scholarly journals Application and Analysis of a Composite Sampling Strategy to Cost-Effectively Compare Nutritive Characteristics of Perennial Ryegrass Cultivars in Field Trials

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1152
Author(s):  
Clare Leddin ◽  
Khageswor Giri ◽  
Kevin Smith
Keyword(s):  
Perennial Ryegrass ◽  
Data Model ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Sampling Strategy ◽  
Field Trials ◽  
Spatial And Temporal Variation ◽  
Full Data ◽  
Composite Sampling ◽  
Composite Samples

Pasture nutritive value is economically important in south-eastern Australian dairy production systems, yet measurement of nutritive characteristics in pasture cultivar evaluation trials is not routinely undertaken, primarily due to cost. An approach aiming to reduce the total laboratory analysis costs in multi-harvest field trials by testing some entries as composite samples is provided. A field trial evaluating 31 trial entries sown in 4 replicates was used. On nine harvest occasions, samples were collected from each plot, dried, ground and analysed using near infrared spectroscopy for key nutritive characteristics (metabolisable energy (ME), crude protein (CP) and neutral detergent fibre (NDF)). Additionally, composite samples of 17 of the 31 entries from each harvest were created by combining sub-samples of material from each of four replicate plots into a single sample that was also analysed. A linear mixed model (LMM) analysis accounting for spatial and temporal variation as well as spatial and temporal correlations was conducted, comparing the full data model where all plots at all harvests were tested individually to a data model where some entries were evaluated as individual plots and others as composites. The precision and accuracy of the estimates for the two models were similar and best linear unbiased prediction (BLUP) means of the composite sampling strategy model were comparable to the full data model. It was concluded that if composite sampling is used in conjunction with testing samples from individual plots on a selection of cultivars, statistically valid inferences are possible and the total cost of determining the nutritive characteristics of perennial ryegrass cultivars in field trials can be reduced.

scholarly journals Tensor P-Spline Smoothing for Spatial Analysis of Plant Breeding Trials

2021 ◽  
Author(s):  
Hans-Peter Piepho ◽  
Martin Boer ◽  
Emlyn R. Williams
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Null Space ◽  
Spatial Interaction ◽  
Natural Extension ◽  
Covariance Structure ◽  
Spatial Modelling ◽  
Field Trials ◽  
Agricultural Field ◽  
Randomized Field Trials

Large agricultural field trials may display irregular spatial trends that cannot be fully captured by a purely randomization-based analysis. For this reason, paralleling the development of analysis-of-variance procedures for randomized field trials, there is a long history of spatial modelling for field trials, starting with the early work of Papadakis on nearest neighbour analysis, which can be cast in terms of first or second differences among neighbouring plot values. This kind of spatial modelling is amenable to a natural extension using P-splines, as has been demonstrated in recent publications in the field. Here, we consider the P-spline framework, focussing on model options that are easy to implement in linear mixed model packages. Two examples serve to illustrate and evaluate the methods. A key conclusion is that first differences are rather competitive with second differences. A further key observation is that second differences require special attention regarding the representation of the null space of the smooth terms for spatial interaction, and that an unstructured variance-covariance structure is required to ensure invariance to translation and rotation of eigenvectors associated with that null space. We develop a strategy that permits fitting this model with ease, but the approach is more demanding than that needed for fitting models using first differences. Hence, even though in other areas second differences are very commonly used in the application of P-splines, our main conclusion is that with field trials first differences have advantages for routine use.

scholarly journals Effect of Herbage Density, Height and Age on Nutrient and Invertebrate Generalist Predator Abundance in Permanent and Temporary Pastures

Land ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 164
Author(s):  
Rémi Toupet ◽  
Alastair T. Gibbons ◽  
Sara L. Goodacre ◽  
Matt J. Bell
Keyword(s):  
Perennial Ryegrass ◽  
Crude Protein ◽  
Dry Matter ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Grass Species ◽  
Nutrient Concentrations ◽  
Generalist Predator ◽  
Diverse Range ◽  
Predator Abundance

