Restricted Maximum Likelihood Analysis Research Articles

Familial aggregation and childhood blood pressure.

There is growing concern about elevated blood pressure (BP) in children. The evidence for familial aggregation of childhood BP is substantial. Twin studies have shown that a large part of the familial aggregation of childhood BP is due to genes. The first part of this review provides the latest progress in gene finding for childhood BP, focusing on the combined effects of multiple loci identified from the genome-wide association studies on adult BP. We further review the evidence on the contribution of the genetic components of other family risk factors to the familial aggregation of childhood BP including obesity, birth weight, sleep quality, sodium intake, parental smoking, and socioeconomic status. At the end, we emphasize the promise of using genomic-relatedness-matrix restricted maximum likelihood (GREML) analysis, a method that uses genome-wide data from unrelated individuals, in answering a number of unsolved questions in the familial aggregation of childhood BP.

Forming Core Collections in Barnyard, Kodo, and Little Millets using Morphoagronomic Descriptors

ABSTRACTMillets are hardy crops adapted to marginal lands in hot, drought‐prone arid and semiarid environments. Among the small millets, barnyard (Echinochloa spp.), kodo (Paspalum scrobiculatum L.), and little (Panicum sumatrense Roth ex Roem. and Schult.) millets are the most underresearched crops in terms of useful genetic and genomic resources available to breeders for genetic enhancement in these crops. A core collection is an important strategy to enhance use of diverse germplasm with agronomically beneficial traits in applied breeding. The entire germplasm collections of barnyard (736 accessions), kodo (656 accessions), and little (460 accessions) millets at ICRISAT were evaluated for 20 to 21 morphoagronomic traits in two to three rainy seasons at Patancheru, India. Quantitative traits data were subjected to residual (or restricted) maximum likelihood analysis and the best linear unbiased predictors were obtained. Qualitative traits data and standardized data on quantitative traits were used to determine Gower distance matrix, which was subjected to hierarchical cluster analysis following Ward method at R2 0.75 to form distinct clusters. About 10% or a minimum of one accession from each cluster were selected to form core collections, which consisted of 89 accessions in barnyard, 75 in kodo, and 56 in little millets. Comparisons of means, variances, frequency distribution, diversity indices, and correlations indicated that the variation in the entire collection has been preserved in the core collections, which can be evaluated multilocationally to identify trait‐specific diverse germplasm for use in genetic improvement of these crops.

Substantial SNP-based heritability estimates for working memory performance.

Working memory (WM) is an important endophenotype in neuropsychiatric research and its use in genetic association studies is thought to be a promising approach to increase our understanding of psychiatric disease. As for any genetically complex trait, demonstration of sufficient heritability within the specific study context is a prerequisite for conducting genetic studies of that trait. Recently developed methods allow estimating trait heritability using sets of common genetic markers from genome-wide association study (GWAS) data in samples of unrelated individuals. Here we present single-nucleotide polymorphism (SNP)-based heritability estimates (h2SNP) for a WM phenotype. A Caucasian sample comprising a total of N=2298 healthy and young individuals was subjected to an N-back WM task. We calculated the genetic relationship between all individuals on the basis of genome-wide SNP data and performed restricted maximum likelihood analyses for variance component estimation to derive the h2SNP estimates. Heritability estimates for three 2-back derived WM performance measures based on all autosomal chromosomes ranged between 31 and 41%, indicating a substantial SNP-based heritability for WM traits. These results indicate that common genetic factors account for a prominent part of the phenotypic variation in WM performance. Hence, the application of GWAS on WM phenotypes is a valid method to identify the molecular underpinnings of WM.

Body Composition Changes Among Female NCAA Division 1 Athletes Across the Competitive Season and Over a Multiyear Time Frame

