Comparison of selective genotyping strategies for prediction of breeding values in a population undergoing selection

Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0), and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection candidates). Lower correlations between genomic-based estimates of breeding values (GEBV) and true breeding values (TBV) were obtained when using the Bottom strategy. For Random, Extreme, and Less Related strategies, the correlation between GEBV and TBV became slightly larger as selection intensity decreased and was largest when no selection occurred. These 3 strategies were better than the Top approach. In addition, the Extreme, Random, and Less Related strategies had smaller predictive mean squared errors (PMSE) followed by the Top and Bottom methods. Overall, the Extreme genotyping strategy led to the best predictive ability of breeding values, indicating that animals with extreme yield deviations values in a reference population are the most informative when training genomic selection models.

Breeding value accuracy estimates for growth traits using random regression and multi-trait models in Nelore cattle

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

Prevalence of Toxoplasma gondii antibodies in ostriches (Struthio camelus) from commercial breeding facilities in the state of São Paulo, Brazil.

Toxoplasmosis is widespread zoonosis caused by Toxoplasma gondii,a protozoan that may infect mammals and birds. The aim of the present study was to assess the prevalence of T. gondii in ostriches (Struthio camelus) from commercial breeding facilities in the state of São Paulo, Brazil, in a way to increase the knowledge on the behavior and importance of the parasite in this animal species. A total of 195 serum samples were collected from ostriches from Sorocaba, Campinas, São Carlos, Aracatuba, São Paulo, Vale do Ribeira, Botucatu and sao Jose do Rio Preto, in the state of São Paulo. These samples were analyzed by means of the Modified Agglutination Test (MAT) in order to investigate the occurrence of Toxoplasmagondii antibodies. The test showed that 14.36% of the animals were seropositive to Toxoplasmagondii. Minimum titer was considered to be equal or greater than 1:16, and the greatest dilution observed was 1:16,384. No statistically significant differences were found between males and females. Seronegative animals occurred in only two regions (São Paulo and Sao Jose do Rio Preto). These results point out the importance of further studies on this infection in ostriches, and on management practices that may minimize the risk of toxoplasmosis transmission in these birds which would, in their turn, decrease the risk for the final consumer.

Isotopic traceability in body tissues and in different breeding periods of broilers

Rastrearam-se a inclusão de farinha de vísceras de aves (FV) em dietas de frangos por ocasião de eventual substituição de dieta contendo FV por dieta estritamente vegetal, e vice-versa, por isótopos estáveis de carbono e de nitrogênio. Foram distribuídos aleatoriamente 192 pintos de um dia de idade, em 12 tratamentos com quatro repetições de quatro aves. Os tratamentos constituíam-se de dieta de vegetais (VG) passando para dietas contendo FV, após certa idade, ou o inverso, em que as aves começaram se alimentando de dieta FV e depois passaram para dieta VG. Aos 42 dias de idade, foram coletadas amostras de músculo peitoral (Pectoralis major), quilha e tíbia, para determinação das razões isotópicas (13C/12C e 15N/14N). A técnica dos isótopos estáveis somente não foi capaz de rastrear a utilização de FV na alimentação de frangos de corte, quando esse ingrediente fez parte da dieta das aves apenas nos primeiros sete, 14 ou 21 dias de idade. Entretanto, há a possibilidade da aplicação dessa técnica em aves mais jovens, amostradas antes de eventual mudança de dieta, pois elas podem ter a assinatura isotópica da alimentação estabilizada em torno de duas semanas de idade.

Use of oocyte transfer in a commercial breeding program for mares with reproductive abnormalities

In some mares with lesions of the reproductive tract, embryo collection and survival rates are low or collection of embryos is not feasible. For these mares, oocyte transfer has been proposed as a method to induce pregnancies. In this report, a method for oocyte transfer in mares and results of oocyte transfer performed over 2 breeding seasons, using mares with long histories of subfertility and various reproductive lesions, are described.Human chorionic gonadotropin or an implant containing a gonadotropin-releasing hormone analog was used to initiate follicular and oocyte maturation. Oocytes were collected by means of transvaginal ultrasound-guided follicular aspiration. Following follicular aspiration, cumulus oocyte complexes were evaluated for cumulus expansion and signs of atresia; immature oocytes were cultured in vitro to allow maturation. The recipient's ovary and uterine tube (oviduct) were exposed through a flank laparotomy with the horse standing, and the oocyte was slowly deposited within the oviduct. Oocyte transfer was attempted in 38 mares between 9 and 30 years old during 2 successive breeding seasons. All mares had a history of reproductive failure while in breeding and embryo transfer programs. Twenty pregnancies were induced. Fourteen of the pregnant mares delivered live foals. Results suggest that oocyte transfer can be a successful method for inducing pregnancy in subfertile mares in a commercial setting..

