Predicting breeding values for milk yield of Guzera (Bos indicus) cows using random regression models

Given the importance of Guzera breeding programs for milk production in the tropics, the objective of this study was to compare alternative random regression models for estimation of genetic parameters and prediction of breeding values. Test-day milk yields records (TDR) were collected monthly, in a maximum of 10 measurements. The database included 20,524 records of first lactation from 2816 Guzera cows. TDR data were analyzed by random regression models (RRM) considering additive genetic, permanent environmental and residual effects as random and the effects of contemporary group (CG), calving age as a covariate (linear and quadratic effects) and mean lactation curve as fixed. The genetic additive and permanent environmental effects were modeled by RRM using Wilmink, All and Schaeffer and cubic B-spline functions as well as Legendre polynomials. Residual variances were considered as heterogeneous classes, grouped differently according to the model used. Multi-trait analysis using finite-dimensional models (FDM) for testday milk records (TDR) and a single-trait model for 305-days milk yields (default) using the restricted maximum likelihood method were also carried out as further comparisons. Through the statistical criteria adopted, the best RRM was the one that used the cubic B-spline function with five random regression coefficients for the genetic additive and permanent environmental effects. However, the models using the Ali and Schaeffer function or Legendre polynomials with second and fifth order for, respectively, the additive genetic and permanent environmental effects can be adopted, as little variation was observed in the genetic parameter estimates compared to those estimated by models using the B-spline function. Therefore, due to the lower complexity in the (co)variance estimations, the model using Legendre polynomials represented the best option for the genetic evaluation of the Guzera lactation records. An increase of 3.6% in the accuracy of the estimated breeding values was verified when using RRM. The ranks of animals were very close whatever the RRM for the data set used to predict breeding values. Considering P305, results indicated only small to medium difference in the animals' ranking based on breeding values predicted by the conventional model or by RRM. Therefore, the sum of all the RRM-predicted breeding values along the lactation period (RRM305) can be used as a selection criterion for 305-day milk production. (c) 2014 Elsevier B.V. All rights reserved.

Multicollinearity and financial constraint in investment decisions: a bayesian generalized ridge regression

This paper addresses the investment decisions considering the presence of financial constraints of 373 large Brazilian firms from 1997 to 2004, using panel data. A Bayesian econometric model was used considering ridge regression for multicollinearity problems among the variables in the model. Prior distributions are assumed for the parameters, classifying the model into random or fixed effects. We used a Bayesian approach to estimate the parameters, considering normal and Student t distributions for the error and assumed that the initial values for the lagged dependent variable are not fixed, but generated by a random process. The recursive predictive density criterion was used for model comparisons. Twenty models were tested and the results indicated that multicollinearity does influence the value of the estimated parameters. Controlling for capital intensity, financial constraints are found to be more important for capital-intensive firms, probably due to their lower profitability indexes, higher fixed costs and higher degree of property diversification.

Prediction of genomic-enabled breeding values and genome-wide association study for feedlot average daily weight gain in Nelore cattle

Pós-graduação em Genética e Melhoramento Animal - FCAV

Re-used progesterone devices efficiently synchronise oestrus and ovulation after autoclaving process in Toggenburg goats during the breeding season

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A new species of hylodes (Anura, Hylodidae) and its secretive underwater breeding behavior

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Aloe vera bathing improved physical and humoral protection in breeding stock after induced spawning in matrinxa (Brycon amazonicus)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Effects of re-stripping on the seminal characteristics of pacu (Piaractus mesopotamicus) during the breeding season