Body composition can affect athletic performance. Numerous studies have documented changes in body composition in female collegiate athletes from pre- to postseason; however, longitudinal studies examining changes across years are scarce. Therefore, the primary purpose of this study was to assess longitudinal body composition changes among female collegiate athletes across 3 years. Two hundred twelve female athletes from basketball (BB; n = 38), soccer (SOC; n = 47), swimming (SW; n = 52), track (sprinters and jumpers; TR; n = 49), and volleyball (VB; n = 26) with an initial mean age of 19.2 ± 1.2 years, height of 172.4 ± 8.9 cm, and total mass of 66.9 ± 9.0 kg had body composition assessments using dual-energy x-ray absorptiometry pre- and postseason over 3 years. A restricted maximum-likelihood linear mixed model regression analysis examined body composition differences by sport and year. Changes (p < 0.05) over 3 years included the following: Lean mass increased in VB from year 1 to 2 (0.7 kg), year 2 to 3 (1.1 kg), and year 1 to 3 (1.8 kg) and in SW from year 1 to 3 (0.6 kg); and percent body fat (%BF) increased in BB from year 1 to 3 (1.7%). There were no changes in SOC or TR. These results indicate that during their college careers, female collegiate athletes can be expected to maintain their %BF and athletes in sports like SW and VB can anticipate an increase in lean mass, but the increases may be less than many athletes, coaches, and trainers envision.

Sarcoidosis in children: HRCT findings and correlation with pulmonary function tests

High-resolution computed tomography (HRCT) plays an important role in the diagnosis and staging of pulmonary sarcoidosis, but implies radiation exposure. In this light, we aimed to describe HRCT findings as well as their relationship with pulmonary function tests (PFT) in children with pulmonary sarcoidosis. In a retrospective study, 18 pediatric patients with sarcoidosis, including 12 with pulmonary abnormalities (PA group) and 6 without pulmonary abnormalities (APA group) were followed over a 16-year period. Relationships between HRCT scores and PFT were studied by non-parametric Spearman's test at diagnosis and by restricted maximum likelihood (REML) analysis during follow-up. Forty-three HRCT were scored. Twelve patients showed abnormal HRCT findings at diagnosis with multiple nodules or micronodules, while ground-glass opacities were seen in 11 patients. Ten patients exhibited pleural thickening or thickening of the fissure and 6 had interlobular septal thickening at diagnosis. No correlation between HRCT and forced vital capacity (FVC), forced expiratory volume in 1 sec (FEV1), forced expiratory flow during the mid-half of the FVC (FEF(25-75)) and specific dynamical compliance (SpecC(Ldyn)) was found at diagnosis. However, linear mixed models showed that changes in total HRCT scores over time were significantly associated with SpecC(Ldyn), FVC, and FEV1 modifications. Radiologic findings in children with pulmonary sarcoidosis were similar to those in adults. HRCT and PFT are both essential investigations at diagnosis; however, the correlation between HRCT pulmonary parenchymal findings and PFT over time suggests the possibility of reducing the number of HRCT during follow-up to decrease unnecessary radiation exposure.

Genetic progress in Dutch crop yields

Crop yields are a result of interactions between genetics, environment and management (G×E×M). As in the Netherlands differences between potential yield and actual farm yields (yield gaps) are relatively small, progress in genetic potential is essential to further increase farm yields. In this paper we study the progress in yields of newly released varieties in official Dutch variety trials as a proxy for the progress in genetic yield potential, i.e., yield under absence of water and nitrogen limitation and pests and diseases. The use of yields from variety trials as a proxy for genetic yield potential is justified as these are well managed and because water is hardly limiting under Dutch climate–soil conditions. We compared the genetic yield progress of winter wheat (Triticum aestivum L.), spring barley (Hordeum vulgare L.), ware and starch potato (Solanum tuberosum L.) and sugar beet (Beta vulgaris L.) over the past ca. 30 years (ca. 1980–2010) with the developments in on-farm yields over the same period. GenStat 14th edition was used to perform modified joint regression analyses (mjra) and residual (or restricted) maximum likelihood (reml) analyses of yields in order to separate year (i.e., climate and/or management) effects from variety effects. Genetic progress in yield has been linear with ca. 100 and 60kgha−1year−1 (15% moisture), respectively, for winter wheat and spring barley, 580kgha−1year−1 payment weight for starch potato, and, partly non-linear for sugar beet, i.e., 80–170kg sugarha−1year−1 depending on resistance type of the varieties. We also analyzed significant year effects (corrected for genetic progress) for most crops in the variety trials, which point at an effect of climate (environment) and/or management in addition to the genetic effect. Farm yields of winter wheat, spring barley and starch potato have increased linearly over the last decades, with ca. 90, 70 and 320kgha−1year−1 (in the same units as above). Increase in sugar yields on farms was concave (20–230kgha−1year−1) and spectacular over the last 10 years. For ware potatoes the genetic yield increase was only 20kg dry matterha−1year−1 and reliable farm statistics for dry matter yields are lacking. We conclude that for the main crops in the Netherlands genetic progress in yield potential of varieties newly released over the past three decades has been substantial and largely linear. Farm yields for these crops also continued to increase, at approximately the same rates, but could not always keep pace with the combined genetic and year effects (G×E×M) in variety trials, suggesting a widening yield gap.

