob or stover. Irrigation applied in July had the highest positive coefficient of determination (R2) with yield. This high positive correlation decreased considerably for irrigation applied in August, and became negative for irrigation applied in September. The best positive correlation between the soil water deficit factor (Ks) and yield occurred during weeks 12-14 from crop emergence, during the "milk" and "dough" growth stages. Yield was poorly correlated to stress during weeks 15 and 16, and the correlation became negative after week 17. Dividing the 150 mm allocation about evenly among July, August and September was a good strategy resulting in the highest yields in 2005, but not in 2006. Applying a larger proportion of the allocation in July was a good strategy during both years, and the opposite resulted when applying a large proportion of the allocation in September. The different results obtained between years indicate that flexible irrigation scheduling techniques should be adopted, rather than relying on fixed timing strategies.

The effect of different levels of inbreeding on self-incompatibility and inbreeding depression in pineapple

A high level of heterozygosity in domesticated pineapple is one of the main obstacles hindering the efficient development of new varieties. Selfing has been proposed as a strategy to minimise this heterozygosity through the development of parentals with a greater level of homozygosity. Selfing and a range of lesser levels of inbreeding were evaluated for their effects on seed production and inbreeding depression in the early growth of seedlings. Selfing produced few seeds, and very few viable seedlings. The paternal backcross and several half-sib combinations exhibited minimal effects on seed development or early growth and in some cases were similar to the outcross. Sibcrosses were generally unsuccessful. The highest inbreeding coefficient that was not associated with severe inbreeding depression was approximately 0.25. The effect of inbreeding depression and the level of homozygosity on several quantitative traits including those related to fruit quality within the inbred populations, is now being assessed.

Non-destructive prediction of 'Hass' avocado dry matter via FT-NIR spectroscopy.

BACKGROUND: The inability to consistently guarantee internal quality of horticulture produce is of major importance to the primary producer, marketers and ultimately the consumer. Currently, commercial avocado maturity estimation is based on the destructive assessment of percentage dry matter (%DM), and sometimes percentage oil, both of which are highly correlated with maturity. In this study the utility of Fourier transform (FT) near-infrared spectroscopy (NIRS) was investigated for the first time as a non-invasive technique for estimating %DM of whole intact 'Hass' avocado fruit. Partial least squares regression models were developed from the diffuse reflectance spectra to predict %DM, taking into account effects of intra-seasonal variation and orchard conditions. RESULTS: It was found that combining three harvests (early, mid and late) from a single farm in the major production district of central Queensland yielded a predictive model for %DM with a coefficient of determination for the validation set of 0.76 and a root mean square error of prediction of 1.53% for DM in the range 19.4-34.2%. CONCLUSION: The results of the study indicate the potential of FT-NIRS in diffuse reflectance mode to non-invasively predict %DM of whole 'Hass' avocado fruit. When the FT-NIRS system was assessed on whole avocados, the results compared favourably against data from other NIRS systems identified in the literature that have been used in research applications on avocados.

Phosphine fumigation of silo bags.

Fumigation with phosphine has the potential to disinfest grain stored in silo bags but only limited research has been conducted on whether phosphine fumigation can be undertaken effectively and safely in this form of storage. Fumigation with phosphine was tested on two (70 m) replicate silo bags each containing 240 t of wheat (9.9 and 9.2% m.c.). The target application rate of phosphine was 1.5 g m 3 with a fumigation period of 17 days. Aluminium phosphide tablets were inserted into each bag at ten release points spaced at 7 m intervals starting 3.5 m from either end of the bag. A total of 14 bioassay cages containing mixed age populations of strongly phosphine resistant Rhyzopertha dominica (F.) were inserted into each fumigated silo bag. Complete control of all life stages of R. dominica was achieved at all locations in the fumigated silo bags. Phosphine concentrations at release points increased rapidly and remained high for the duration of the fumigation. Concentrations at midway points were always lower than at the release points but exceeded 215 ppm for ten days. The diffusion coefficient of available phosphine averaged over the first three full days of the fumigation for both fumigated silo bags was 2.8 x 10 7. Venting the silo bag with an aeration fan reduced the phosphine concentration by 99% after 12 h. Relatively small amounts of phosphine continued to desorb after the venting period. Although grain temperature at the core of the silo bags remained stable at 29degreesC for 17 days, grain at the surface of the silo bags fluctuated daily with a mean of 29degreesC. The results demonstrate that silo bags can be fumigated with phosphine for complete control of infestations of strongly phosphine resistant R. dominica and potentially other species.

