Genetic parameters and predicted response to selection for lean growth in an Australian commercial nucleus pig herd

Genetic parameters for performance traits in a pig population were estimated using a multi-trait derivative-free REML algorithm. The 2590 total data included 922 restrictively fed male and 1668 ad libitum fed female records. Estimates of heritability (standard error in parentheses) were 0.25 (0.03), 0.15 (0.03), and 0.30 (0.05) for lifetime daily gain, test daily gain, and P2-fat depth in males, respectively; and 0.27 (0.04) and 0.38 (0.05) for average daily gain and P2-fat depth in females, respectively. The genetic correlation between P2-fat depth and test daily gain in males was -0.17 (0.06) and between P2-fat and lifetime average daily gain in females 0.44 (0.09). Genetic correlations between sexes were 0.71 (0.11) for average daily gain and -0.30 (0.10) for P2-fat depth. Genetic response per standard deviation of selection on an index combining all traits was predicted at $AU120 per sow per year. Responses in daily gain and backfat were expected to be higher when using only male selection than when using only female selection. Selection for growth rate in males will improve growth rate and carcass leanness simultaneously.

Robust automatic mapping algorithms in a network monitoring scenario

Automatically generating maps of a measured variable of interest can be problematic. In this work we focus on the monitoring network context where observations are collected and reported by a network of sensors, and are then transformed into interpolated maps for use in decision making. Using traditional geostatistical methods, estimating the covariance structure of data collected in an emergency situation can be difficult. Variogram determination, whether by method-of-moment estimators or by maximum likelihood, is very sensitive to extreme values. Even when a monitoring network is in a routine mode of operation, sensors can sporadically malfunction and report extreme values. If this extreme data destabilises the model, causing the covariance structure of the observed data to be incorrectly estimated, the generated maps will be of little value, and the uncertainty estimates in particular will be misleading. Marchant and Lark [2007] propose a REML estimator for the covariance, which is shown to work on small data sets with a manual selection of the damping parameter in the robust likelihood. We show how this can be extended to allow treatment of large data sets together with an automated approach to all parameter estimation. The projected process kriging framework of Ingram et al. [2007] is extended to allow the use of robust likelihood functions, including the two component Gaussian and the Huber function. We show how our algorithm is further refined to reduce the computational complexity while at the same time minimising any loss of information. To show the benefits of this method, we use data collected from radiation monitoring networks across Europe. We compare our results to those obtained from traditional kriging methodologies and include comparisons with Box-Cox transformations of the data. We discuss the issue of whether to treat or ignore extreme values, making the distinction between the robust methods which ignore outliers and transformation methods which treat them as part of the (transformed) process. Using a case study, based on an extreme radiological events over a large area, we show how radiation data collected from monitoring networks can be analysed automatically and then used to generate reliable maps to inform decision making. We show the limitations of the methods and discuss potential extensions to remedy these.

Juvenile-mature genetic correlations in Pinus taeda clones propagated via somatic embryogenesis.

Objetivou-se com o presente trabalho, estimar a correlação genética entre idades de seleção (juvenil-adulta) e eficiência da seleção precoce para as características altura, diâmetro e volume de indivíduos de famílias de Pinus taeda propagados via embriogênese somática. O estudo foi realizado por meio de análise genético-estatística pelo procedimento de estimação de componentes de variância (Reml) e de predição de valores genéticos (Blup), usando-se o software Selegen-Reml/Blup. As correlações genéticas entre idades juvenis e idade de rotação foram realizadas aplicando o modelo linear desenvolvido por Lambeth (1980). Segundo os resultados do modelo estabelecido, a seleção precoce pode ser realizada em clones de Pinus taeda com alta eficiência de seleção. As idades de 4 a 6 anos são suficientes para selecionar clones de Pinus taeda propagados via embriogênese somática para colheita aos 8 e 12 anos e, as idades de 6 a 10 anos são suficientes para selecionar para colheita aos 20 anos. De acordo com as estimativas de correlação genotípicaa partir dos ambientes, a seleção de clones de Pinus taeda propagados via embriogênese somática deve ser praticada de forma específica para cada ambiente. Pode-se realizar a seleção de clones considerando o diâmetro, visto a alta correlação observada entre volume e diâmetro.