Bayesian methods for the analysis of small sample multilevel data with a complex variance structure.

Inferences from multilevel models can be complicated in small samples or complex data structures. When using (restricted) maximum likelihood methods to estimate multilevel models, standard errors and degrees of freedom often need to be adjusted to ensure that inferences for fixed effects are correct. These adjustments do not address problems in estimating variance/covariance components. An alternative to the adjusted likelihood method is to use Bayesian methods, which can produce accurate inferences about fixed effects and variance/covariance parameters. In this article, the authors contrast the benefits and limitations of likelihood and Bayesian methods in the estimation of multilevel models. The issues are discussed in the context of a partially clustered intervention study, a common intervention design that has been shown to require an adjusted likelihood analysis. The authors report a Monte Carlo study that compares the performance of an adjusted restricted maximum likelihood (REML) analysis to a Bayesian analysis. The results suggest that for fixed effects, the models perform equally well with respect to bias, efficiency, and coverage of interval estimates. Bayesian models with a carefully selected gamma prior for the variance components were more biased but also more efficient with respect to estimation of the variance components than the REML model. However, the results also show that the inferences about the variance components in partially clustered studies are sensitive to the prior distribution when sample sizes are small. Finally, the authors compare the results of a Bayesian and adjusted likelihood model using data from a partially clustered intervention trial.

Cotton farming systems in Australia: factors contributing to changed yield and fibre quality

This study was undertaken to identify factors in Australian cotton farming systems that influence yield and fibre quality of cotton and how these have changed with time after the wide adoption of Bollgard II® cultivars (containing the proteins Cry1Ac and Cry2Ab, providing easier control of Helicoverpa spp.) in the 2003–04 season. Data from Australian commercial cotton variety trials conducted from 2004 to 2011 were used to link management inputs, yield, and fibre quality. Restricted (residual) maximum likelihood (REML) and regression analyses were used to determine which factors had a significant effect on yield and fibre quality. Results showed that lint yield was significantly influenced by cultivar and growing region, and the interaction between region and the amount of applied nitrogen and phosphorus (kg ha–1), plant stand (plants ha–1), in-crop rainfall (mm) and the number of irrigations, season length (days), and days to defoliation. Generally, the same factors also influenced fibre quality. Regression analysis captured 41, 71, 50, 30, and 36% of the variability in lint yield, fibre length, micronaire, fibre strength, and trash, respectively, for irrigated systems. For dryland systems the variability captured was 97, 87, 77 80, and 78%, respectively. Changes in cotton farming systems from 2004 to 2011 have occurred with applied nitrogen fertiliser increasing under irrigation and decreasing under dryland systems. However, phosphorus fertiliser use has remained steady under irrigated and decreased under dryland systems, and the number of insect sprayings has decreased under both systems. Under irrigated systems, lint yield, fibre length, and trash levels increased while micronaire and fibre strength decreased. Under dryland systems, lint yield decreased while micronaire, fibre length, strength, and trash levels increased. All fibre quality parameters satisfied criteria that would not incur a penalty. The results considering which factors are the most important and which are of lesser importance provide some insight to changes in management in both irrigated and dryland systems and the effect on lint yield and fibre quality and provide some basis for future investment in research and development and extension to the Australian cotton industry.

Effects of feed intake on enteric methane emissions from sheep fed fresh white clover (Trifolium repens) and perennial ryegrass (Lolium perenne) forages