Seminal characteristics in teleost fish with an annual reproductive period, such as pacu (Piaractus mesopotamicus), may vary during the breeding season. The sperm formed before the beginning of the spawning period may be stored for a long time, causing damage to the cells. Therefore, re-stripping may be an important way to eliminate the old and allow for the collection of new spermatozoids. In this study, we analyzed the seminal characteristics of hormonally induced pacu at the beginning, middle and end of the breeding season, and we analyzed samples from re-stripped males (stripped first at the beginning, re-stripped in the middle, and re-stripped again at the end of the season) during two breeding seasons. The sperm density, ionic composition, pH, and osmolality were similar among the groups. The semen volume, seminal plasma protein concentration and incidence of morphologically anomalous sperm increased over time. In addition, some parameters that are associated with good-quality semen decreased, such as sperm motility, viability and DNA integrity. Moreover, we observed a positive association among motility, viability and DNA integrity for sperm with elevated 11-ketotestosterone, but there was no such association for fshb or lhb mRNA levels in the pituitary. The semen that was obtained earlier (at the beginning) or from re-stripped males exhibited better characteristics than the other samples collected. In conclusion, collecting semen from pacu at the end of breeding season should be avoided; it is preferable to strip early and then re-strip later in the season, and this approach may be used for diverse aquaculture purposes.

Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

Breeding season diet of Scarlet Ibises and Little Blue Herons in a Brazilian mangrove swamp

We studied the diet composition and overlap of Scarlet Ibises (Eudocimus ruber) and Little Blue Herons (Egretta caerulea in a mangrove swamp in southeast Brazil during the 1996-1997 breeding season, which occurs during the rainiest period. Crabs comprised 95% of all prey taken by the ibises and 80% of the prey of the herons, Nevertheless, diet overlap was small (similar to 30%) due to ibises feeding mostly on Uca spp. and Eurythium limosum crabs, which were taken from their burrows; the herons fed on the arboreal and semi-arboreal Aratus Pisonii and Metasesarma rubripes crabs. Divergent hunting strategies of ibises (tactile foragers) and herons visually-oriented predators) explains the diet segregation when preying on an ecologically diverse crab guild, but it is unclear why herons prey rarely on fiddler crabs. Scarlet Ibises bred successfully while feeding oil estuarine organisms living in low salinities in the mangroves, showing that mangroves may be adequate foraging habitats for chick-rearing ibises during periods of low salinity.

Seasonal home ranges and fidelity to breeding sites among ringed seals

Population structure and patterns of habitat use among ringed seals (Phoca hispida) are poorly known, in part because seasonal movements have not been adequately documented. We monitored the movements of 98 ringed seals in the Beaufort and Chukchi seas between 1990 and 2006 using three forms of telemetry. In the winter—spring period (when the seals were occupying shorefast ice), we used radio and ultra-sonic tags to track movements above and below the ice, respectively. We used satellite-linked transmitters in summer and fall (when the seals ranged away from their winter sites) to track at-sea movements. In the shorefast ice habitat, the home ranges of 27 adult males ranged from\1 to 13.9 km2 (median = 0.628) while the home ranges of 28 adult females ranged from \1 to 27.9 km2 (median = 0.652). The 3-dimensional volumes used by 9 seals tracked acoustically under the ice averaged 0.07 (SD = 0.04) km3 for subadults and adult males and 0.13 (SD = 0.04) km3 for adult females. Three of the radio-tracked seals and 9 tracked by satellite ranged up to 1,800 km from their winter/spring home ranges in summer but returned to the same small (1–2 km2) sites during the ice-bound months in the following year. The restricted movements of ringed seals during the ice-bound season— including the breeding season—limits their foraging activities for most of the year and may minimize gene flow within the species.

Two and a Half Cheers for the Midwestern Bourgeoisie: Role of the Virtues in Tempering Business Decisions

A recent book (The Bourgeois Virtues: Ethics for an Age of Commerce, D. N. McCloskey), raises the matter of the role of the virtues in business and economic choice, arguing that capitalism can indeed, be virtuous or at least better than the alternative(s). This argument is especially timely in light of the apparent excesses on Wall Street and in some banking/financial institutions. Excessive greed and often the lack of business ethics contributed in substantive ways to the financial crisis and near economic meltdown we have been experiencing. As McCloskey, (2006, pp. 1-2) argues (in setting the stage for the complex argument made in this 616-page book!): “The book … is directed toward you who are suspicious of the phrase ‘bourgeois virtues,’ pretty sure that it is a contradiction in terms. And the book is directed, with less optimism about changing their minds, toward you who think the phrase is worse: a lie. ‘Bourgeois virtues’ is neither. The claim here is that modern capitalism does not need to be offset to be good. Capitalism can on the contrary be virtuous. In a fallen world bourgeois life is not perfect. But it’s better than any available alternative. American capitalism needs to be inspirited, moralized, completed. Two and a half cheers for the Midwestern bourgeoisie (middle-class, small business owners…. yet)… Many a businessman is an ethical shell or worse. Even the virtues of the bourgeoisie, … do not lead straight to heaven.”