Estimating winter crop area across seasons and regions using time-sequential MODIS imagery.

The wheat grain industry is Australia's second largest agricultural export commodity. There is an increasing demand for accurate, objective and near real-time crop production information by industry. The advent of the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite platform has augmented the capability of satellite-based applications to capture reflectance over large areas at acceptable pixel scale, cost and accuracy. The use of multi-temporal MODIS-enhanced vegetation index (EVI) imagery to determine crop area was investigated in this article. Here the rigour of the harmonic analysis of time-series (HANTS) and early-season metric approaches was assessed when extrapolating over the entire Queensland (QLD) cropping region for the 2005 and 2006 seasons. Early-season crop area estimates, at least 4 months before harvest, produced high accuracy at pixel and regional scales with percent errors of -8.6% and -26% for the 2005 and 2006 seasons, respectively. In discriminating among crops at pixel and regional scale, the HANTS approach showed high accuracy. The errors for specific area estimates for wheat, barley and chickpea were 9.9%, -5.2% and 10.9% (for 2005) and -2.8%, -78% and 64% (for 2006), respectively. Area estimates of total winter crop, wheat, barley and chickpea resulted in coefficient of determination (R(2)) values of 0.92, 0.89, 0.82 and 0.52, when contrasted against the actual shire-scale data. A significantly high coefficient of determination (0.87) was achieved for total winter crop area estimates in August across all shires for the 2006 season. Furthermore, the HANTS approach showed high accuracy in discriminating cropping area from non-cropping area and highlighted the need for accurate and up-to-date land use maps. The extrapolability of these approaches to determine total and specific winter crop area estimates, well before flowering, showed good utility across larger areas and seasons. Hence, it is envisaged that this technology might be transferable to different regions across Australia.

Genetic effects and genetic relationships among shrunken (sh2) sweet corn lines and F1 hybrids

The objectives of this study were to quantify the components of genetic variance and the genetic effects, and to examine the genetic relationship of inbred lines extracted from various shrunken2(sh2) breeding populations. Ten diverse inbred lines developed from genetic background, were crossed in half diallel. Parents and their F1 hybrids were evaluated at three environments. The parents were genotyped using 20 polymorphic simple sequence repeats (SSR). Agronomic and quality traits were analysed by a mixed linear model according to additive-dominance genetic model. Genetic effects were estimated using an adjusted unbiased prediction method. Additive variance was more important than dominance variance in the expression of traits related to ear aspects (husk ratio and percentage of ear filled) and eating quality (flavour and total soluble solids). For agronomic traits, however, dominance variance was more important than additive variance. The additive genetic correlation between flavour and tenderness was strong (r = 0.84, P <0.01). Flavour, tenderness and kernel colour additive genetic effects were not correlated with yield related traits. Genetic distance (GD), estimated from SSR profiles on the basis of Jaccard's similarity coefficient varied from 0.10 to 0.77 with an average of 0.56. Cluster analysis classified parents according to their pedigree relationships. In most studied traits, F1 performance was not associated with GD.

Modelling temperature, photoperiod and vernalization responses of Brunonia australis (Goodeniaceae) and Calandrinia sp (Portulacaceae) to predict flowering time

Crop models for herbaceous ornamental species typically include functions for temperature and photoperiod responses, but very few incorporate vernalization, which is a requirement of many traditional crops. This study investigated the development of floriculture crop models, which describe temperature responses, plus photoperiod or vernalization requirements, using Australian native ephemerals Brunonia australis and Calandrinia sp. A novel approach involved the use of a field crop modelling tool, DEVEL2. This optimization program estimates the parameters of selected functions within the development rate models using an iterative process that minimizes sum of squares residual between estimated and observed days for the phenological event. Parameter profiling and jack-knifing are included in DEVEL2 to remove bias from parameter estimates and introduce rigour into the parameter selection process. Development rate of B. australis from planting to first visible floral bud (VFB) was predicted using a multiplicative approach with a curvilinear function to describe temperature responses and a broken linear function to explain photoperiod responses. A similar model was used to describe the development rate of Calandrinia sp., except the photoperiod function was replaced with an exponential vernalization function, which explained a facultative cold requirement and included a coefficient for determining the vernalization ceiling temperature. Temperature was the main environmental factor influencing development rate for VFB to anthesis of both species and was predicted using a linear model. The phenology models for B. australis and Calandrinia sp. described development rate from planting to VFB and from VFB to anthesis in response to temperature and photoperiod or vernalization and may assist modelling efforts of other herbaceous ornamental plants. In addition to crop management, the vernalization function could be used to identify plant communities most at risk from predicted increases in temperature due to global warming.