Published analyses of enteric methane (CH4) emissions from sheep and cattle show an inverse relationship between feed intake and CH4 yield (gCH4/kg dry matter (DM) intake), which suggests opportunities for reducing CH4 emissions from feed eaten and per unit of animal production. Most relationships between feed intake and CH4 yield have been based on animals fed conserved feeds, especially silages and grains. Our research is a series of experiments with fresh white clover (Trifolium repens) and perennial ryegrass (Lolium perenne; ryegrass) forages fed to sheep at a range of feed intake levels. This study was comprised of four experiments where good quality freshly harvested white clover or ryegrass were fed to sheep over a three-fold range in DM intake, and CH4 emissions were measured in respiration chambers for two consecutive days in each experiment. Measurements were made from 16 sheep in Experiment 1 (fed at 1.6×metabolizable energy requirements for maintenance; MEm), 28 sheep in Experiment 2 (at 0.8 and 2.0×MEm), eight sheep and two measurement periods in Experiment 3 (at 1.6×MEm), and 30 sheep in Experiment 4 (fed at 0.8, 1.2, 1.6, 2.0 and 2.5×MEm). Prior to each experiment, sheep had a 10d acclimatization period to diets. Apparent digestibility was measured over 7d from sheep in Experiments 1, 3 and 4, along with collection of rumen digesta for volatile fatty acid (VFA) determination. Although CH4 yields differed when sheep were fed white clover or ryegrass at similar intakes, the differences were inconsistent and mean values similar across all experiments. This, and a similar structure of all experiments, enabled combined analysis of data from all four experiments using the restricted maximum likelihood (REML) procedure to estimate effects of feed intake level on digestibility, digestible nutrient intake, gas emissions, and VFA concentrations in the rumen. The REML analysis showed that when DM intake increased from 0.40 to 1.60kg/d, the predicted responses were an increase in CH4 production (g/d) of 187% (12.4–35.6g/d; P<0.001), and a decline in CH4 yield of 21% (25.6–20.2g/kg DM intake; P<0.001). High feed intake levels were associated with increased molar proportions (mM of total VFA) of propionate from 0.17 to 0.21 (P=0.038). Single and multiple regressions were completed on the data from all experiments, with organic matter (OM) intake predicting 0.87 of the variation in CH4 production, and molar proportion of propionate predicting 0.60 of the variation in CH4 yield. Increasing feed intakes by 1kg/d of DM reduced CH4 yield by 4.5g/kg DM intake. Plant chemical composition was weakly related to CH4 yield. High intakes of fresh forages will lower CH4 yield from fermentation, but effects of feed composition on CH4 emissions were minor. The interaction between effects of feed intake and rumen function requires further investigation to understand relationships with CH4 emissions.

Advanced complex trait analysis.

The Genome-wide Complex Trait Analysis (GCTA) software package can quantify the contribution of genetic variation to phenotypic variation for complex traits. However, as those datasets of interest continue to increase in size, GCTA becomes increasingly computationally prohibitive. We present an adapted version, Advanced Complex Trait Analysis (ACTA), demonstrating dramatically improved performance. We restructure the genetic relationship matrix (GRM) estimation phase of the code and introduce the highly optimized parallel Basic Linear Algebra Subprograms (BLAS) library combined with manual parallelization and optimization. We introduce the Linear Algebra PACKage (LAPACK) library into the restricted maximum likelihood (REML) analysis stage. For a test case with 8999 individuals and 279,435 single nucleotide polymorphisms (SNPs), we reduce the total runtime, using a compute node with two multi-core Intel Nehalem CPUs, from ∼17 h to ∼11 min. The source code is fully available under the GNU Public License, along with Linux binaries. For more information see http://www.epcc.ed.ac.uk/software-products/acta. a.gray@ed.ac.uk Supplementary data are available at Bioinformatics online.

Estimação de parâmetros genéticos de uma população F2 de suínos

Objetivou-se estimar parâmetros genéticos de características de carcaça, cortes de carcaça, qualidade de carne e desempenho de suínos em uma população F2 (Piau x linhagem comercial), para melhor se compreender a herança e a associação entre essas características. Para obter as estimativas de herdabilidades e correlações genéticas foi utilizado um modelo animal unicaracterístico e bicaracterístico, respectivamente, e os parâmetros foram estimados a partir dos componentes de variância e covariância, obtidos pelo método da máxima verossimilhança restrita por meio do programa MTDFREML. As herdabilidades estimadas, em modelo unicaracterístico, variaram de 0,10 a 0,43 para o grupo de características de carcaça, de 0,07 a 0,47 para cortes de carcaça, de 0,14 a 0,40 para qualidade de carne e de 0,18 a 0,86 para características de desempenho. As correlações genéticas estimadas em modelo bicaracterístico foram altas para algumas características, o que pode ser indicativo de que estas são controladas pelos mesmos genes ou genes ligados. Estudos futuros de mapeamento dos locos de características quantitativas, nesta população permitirão uma melhor compreensão das causas das correlações genéticas existentes entre as características, bem como determinar em qual região cromossômica localiza-se os locos de características quantitativas.