Energy Restriction During Breeding Gilt Development: An Economic Analysis

Swine production has increasingly become a lowmargin business. As costs of production have increased, producers are continuing to increase efficiency in both market pig production and gilt development. Restricting energy during gilt development reduces feeding costs and can enhance some productivity measures, but can also negatively impact other areas of production. Thus, the net economic returns from a restricted energy gilt development program are unclear. This study utilized gilt development and market pig production data for two genetic lines of hogs, LWxLR (a cross between industry Large White and Landrace) and L45X (a Nebraska line selected 23 generations for increased litter size) from Johnson and Miller and Johnson et al., to estimate the returns to finishing market hogs using conventional and restricted energy gilt development programs.

Analyzing ACRE: Results for 2009 and Decisions for 2010

In 2009, agricultural producers participating in federal farm programs had to decide between staying in the existing Direct and Counter-Cyclical Program (DCP), and the new Average Crop Revenue Election Program (ACRE). If producers chose to keep the DCP, their farm income safety net is strictly tied to crop prices, with a combination of marketing loans, counter-cyclical payments and direct payments. If producers chose the new ACRE program, they changed their farm income safety net to a combination of price and revenue. The new ACRE component is based on revenue and replaces the counter-cyclical payment. The other parts of the safety net for ACRE participants remain tied to price, albeit at lower levels (direct payments reduced 20 percent, marketing loan rates reduced 30 percent).

Breeding system can affect the offspring sex ratio in Syrian hamsters

Nulliparous female Syrian hamsters were used to investigate the effect of two different breeding systems on the fertility of the female Syrian hamster. We hypothesized that females submitted to a harem system (HS) would deliver smaller and more female-biased litters than in a monogamic system. Ten female and 10 adult male hamsters housed individually (G1) were kept in a monogamic temporary breeding system, while 10 females and five males (G2) were submitted to HS with two females and a male permanently housed together since female weaning. Females from G1 and G2 delivered, respectively, 47 and 50 litters, and produced 364 (G1) and 383 (G2) weaned pups without any difference in litter size, mean weight of weaned pups and body condition of dams. Interparturition intervals were shorter and the percentage of male pups per litter was higher in the HS possibly as a result of different endocrine conditions provided by different breeding systems. Besides providing evidence that housing conditions can influence the sex of hamster offspring, our findings suggest a mechanism for the non-random distribution of male and female pups in hamster litters.

Skeletal abnormalities in humpback whales Megaptera novaeangliae stranded in the Brazilian breeding ground

Skeletal tissues of 49 humpback whales Megaptera novaeangliae that stranded between 2002 and 2011 along the Abrolhos Bank seashore and its adjacent waters in Brazil were studied. Twelve (24.5%) animals presented pathological changes in one or more bones. Degenerative changes and developmental malformations were most frequent (10.2% each), followed by inflammatory/infectious and traumatic lesions (8.2% each). Infectious diseases led to severe lesions of the caudal vertebrae of 2 whales. In one of these individuals, the lesions involved 6 caudal vertebrae, leading to ankylosis of 3 vertebrae. Degenerative changes were observed in the vertebral columns of 3 animals, involving the joints of 13 ribs of 1 individual, and in the humerus of 1 whale. Traumatic lesions, such as osseous callus in the ribs, were observed in 4 animals. In 1 whale, the rib showed severe osteomyelitis, possibly resulting from the infection of multiple fractures. Developmental abnormalities such as spina bifida on 3 cervical vertebrae of 1 whale, fusion of spinal processes on thoracic vertebrae of 1 individual and fusion of the first 2 ribs unilaterally or bilaterally in 4 animals were found. Chronic infectious conditions found in the axial skeleton may have restrained spinal mobility and had detrimental effects on the general health of the animals, contributing to stranding and death. To our knowledge, this is the first systematic study on skeletal lesions in stranded humpback whales.