The aim of this research was to assess differences in the quantity and quality of herbage and invertebrate generalist predator abundance among permanent and temporary pastures. Two permanent pastures and four temporary ley pastures (either one year or two years since being sown) were monitored weekly for 10 weeks in the spring. Permanent pastures included a diverse range of native UK grass species, and temporary ley pastures were predominantly perennial ryegrass (Lolium perenne) with or without white clover (Trifolium repens). Weekly measurements of herbage height (in centimeters), herbage cover (fresh and dry matter in kg per hectare) and herbage density (fresh and dry matter in kg per hectare per centimeter) were obtained for each field, along with lycosid spider and carabid beetle abundance. Weekly pasture samples were used to obtain nutrient concentrations of dry matter, crude protein, neutral detergent fibre (NDF), acid detergent fibre (ADF), ash, oil, sugars, digestible organic matter in the dry matter (DOMD) and metabolisable energy (ME) in the herbage as a measure of forage quality for grazing or harvesting. A linear mixed model was used to assess the effect of sward age, herbage density and height on herbage production, nutrient concentrations and invertebrate abundance. Although this study showed that permanent pastures were associated with lower nutrient concentrations of crude protein, ash, oil and ME compared to younger and predominantly perennial ryegrass pastures, the older pastures were associated with higher carabid numbers. Furthermore, permanent pastures had a higher density of dry matter herbage compared to younger pastures, and more dense and taller swards were associated with higher lycosid numbers. The study suggests that within pastures of 3 to 20 cm height, increasing the height and density of swards increases both ME and oil concentrations in herbage, therefore enhancing forage nutrient quality. Older and more permanent pastures can be beneficial for plant and invertebrate generalist predator populations, and still provide a useful source of nutrients for forage production.

scholarly journals 15 EFFECT OF SEMEN THAW METHOD ON CONCEPTION RATE IN DAIRY HEIFER HERDS

2005 ◽  
Vol 17 (2) ◽  
pp. 157 ◽  
Author(s):  
M. Kaproth ◽  
H. Rycroft ◽  
G. Gilbert ◽  
G. Abdel-Azim ◽  
B. Putnam ◽  
...  
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Semen Quality ◽  
Sperm Quality ◽  
Field Trials ◽  
Conception Rate ◽  
Warm Water ◽  
Dairy Heifer

Semen processed with procedures permitting a flexible thaw method is used to breed millions of cows yearly. “Pocket thawing” is widely used as an alternative to warm-water thawing with such semen. To pocket thaw, a straw is retrieved from cryostorage, immediately wrapped in a folded paper towel, and moved to a thermally protected pocket for 2 to 3 min of thawing within the pocket before AI gun loading. Published field data are lacking for comparisons of such a thaw method with those for semen prepared to permit flexible-thawing. We measured the effect of warm-water or pocket thaw on conception rate in four dairy heifer herds using semen prepared with methods previously optimized for flexible-thawing success. Semen processing (Anderson S et al. 1994 J. Dairy Sci. 77, 2302–2307) includes two-step whole-milk extension, static vapor tank freezing (0.5-mL straws), and IMV Digitcool mechanical freezing (0.25-mL straws). It is unclear which specific processing steps permit flexible thawing. These procedures have been developed using breeding results from decades of field trials by professional inseminators using both pocket and warm-water thaw. Semen prepared from each of 12 sires produced equal straw units at 10 and 15 million total sperm per straw, in both 0.5- and 0.25-mL straw packages. Professional inseminators used each combination evenly over 16 months. Additional commercial semen (55% of total) from the same source was used. The thaw methods alternated weekly. Thaw effect on conception status, from 70 day non-return data for 11,215 services (67.6% conception rate), was estimated by a generalized linear mixed model. Neither thaw method nor total sperm per straw significantly affected conception rate (P = 0.658, 0.769, respectively). Bull, herd, inseminator within herd, year, season, and straw size did significantly affect conception rate (P < 0.05). No thaw method interactions with herd, sperm number, season, and straw package size were significant (P = 0.297, 0.526, 0.365, 0.723, respectively). This suggests that if semen has been prepared with procedures specific to flexible-thawing, it can be either pocket thawed or warm-water thawed within a range of herdsman or inseminator practices, season, or straw packaging choices. Even at 10 million, the lowest total sperm per straw, pocket thaw was equally as successful as warm-water thaw. We generally observe that in vitro sperm quality, as expected, is maximal for rapidly thawed straws, with slower thawing resulting in lower values. However, while it appears that conventional measures of in vitro semen quality are improved with fast thaw rates, these measures do not appear to correspond to higher in vivo fertility for semen prepared intentionally to be flexibly thawed. We conclude that, for semen prepared with procedures that permit flexible thawing, the thaw method, whether pocket or warm-water thaw, does not affect conception under commercial conditions and with routine semen handling methods. We thank the herd owners and their staff, the inseminators, and Hap Allen, Ron Hunt, Gordon Nickerson, and Bryan Krick of Genex for their help and cooperation.