(Co)variance components and genetic parameters for growth traits in Arabi sheep using different animal models

The objective of the present study was to estimate genetic parameters for body weight at different ages in Arabi sheep using data collected from 1999 to 2009. Investigated traits consisted of birth weight (N = 2776), weaning weight (N = 2002) and weight at six months of age (N = 1885). The data were analyzed using restricted maximum likelihood analysis, by fitting univariate and multivariate animal models. All three weight traits were significantly influenced by birth year, sex and birth type. Age of dam only significantly affected birth weight. Log-likelihood ratio tests were conducted to determine the most suitable model for each growth trait in univariate analyses. Direct and total heritability estimates for birth weight, weaning weight and weight at six months of age (based on the best model) were 0.42 and 0.16 (model 4), 0.38 and 0.13 (model 4) and 0.14 and 0.14 (model 1), respectively. Estimation of maternal heritability for birth weight and weaning weight was 0.22 and 0.18, respectively. Genetic and phenotypic correlations among these traits were positive. Phenotypic correlations among traits were low to moderate. Genetic correlations among traits were positive and higher than the corresponding phenotypic correlations. Weaning weight had a strong and significant correlation with weight at six months of age (0.99). We conclude that selection can be made in animals based on weaning weight instead of the present practice of selection based on weight at six months.

An Investigation Into The Fruit Firmness Properties of Some Progeny and Cultivars of Red Raspberry (Rubus Idaeus)

Raspberries (Rubus ideaus L.) are popular and a major UK soft fruit crop. Several efforts have been geared towards developing an improved cultivar that will have a longer shelf-life. A 1 to 2 days improvement in fruit shelf-life would increase the value of harvested fruit and reduce waste. This research work investigated the firmness characteristics of 22 progeny (clones) derived from a Glen Moy x Latham mapping population by recording the various hardness values at 4 0 C over a 7 day storage period. A QTS-Texture Analyser was used to measure hardness values and the results were analyzed using Restricted Maximum Likelihood (REML) analysis. The parameters measured were: hardness, hardness1_workdone, final load, and sample length (diameter). Overall, there were significant differences (p<0.001) in the total hardness measurements between progeny. This research shows that some red raspberry clones from Glen Moy x Latham mapping population can stay wholesome after 7 days of storage at 4 0 C. This is a good development for red raspberry processors and the

Cryptic genetic variability in Swainsona sericea (A. Lee) H. Eichler (Fabaceae): lessons for restoration

Grassland communities worldwide have been extensively modified or lost following broadscale agricultural expansion. In south-eastern Australia few natural grasslands remain, with most now being small, isolated and degraded. Conservation and restoration of grassland communities requires an understanding of the impacts of fragmentation on genetic and demographic processes. Swainsona sericea is a perennial grassland herb with conservation listing in New South Wales, Victoria and South Australia. Reproductive output, progeny fitness and genetic diversity were assessed in nine S. sericea populations occupying fragmented grasslands across the southern tablelands of New South Wales. Unexpectedly, four chromosome classes were observed among the populations (2n = 4x = 32, 2n = 10x = 80, 2n = 14x = 112, 2n = 16x = 128), suggesting a more complex taxonomy than is currently recognised. There was no association between reproductive output and population size or ploidy level whereas population size influenced the number of alleles and percentage of polymorphic loci while ploidy influenced effective alleles and expected heterozygosity. Restricted maximum likelihood analyses of progeny growth indicated that ploidy had a significant influence on height, shoot weight, shoot to root ratio and days to germination. The cytological complexity in S. sericea requires clarification, including delineating the cytological boundaries to enable land managers to include this in their conservation and management plans.