Reproductive characteristics of stallions during the breeding and non-breeding season in a tropical region

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

Genetic monitoring of the Amazonian fish matrincha (Brycon cephalus) using RAPD markers: insights into supportive breeding and conservation programmes

The importance of genetic evaluations in aquaculture programmes has been increased significantly not only to improve effectiveness of hatchery production but also to maintain genetic diversity. In the present study, wild and captive populations of a commercially important neotropical freshwater fish, Brycon cephalus (Amazonian matrincha), were analyzed in order to evaluate the levels of genetic diversity in a breeding programme at a Brazilian research institute of tropical fish. Random Amplified Polymorphic DNA fingerprinting was used to access the genetic variability of a wild stock from the Amazon River and of three captive stocks that correspond to consecutive generations from the fishery culture. Although farmed stocks showed considerably lower genetic variation than the wild population, a significantly higher level of polymorphism was detected in the third hatchery generation. The results seem to reflect a common breeding practice on several hatchery fish programmes that use a small number of parents as broodstocks, obtaining reproductive success with few non-identified mating couples. The obtained data were useful for discussing suitable strategies for the genetic management and biodiversity conservation of this species.

Population structure and breeding season of the South Atlantic hermit crab, Loxopagurus loxochelis (Anomura, Diogenidae) from the Ubatuba region, Brazil

A population of Loxopagurus loxochelis was studied in terms of seasonal abundance, size frequency distribution, sex ratio, and reproductive period (percentage of ovigerous females). Specimens were collected monthly over a period of two years (from September 1995 to August 1997) in the non-consolidated areas of the Ubatuba, Mar Virado, and Ubatumirim bays (northern coast of São Paulo State, Brazil) with a double-rig trawl net. A total of 1,084 individuals were analysed. Animal size (minimum, maximum, and mean +/- SD shield length) was 2.8, 9.1, and 6.88 +/- 1.13 mm for 625 males; 2.8, 8.2, and 5.78 +/- 0.98 mm for 236 non-ovigerous females; and 4.6, 8.0, and 6.24 +/- 0.68 mm for 223 ovigerous females, respectively. Sexual dimorphism was recorded by the presence of males in the largest size classes. The sex ratio was 1.4 : 1 in favour of males. The highest incidence of ovigerous females occurred during winter and spring (June to October), with a low percentage in summer and fall (November to May), indicating continuity in the reproductive cycle. This strategy of reproduction is related to temperature. The occurrence of L. loxochelis in the Ubatuba region represents the final point of northern distribution of this species as a function of water mass influence, and could be its real limit on the Atlantic coast of South America.

Breeding season of the hermit crab petrochirus diogenes (anomura : diogenidae) in the north coast of São Paulo state, Brazil

Petrochirus diogenes, one of the largest hermit crabs in the western Atlantic, was studied in the north coast of the State of São Paulo, Brazil, to determine its breeding season through the analysis of gonad development at a macroscopic level. The analysis of 999 crabs collected from 1995 to 1999, based on four categories of gonad development, showed that males present gonads in the advanced stage during all seasons, and although females present developed ovaries all year as well, the peak incidence is in the summer. The peak of recruitment occurs in the winter.

Population structure and breeding period of Pachycheles monilifer (Dana) (Anomura, Porcellanidae) inhabiting sabellariid sand reefs from the littoral coast of São Paulo State, Brazil

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

Breeding of the Spot-billed Toucanet (Selenidera maculirostris) in the Wild

The Spot-billed Toucanet (Selenidera maculirostris) is an endemic member of the Ramphastidae occurring in the Atlantic Forest in Brazil. There is anecdotal literature about this species breeding in the wild, but no data are available about parental behavior and nest morphometry. We describe observations of parental behavior of the Spot-billed Toucanet including measurements of one nest in Ilha do Cardoso State Park, São Paulo, Brazil. The nest was inside a hollow of a Lauraceae tree with the entrance hidden by leaves of Aechmea sp. (Bromeliaceae). The Spot-billed Toucanet, based on our observations and review of the literature, nests in tree cavities between 2 and 7 to above ground and both parents provision the nestlings. Received 13 July 2008. Accepted 7 June 2009.

Genetic structure in a tropical lek-breeding bird, the blue manakin (Chiroxiphia caudata) in the Brazilian Atlantic Forest

Determining the genetic structure of tropical bird populations is important for assessing potential genetic effects of future habitat fragmentation and for testing hypotheses about evolutionary mechanisms promoting diversification. Here we used 10 microsatellite DNA loci to describe levels of genetic differentiation for five populations of the lek-mating blue manakin (Chiroxiphia caudata), sampled along a 414-km transect within the largest remaining continuous tract of the highly endangered Atlantic Forest habitat in southeast Brazil. We found small but significant levels of differentiation between most populations. F-ST values varied from 0.0 to 0.023 (overall F-ST = 0.012) that conformed to a strong isolation by distance relationship, suggesting that observed levels of differentiation are a result of migration-drift equilibrium. N(e)m values estimated using a coalescent-based method were small (<= 2 migrants per generation) and close to the minimum level required to maintain genetic similarity between populations. An implication of these results is that if future habitat fragmentation reduces dispersal between populations to even a small extent, then individual populations may undergo a loss of genetic diversity due to an increase in the relative importance of drift, since inbreeding effective population sizes are relatively small (N-e similar to 1000). Our findings also demonstrate that population structuring can occur in a tropical bird in continuous habitat in the absence of geographical barriers possibly due to behavioural features of the species.