Development of a system to rank perennial ryegrass cultivars according to their economic value to dairy farm businesses in south-eastern Australia

2018 ◽  
Vol 58 (8) ◽  
pp. 1552 ◽  
Author(s):  
C. M. Leddin ◽  
J. L. Jacobs ◽  
K. F. Smith ◽  
K. Giri ◽  
B. Malcolm ◽  
...  
Keyword(s):  
Perennial Ryegrass ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Economic Value ◽  
Dairy Farm ◽  
Grass Species ◽  
South Eastern ◽  
Eastern Australia ◽  
Forage Value ◽  
South Eastern Australia

Dairy production systems in south-eastern Australia are based primarily on grazed pasture. Perennial ryegrass (Lolium perenne L.) is the major grass species used in this region and farmers are faced with the challenge of choosing from more than 60 commercially available cultivars. This paper describes the development of a system termed as a forage value index that ranks the overall performance of perennial ryegrass cultivars relative to cultivar Victorian according to the summation of the estimated difference in the value of seasonal dry-matter (DM) yield of the cultivars. Average predicted seasonal DM yields were calculated by analysing the results of eight available perennial ryegrass plot trials across south-eastern Australia, using a multi-environment, multi-harvest linear mixed model. The differences in the model-predicted DM yield of each cultivar was compared with cultivar Victorian in each of five seasonal periods (autumn, winter, early spring, late spring, summer) to generate a series of performance values (1 per period) for each cultivar. Each performance value was then multiplied by an economic value (AU$/kg extra pasture grown) relating to each of four regions (Gippsland, northern Victoria, south-western Victoria, Tasmania) and seasonal period and aggregated to generate an overall forage value index rating for each cultivar. Economic values ranged from AU$0.11 to AU$0.39 per extra kilogram of DM grown, depending on the season and region, which translated into estimated benefits on dairy farms of up to AU$183 per ha per year for farmers that use high-yielding cultivars in place of cultivar Victorian perennial ryegrass.

Establishing phenotypic performance of grass varieties on Irish grassland farms

2017 ◽  
Vol 155 (10) ◽  
pp. 1633-1645 ◽  
Author(s):  
N. BYRNE ◽  
T. J. GILLILAND ◽  
N. McHUGH ◽  
L. DELABY ◽  
A. GEOGHEGAN ◽  
...  
Keyword(s):  
Perennial Ryegrass ◽  
Dry Matter ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Phenotypic Variance ◽  
Total Production ◽  
Dry Matter Digestibility ◽  
Herbage Yield ◽  
Significant Performance ◽  
Commercial Farms

SUMMARYConventionally perennial ryegrass evaluations are conducted under simulated grazing studies to identify varieties with the best phenotypic performance. However, cut-plot environments differ greatly to those experienced on commercial farms as varieties are not exposed to the same stress levels in test environments. It could be argued that plot-based testing regimes provide little direction to plant breeders in the development of advanced varieties. Varietal phenotypic performance needs to be quantified in ‘commercial’ situations. The objective of the current study was to evaluate the phenotypic performance of a range of perennial ryegrass varieties under commercial farm conditions. Monocultures of 11 Irish Recommended List perennial ryegrass varieties were sown on 66 commercial farms throughout Ireland where performance was evaluated over a 3-year period from 2013 to 2015, inclusive. A linear mixed model was used to quantify variety effects on grassland phenotypic performance characteristics. No significant variety effect was estimated for total, seasonal or silage herbage production. Despite the lack of variety effects, pairwise comparisons found significant performance differences between individual varieties. Grazed herbage yield is of primary importance and was shown to be correlated strongly with total production (0.71); Grazed herbage yield differed significantly by variety, with a range of 1927 kg dry matter (DM)/ha between the highest and lowest performing varieties. Sward quality (dry matter digestibility [DMD]) and density were influenced by variety with a range of 44 g/kg DM for DMD and 0.7 ground score units between the highest and lowest performing varieties. Results of the current study show that on-farm evaluation is effective in identifying the most suitable varieties for intensive grazing regimes, and the phenotypic variance identified among varieties performance for many traits should allow for improved genetic gain in areas such as DM production, persistence and grazing efficiency.

Analyzing discontinuities in longitudinal count data: A multilevel generalized linear mixed model.