Effect of automatic feeding of total mixed rations on the diurnal visiting pattern of dairy cows to an automatic milking system

Automatic feeding systems (AFSs) enable more frequent delivery of feedstuffs compared to conventional feeding systems (CFSs). The objective was to estimate the effect of the feeding system (CFS versus AFS) and of the associated feeding and milking related actions on the visiting patterns to automatic milking systems (AMSs). The AMS log files of 20 Dutch dairy farms that fed total mixed rations (TMR) and milked automatically for the year 2009 were analysed: 9 farms used a CFS, 11 farms fed with an AFS. The effects of the feeding system on the mean daily AMS visits were determined using an F-test and on the hourly AMS visits using a restricted maximum likelihood (REML) analysis. To assess the effect of feeding and milking related actions on the AMS visiting patterns the patterns were decomposed into Fourier harmonics, the effects of the actions were analysed with transfer functions and lagged variables and parameters were estimated with REML. No statistical differences were found for the mean daily AMS visits between the CFS (2.567 milkings day-1, 2.056 refusals day-1 and 0.105 failures day-1) and AFS farms (2.614 milkings day-1, 2.483 refusals day-1 and 0.118 failures day-1). The cows at the AFS farms were milked significantly earlier (at 7:00 and 8:00 AM) than at the CFS farms. Feed delivery reduced the milkings cow-1 h-1 slightly and almost significantly in the hour of feed delivery, while AMS cleanings and fetching of cows had a more significant effect on the hourly cow visits to the AMS.

Phenotypic plasticity of introduced versus native purple loosestrife: univariate and multivariate reaction norm approaches

The plastic responses to environmental change by Lythrum salicaria (purple loosestrife) were compared between native plants derived from seeds collected in Europe and those introduced into North America. Plants from nine populations each were grown under two levels of water and nutrient conditions. At the end of the growing season, samples were evaluated for eight traits related to their life history, plant size/architecture, and reproduction. Genetic (G), environmental (E), and G × E interactions were assessed by restricted maximum likelihood (REML) analysis of covariance (ANCOVA) and multivariate analysis of covariance (MANCOVA). Both univariate and multivariate reaction norm analyses were used to test for differences in the magnitude and direction of phenotypic plasticity between introduced and native plants. Under high-nutrient conditions, introduced plants were taller and had more branches and greater aboveground biomass. They also exhibited significantly greater amounts of phenotypic plasticity for aboveground biomass than did the natives in response to changing nutrient levels in standing water. This difference in univariate plasticity contributed to the general contrast in multivariate plasticity between introduced and native plants. These results support the idea that introduced plants may successfully invade a habitat and grow better than native plants in response to increased resources.

A DECISION SUPPORT SYSTEM FOR SUGARCANE VARIETY SELECTION IN SOUTH AFRICA BASED ON GENOTYPE-BY-ENVIRONMENT ANALYSES

SUMMARYThe objective of this study was to develop a basic variety selection decision support system (DSS) based on industry legalities, varietal characteristics and structured genotype-by-environment (G × E) analyses. Trial data extracted from a variety trial database at the South African Sugarcane Research Institute (SASRI) were categorized into different regions, harvest ages (12, 18, 24 months) and harvest seasons (early, mid, late season harvests). Restricted maximum likelihood analyses were conducted regionally to determine varietal adaptability to different harvest ages and seasons. Highly significant variety × harvest age and variety × season interactions allowed for the appropriate categorization of varieties. Varietal adaptability to different yield potential conditions was determined using the sites regression technique, and varietal adaptability was interpreted from the slope of the regression curves. The analysed data were used to create simplistic ‘yes/no’ spreadsheets, which were housed within a relational database. A web interface linked to the database allows users to specify characteristics of their production environment. The system then selects appropriate varieties that conform to specified criteria and eliminates non-compliers in a stepwise approach. The system was subsequently validated against expert extension specialist opinion and acceptable performance was observed.

Variation of fibre diameter coefficient of variation and fibre curvature across mohair fleeces: Implications for animal selection, genetic selection and fleece evaluation