Modelos linear e não linear em análises genéticas para sobrevivência de crias de ovinos da raça Santa Inês.

Resumo: Registros de sobrevivência do nascimento ao desmame de 3846 crias de ovinos da raça Santa Inês foram analisados por modelos de reprodutor linear e não linear (modelo de limiar), para estimar componentes de variância e herdabilidade. Os modelos usados para sobrevivência, analisada como característica da cria, incluíram os efeitos fixos de sexo, da combinação tipo de nascimento-criação da cria e da idade da ovelha ao parto, efeito da covariável peso da cria ao nascer e efeitos aleatórios de reprodutor, da classe rebanho-ano-estação e do resíduo. Componentes de variância para o modelo linear foram estimados pelo método da máxima verossimilhança restrita (REML) e para o modelo não linear por uma aproximação da máxima verossimilhança marginal (MML), pelo programa CMMAT2. O coeficiente de herdabilidade (h2) estimado pelo modelo de limiar foi de 0,29, e pelo modelo linear, 0,14. A correlação de ordem de Spearman entre as capacidades de transmissão dos reprodutores, com base nos dois modelos foi de 0,96. As estimativas de h2 obtidas indicam a possibilidade de se obter, por seleção, ganho genético para sobrevivência. [Linear and nonlinear models in genetic analyses of lamb survival in the Santa Inês hair sheep breed]. Abstract: Records of 3,846 lambs survival from birth to weaning of Santa Inês hair sheep breed, were analyzed by linear and non linear sire models (threshold model) to estimate variance components and heritability (h2). The models that were used to analyze survival, considered in this study as a lamb trait, included the fixed effects of sex of the lamb, combination of type of birth-rearing of lamb, and age of ewe, birth weight of lamb as covariate, and random effects of sire, herd-year-season and residual. Variance components were obtained using restricted maximum likelihood (REML), in linear model and marginal maximum likelihood in threshold model through CMMAT2 program. Estimate of heritability (h2) obtained by threshold model was 0.29 and by linear model was 0.14. Rank correlation of Spearman, between sire solutions based on the two models was 0.96. The obtained estimates in this study indicate that it is possible to acquire genetic gain to survival by selection.

Coarser wool is not a necessary consequence of sheep aging: allometric relationship between fibre diameter and fleece-free liveweight of Saxon Merino sheep