2020 ◽  
Author(s):  
James L. Peugh ◽  
Sarah J. Beal ◽  
Meghan E. McGrady ◽  
Michael D. Toland ◽  
Constance Mara
Keyword(s):  
Count Data ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Generalized Linear Mixed Model ◽  
Longitudinal Count Data

Predicting bycatch hotspots based on suitable habitat derived from fishery-independent data

2020 ◽  
Vol 641 ◽  
pp. 159-175
Author(s):  
J Runnebaum ◽  
KR Tanaka ◽  
L Guan ◽  
J Cao ◽  
L O’Brien ◽  
...  
Keyword(s):  
Habitat Suitability ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Gulf Of Maine ◽  
Homarus Americanus ◽  
Management Tool ◽  
American Lobster ◽  
Suitable Habitat ◽  
Climate Conditions ◽  
Suitability Index

Bycatch remains a global problem in managing sustainable fisheries. A critical aspect of management is understanding the timing and spatial extent of bycatch. Fisheries management often relies on observed bycatch data, which are not always available due to a lack of reporting or observer coverage. Alternatively, analyzing the overlap in suitable habitat for the target and non-target species can provide a spatial management tool to understand where bycatch interactions are likely to occur. Potential bycatch hotspots based on suitable habitat were predicted for cusk Brosme brosme incidentally caught in the Gulf of Maine American lobster Homarus americanus fishery. Data from multiple fisheries-independent surveys were combined in a delta-generalized linear mixed model to generate spatially explicit density estimates for use in an independent habitat suitability index. The habitat suitability indices for American lobster and cusk were then compared to predict potential bycatch hotspot locations. Suitable habitat for American lobster has increased between 1980 and 2013 while suitable habitat for cusk decreased throughout most of the Gulf of Maine, except for Georges Basin and the Great South Channel. The proportion of overlap in suitable habitat varied interannually but decreased slightly in the spring and remained relatively stable in the fall over the time series. As Gulf of Maine temperatures continue to increase, the interactions between American lobster and cusk are predicted to decline as cusk habitat continues to constrict. This framework can contribute to fisheries managers’ understanding of changes in habitat overlap as climate conditions continue to change and alter where bycatch interactions could occur.

Long-term seizure outcomes after pediatric temporal lobectomy: does brain MRI lesion matter?

2019 ◽  
Vol 24 (2) ◽  
pp. 200-208
Author(s):  
Ravindra Arya ◽  
Francesco T. Mangano ◽  
Paul S. Horn ◽  
Sabrina K. Kaul ◽  
Serena K. Kaul ◽  
...  
Keyword(s):  
Repeated Measures ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Hippocampal Sclerosis ◽  
Brain Mri ◽  
Temporal Lobectomy ◽  
Seizure Freedom ◽  
Seizure Onset

OBJECTIVEThere is emerging data that adults with temporal lobe epilepsy (TLE) without a discrete lesion on brain MRI have surgical outcomes comparable to those with hippocampal sclerosis (HS). However, pediatric TLE is different from its adult counterpart. In this study, the authors investigated if the presence of a potentially epileptogenic lesion on presurgical brain MRI influences the long-term seizure outcomes after pediatric temporal lobectomy.METHODSChildren who underwent temporal lobectomy between 2007 and 2015 and had at least 1 year of seizure outcomes data were identified. These were classified into lesional and MRI-negative groups based on whether an epilepsy-protocol brain MRI showed a lesion sufficiently specific to guide surgical decisions. These patients were also categorized into pure TLE and temporal plus epilepsies based on the neurophysiological localization of the seizure-onset zone. Seizure outcomes at each follow-up visit were incorporated into a repeated-measures generalized linear mixed model (GLMM) with MRI status as a grouping variable. Clinical variables were incorporated into GLMM as covariates.RESULTSOne hundred nine patients (44 females) were included, aged 5 to 21 years, and were classified as lesional (73%), MRI negative (27%), pure TLE (56%), and temporal plus (44%). After a mean follow-up of 3.2 years (range 1.2–8.8 years), 66% of the patients were seizure free for ≥ 1 year at last follow-up. GLMM analysis revealed that lesional patients were more likely to be seizure free over the long term compared to MRI-negative patients for the overall cohort (OR 2.58, p < 0.0001) and for temporal plus epilepsies (OR 1.85, p = 0.0052). The effect of MRI lesion was not significant for pure TLE (OR 2.64, p = 0.0635). Concordance of ictal electroencephalography (OR 3.46, p < 0.0001), magnetoencephalography (OR 4.26, p < 0.0001), and later age of seizure onset (OR 1.05, p = 0.0091) were associated with a higher likelihood of seizure freedom. The most common histological findings included cortical dysplasia types 1B and 2A, HS (40% with dual pathology), and tuberous sclerosis.CONCLUSIONSA lesion on presurgical brain MRI is an important determinant of long-term seizure freedom after pediatric temporal lobectomy. Pediatric TLE is heterogeneous regarding etiologies and organization of seizure-onset zones with many patients qualifying for temporal plus nosology. The presence of an MRI lesion determined seizure outcomes in patients with temporal plus epilepsies. However, pure TLE had comparable surgical seizure outcomes for lesional and MRI-negative groups.

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