The present work aimed to determine how the average fibre diameter coefficient of variation (CVD) and fibre curvature (FC) differences between nine sampling sites vary between sex and flock, to identify differences in variability between sampling sites as a result of between animal and between sire variability and to determine correlations between sampling sites in between animal and between sire variability. Australian Angoras ( n = 313) from two farms in southern Australia were sampled at 12 and 18 months of age at nine sites (mid side, belly, brisket, hind flank, hip, hock, mid back, neck, shoulder). Staples were taken prior to shearing at skin level and CVD and FC determined. For each shearing, differences in CVD and FC between sampling sites, how these differences were affected by farm, sex, and sire, and the covariance between sites for sire and individual animal effects were investigated by restricted maximum likelihood (REML) analyses. The median mid side CVD at 12 and 18 months of age ranged from 23.6 to 25.1% but the actual range was 16.8–34.2%. The median mid side FC at 12 and 18 months of age ranged from 14.4 to 18.6°/mm but the actual range was 10.5–26.3°/mm. The general pattern for CVD was for the mid back, hip and neck sites to have similar CVD, the brisket, hind flank and hock sites to have larger CVD and the belly to have smaller CVD than the mid side site. The between animal variation for CVD was lowest at the mid back site. This implies that the mid back would be the most effective site for between animal selection for CVD. Heritabilities for CVD (range at 18 months 0.18–0.30) were only about half the heritabilities for mean fibre diameter in the same study. There was a marked anterior–posterior increase in FC at both farms and with both ages. The results give no clear indication of the best site for between animal selection for FC, other than that the hock should be avoided. Heritabilities for FC are moderate to high (range at 18 months 0.44–0.77) and the genetic correlations are high except for the hock. Thus genetic selection for FC at any site, other than the hock, should be effective for changing FC over the entire fleece. There was more variability between animals than between sites and sires. These results are put into context with associated research on variation in mean fibre diameter and staple length.

Variation of mohair staple length across Angora goat fleeces: implications for animal selection and fleece evaluation

SUMMARYThe present study aimed to determine how the average mohair staple length (SL) differences between nine sampling sites vary between sex and flock, to identify differences in SL variability between sampling sites as a result of between-animal and between-sire variability and to determine SL correlations between sampling sites in between-animal and between-sire variability. Australian Angora goats (n=301) from two farms in southern Australia were sampled at 12 and 18 months of age at nine sites (mid side, belly, brisket, hind flank, hip, hock, mid back, neck and shoulder). Staples were taken prior to shearing at skin level and stretched SL determined. For each shearing, differences in SL between sampling sites, how these differences were affected by farm, sex and sire, and the covariance between sites for sire and individual animal effects were investigated by restricted maximum likelihood (REML) analyses. The median mid-side SL at 12 and 18 months of age was 110 and 130 mm, respectively, but the actual range in mid-side SL was 65–165 mm. There was an anterior–posterior decline in SL with the hock being particularly short. There was no evidence that the between-site correlation of the sire effects differed from 1, indicating that genetic selection for SL at one site will be reflected in SL over the whole fleece. However, low heritabilities of SL at the hock, belly and brisket or at any site at 12 months of age were obtained. There was more variability between sites than between sires, but the between-animal variation was greater. The hip and mid-back sites can be recommended for within-flock (culling) and genetic selection for SL due to their low sampling variability, moderate heritability and ease of location.

REML IS AN EFFECTIVE ANALYSIS FOR MIXED MODELLING OF UNBALANCED ON-FARM VARIETAL TRIALS

SUMMARYOn-farm participatory varietal selection (PVS) trials are often of two types: mother trials (with all of the entries) and baby trials (each having one, or very few of the entries from the mother trials). We conducted PVS trials on 17 wheat varieties in 12 villages of four districts of Bangladesh over three years but the data were highly unbalanced. Both quantitative and qualitative traits were measured in the on-farm trials. The factors in the trials were both fixed effects (varieties and districts) and random (years and farmers). We used the residual or restricted maximum likelihood (REML) analysis for the mixed model for quantitative traits. For qualitative data on farmers' perceptions, logistic regression procedures were used that are equally applicable to balanced and unbalanced data sets. The REML analysis provided adjusted mean values for quantitative traits for all the varieties, for the mother and baby trials separately, using the data from all years and all locations. It identified varieties BAW 1006 and BAW 1008 that yielded 19–30% more than the control Kanchan and also had a higher 1000-grain weight, were at least as early to flower and had a high overall ranking by farmers in the mother trials. The logistic regression analysis of perception data agreed with the results of the REML analysis as these varieties were most preferred by farmers for grain yield, earlier maturity and better chapatti making quality. The less labour-intensive method of recording qualitative perceptions can usefully replace actual yield measurements, particularly when validated by other participatory measures such as intended and actual adoption. In 2005, BAW 1006 was released as BARI Gom 23 or Bijoy and BAW 1008 as BARI Gom 24 or Prodip for the whole of Bangladesh. The validity of the results of the REML analysis was confirmed by the high early adoption trends of the identified varieties. Since REML is an effective analysis for unbalanced PVS trial data using a mixed model, its wider use by researchers would increase the value of the PVS process.