The mean fibre diameter (MFD) of wool is the primary determinant of price, processing performance and textile quality. This study determines the primary influences on MFD as Saxon Merino sheep age, by allometrically relating MFD to fleece-free liveweight (FFLwt). In total, 79 sheep were grazed in combinations of three stocking rates and two grazing systems (GS: sheep only; mixed with Angora goats) and studied over 3 years. Measurements were made over 14 consecutive periods (Segments), including segments of FFLwt gain or FFLwt loss. Using shearing and liveweight records and dye-bands on wool, the FFLwt and average daily gain (ADG) of each sheep were determined for each segment. The mean and range in key measurements were as follows: FFLwt, 40.1 (23.1 to 64.1) kg; MFD, 18.8 (12.7 to 25.8) μm. A random coefficient restricted maximum likelihood (REML) regression mixed model was developed to relate the logarithm of MFD to the logarithm of FFLwt and other effects. The model can be written in the form of ${\rm MFD}\,{\equals}\,\rkappa \left( {{\rm GS,}\,{\rm A}{\rm ,}\,{\rm Segment}{\rm .Plot,}\,{\rm Segment,}\,{\rm ADG}} \right){\times}{\rm FFLwt}^{{\left( {\ralpha \left( {{\rm GS}} \right){\plus}\rbeta \left(\rm A \right){\plus}\rgamma \left( {{\rm Segment}{\rm .Plot}} \right)} \right)}} $ , where $\ralpha \left( {{\rm GS}} \right)\,{\equals}\,\;\left\{ {\matrix{\!\! {0.32\left( {{\rm SE}\,{\equals}\,{\rm 0}{\rm .038}} \right)\,{\rm when}\,{\rm sheep}\,{\rm are}\,{\rm grazed}\,{\rm alone}} \hfill \cr \!\!\!\!{0.49\left( {{\rm SE}\,{\equals}\,{\rm 0}{\rm .049}} \right)\,{\rm when}\,{\rm sheep}\,{\rm are}\,{\rm mixed}\,{\rm with}\,{\rm goats}} \hfill \cr } } \right.$ β(A) is a random animal effect, γ(Segment.Plot) a random effect associated with Segment.plot combinations, and κ a constant that depends on GS, random animal effects, random Segment.plot combination effects, Segment and ADG. Thus, MFD was allometrically related to the cube root of FFLwt over seasons and years for sheep, but to the square root of FFLwt for sheep grazed with goats. The result for sheep grazed alone accords with a primary response being that the allocation of nutrients towards the cross-sectional growth of wool follicles is proportional to the changes in the skin surface area arising from changes in the size of the sheep. The proportionality constant varied systematically with ADG, and in sheep only grazing, was about 5 when sheep lost 100 g/day and about 6 when sheep gained 100 g/day. The proportionality constant did not systematically change with chronological age. The variation in the allometric coefficient between individual sheep indicates that some sheep were more sensitive to changes in FFLwt than other sheep. Key practical implications include the following: (a) the reporting of systematic increases in MFD with age is likely to be a consequence of allowing sheep to increase in size during shearing intervals as they age; (b) comparisons of MFD between sheep are more likely to have a biological basis when standardised to a common FFLwt and not just to a common age;

Estimates of genetic parameters using RELM/BLUP for intrapopulational genetic breeding of Platonia insignis Mart.

The aim of this study was to estimate genetic parameters to support the selection of bacuri progenies for a first cycle of recurrent selection, using the REML/BLUP (restricted maximum likelihood/best linear unbiased prediction) procedure to estimate the variance components and genotypic values. Were evaluated twelve variables in a total of 210 fruits from 39 different seed trees, from a field trial with an experimental design of incomplete blocks with clonal replies among subplots. The three variables related with the fruit development (weight, diameter, length) showed strong correlation, and where fruit length showed higher heritability and potential to be used for indirect selection. Among the 39 progenies evaluated in this study, five present potential to compose the next cycle of recurrent selection, due they hold good selection differential either to agrotechnological variables as to development of bacuri fruit.

Predição de ganhos genéticos via modelos mistos em progênies de café Conilon.

Objetivou-se, neste trabalho, avaliar os ganhos genéticos preditos por meio de diferentes índices de seleção pela metodologia REML/BLUP, em cinco caracteres de interesse ao programa de melhoramento do café conilon do Incaper. Foram avaliadas 8 progênies de meios-irmãos, de ciclo de maturação precoce, média de duas safras, com três repetições, o que totalizou 1368 observações, utilizados os índices de seleção clássico, multiplicativo e com base na soma de postos. Avaliaramse, na época de colheita, as características tamanho dos grãos (TG), produtividade (PRO), porte (PT), vigor vegetativo (VIG) e grau de inclinação (GI). A população foi avaliada na Fazenda Experimental de Marilândia, região Noroeste do estado do Espírito Santo. As análises genético-estatísticas foram realizadas pelo programa Selegen - REM/BLUP. Verificou-se, a partir da análise dos parâmetros genéticos, um excelente potencial seletivo entre famílias, para todas as características avaliadas. O índice Mulamba e Mock foi o que mostrou maior eficiência de seleção entre famílias de meios-irmãos de café conilon.

Bunch yield of interspecific hybrids of American oil palm with oil palm in the juvenile phase.

To identify superior genotypes, 42 progenies of interspecific hybrids between American oil palm and oil palm were evaluated in an area with incidence of bud rot. The following variables were assessed: total bunch yield (TBY), number of bunches (NB) and mean bunch weight (MBW) from the third to the sixth year of cultivation and estimates of genetic parameters obtained by REML/BLUP procedures.