Estimating Hydrogen Cyanide in Forage Sorghum (Sorghum bicolor) by Near-Infrared Spectroscopy

Hydrogen cyanide (HCN) is a toxic chemical that can potentially cause mild to severe reactions in animals when grazing forage sorghum. Developing technologies to monitor the level of HCN in the growing crop would benefit graziers, so that they can move cattle into paddocks with acceptable levels of HCN. In this study, we developed near-infrared spectroscopy (MRS) calibrations to estimate HCN in forage sorghum and hay. The full spectral NIRS range (400-2498 nm) was used as well as specific spectral ranges within the full spectral range, i.e., visible (400-750 nm), shortwave (800-1100 nm) and near-infrared (NIR) (1100-2498 nm). Using the full spectrum approach and partial least-squares (PLS), the calibration produced a coefficient of determination (R-2) = 0.838 and standard error of cross-validation (SECV) = 0.040%, while the validation set had a R-2 = 0.824 with a low standard error of prediction (SEP = 0.047%). When using a multiple linear regression (MLR) approach, the best model (NIR spectra) produced a R-2 = 0.847 and standard error of calibration (SEC) = 0.050% and a R-2 = 0.829 and SEP = 0.057% for the validation set. The MLR models built from these spectral regions all used nine wavelengths. Two specific wavelengths 2034 and 2458 nm were of interest, with the former associated with C=O carbonyl stretch and the latter associated with C-N-C stretching. The most accurate PLS and MLR models produced a ratio of standard error of prediction to standard deviation of 3.4 and 3.0, respectively, suggesting that the calibrations could be used for screening breeding material. The results indicated that it should be feasible to develop calibrations using PLS or MLR models for a number of users, including breeding programs to screen for genotypes with low HCN, as well as graziers to monitor crop status to help with grazing efficiency.

Sorghum dwarfing genes can affect radiation capture and radiation use efficiency

Presence of the dw3 sorghum dwarfing gene had negative effects on grain yield in some genetic backgrounds and environments. In a previous study we showed that this was due to a significant reduction in shoot biomass (mainly via reduced stem mass), which in turn negatively affected grain size. The current study examines whether shoot biomass was reduced via effects of dw3 on traits associated with resource capture, such as leaf area index (LAI), light interception (LI), and canopy extinction coefficient (k) or with resource use efficiency, such as radiation use efficiency (RUE). Three pairs of near-isogenic sorghum lines differing only in the presence or absence of the dwarfing allele dw3 (3-dwarfs vs 2-dwarfs) were grown in large field plots. Biomass accumulation and LI were measured for individual canopy layers to examine canopy characteristics of tall and short types. Similar to the previously reported effects on grain yield, the effects of dw3 on RUE, LI and k varied among genetic backgrounds and environments. Interactions between dw3 and genetic background, but also interactions with environment are likely to have modulated the extent to which RUE, LI, or k contributed to biomass differences between tall and short sorghum. © 2013 .

A novel method for the age estimation of Saddletail snapper (Lutjanus malabaricus) using Fourier Transform-near infrared (FT-NIR) spectroscopy

Near infrared (NIR) spectroscopy was investigated as a potential rapid method of estimating fish age from whole otoliths of Saddletail snapper (Lutjanus malabaricus). Whole otoliths from 209 Saddletail snapper were extracted and the NIR spectral characteristics were acquired over a spectral range of 800–2780 nm. Partial least-squares models (PLS) were developed from the diffuse reflectance spectra and reference-validated age estimates (based on traditional sectioned otolith increments) to predict age for independent otolith samples. Predictive models developed for a specific season and geographical location performed poorly against a different season and geographical location. However, overall PLS regression statistics for predicting a combined population incorporating both geographic location and season variables were: coefficient of determination (R2) = 0.94, root mean square error of prediction (RMSEP) = 1.54 for age estimation, indicating that Saddletail age could be predicted within 1.5 increment counts. This level of accuracy suggests the method warrants further development for Saddletail snapper and may have potential for other fish species. A rapid method of fish age estimation could have the potential to reduce greatly both costs of time and materials in the assessment and management of commercial fisheries.