Fine mapping and replication of QTL in outbred chicken advanced intercross lines

Background: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature. Methods: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight. Results: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL. Conclusions: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.

Quantitative Analysis of Diepoxybutane Damage within the Chicken β-globin Domain

In industrial polymer and synthetic rubber production facilities, workers are exposed to 1,3-butadiene. This compound is converted in vivo to 1,2,3,4-diepoxybutane (DEB) and has been linked to increased incidences of cancer in these individuals. Carcinogenesis has been attributed to formation of DEB induced DNA interstrand cross-links. Previous studies have demonstrated that DEB cross-links deoxyguanosine residues within 5'-GNC sequences in synthetic DNA, in restriction fragments, and in defined sequence nucleosomes. The current study utilized the polymerase chain reaction (PCR) to examine DEB damage frequencies within nuclear genes, found within "open" regions of chromatin, as compared to regions of unexpressed sequence that reside in tightly packed, "closed" chromatin, to more closely model DEB reactivity in vivo. These initial studies have been performed in chicken liver homogenates. Preliminarily, we have found a dose-dependent DEB lesion-forming response within "open" chromatin. DEB appears to have little-to-no effect upon regions of "closed" chromatin.

Mapping of Diepoxybutane Damage in the Cytochrome b Domain of Mitochondrial DNA and the β-globin Domain of Nuclear Chicken DNA Using Quantitative PCR

Diepoxybutane (DEB), a known industrial carcinogen, reacts with DNA primarily at the N7 position of deoxyguanosine residues and creates interstrand cross-links at the sequence 5'-GNC. Since N7-N7 cross-links cause DNA to fragment upon heating, quantative polymerase chain reaction (QPCR) is being used in this experiment to measure the amount of DEB damage (lesion frequency) with three different targets-mitochondrial (unpackaged), open chromatin region, and closed chromatin region. Initial measurements of DEB damage within these three targets were not consistent because the template DNA was not the limiting reagent in the PCR. Follow-up PCR trials using a limiting amount of DNA are still in progress although initial experimentation looks promising. Sequencing of these three targets to confirm the primer targets has only been successfully performed for the closed chromatin target and does not match the sequence from NIH used to design that primer pair. Further sequencing trials need to be conducted on all three targets to assure that a mitochondrial, open chromatin, and closed chromatin region are actually being amplified in this experimental series.

Effect of poultry viscera meal inclusion in broiler diets in different rearing periods on performance, carcass and parts yields

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Digestibility and performance of pacu (Piaractus mesopotamicus) juveniles - fed diets containing different protein, lipid and carbohydrate levels

Due to lack of information on the use of non-protein energy sources in diets for pacu (Piaractus mesopotamicus), a 2 x 2 x 3 factorial experiment was conducted to evaluate the performance and digestibility of 12 diets containing approximately two crude protein (CP; 220 and 250 g kg(-1)), two lipid (40 and 80 g kg(-1)) and three carbohydrate levels (410, 460 and 500 g kg(-1)). The pacu juveniles-fed diets containing 220 g kg(-1) CP did not respond (P > 0.05) to increased dietary lipid and carbohydrate levels, but the fish-fed diets containing 250 g kg(-1) CP showed a better feed conversion ratio. There were interactions in weight gain (WG), specific growth rate (SGR), crude protein intake (CPI) and feed conversion rate (FCR) dependent on dietary carbohydrate and lipid levels, showing positive effects of increasing carbohydrate levels only for fish-fed diets containing 80 g kg(-1) lipid level. However, when the diets contained 40 g kg(-1) lipid, the best energy productive value (EPV) results were obtained at 460 g kg(-1) carbohydrate. A higher usage of lipids (80 g kg(-1)) reduced CPI and was detrimental to protein [apparent digestibility coefficient (ADC)(CP)] and energy (ADC(GE)), but did not affect growth. The ADC(GE) improved proportionally as dietary carbohydrate levels increased (P < 0.05), increasing the concentration of digestible energy. In addition, the WG, CPI, ADC(GE) results showed best use of the energy from carbohydrates when dietary protein level was 250 g kg(-1) CP. The utilization of 250 g kg(-1) CP in feeds for juvenile pacu for optimal growth is suggested. Therefore, the optimum dietary lipid and carbohydrate levels depend on their combinations. It can be stated that pacu uses carbohydrates as effectively as lipids in the maximization of protein usage, as long as it is not lower than 250 g kg(-1) CP or approximately 230 g kg(-1) digestible protein.

Growth performance and energetic metabolism of pacu, Piaractus mesopotamicus (Holmberg, 1887), fed diets supplemented with ammonium metavanadate

Vanadium compounds mimic most of the metabolic effects of insulin, suggesting that it might be useful to improve utilization of dietary carbohydrate. This work evaluated the effect of dietary ammonium metavanadate (H(4)NO(3)V) on the growth performance and energy metabolism of pacu, an omnivorous South America characin. Two hundred and eighty-eight fish were distributed into four blocks according to the body weight (21.8 +/- 1.7, 28.5 +/- 2.0, 28.4 +/- 1.9, 35.7 +/- 1.9 g), stocked in 24 plastic tanks and fed twice daily with isonitrogenous and isoenergetic diets containing six levels of H(4)NO(3)V (0, 10, 50, 100, 300 and 1000 mg kg(-1)) for 60 days. Increasing levels of dietary ammonium metavanadate did not improve growth (P > 0.05), and the highest level of inclusion (1000 mg kg(-1)) reduced performance (P < 0.05). Blood glucose levels decreased (P < 0.05) in fish fed 300 and 1000 mg kg(-1) H(4)NO(3)V, but no differences were observed in other blood metabolites. A slight increase in muscle lipid content was observed in fish fed a diet containing 300 mg kg(-1) H(4)NO(3)V. Based on the results of this study, there is no benefit in supplementing pacu diets with metavanadate.

Challenge of pacu (Piaractus mesopotamicus) fed diets supplemented with vitamins C and E by Aeromonas hydrophila under different temperature

Pacus Piaractus mesopotamicus alimentados com dietas contendo três níveis de vitaminas C e E (zero, 250 e 500mg/kg de ração) foram desafiados, em diferentes temperaturas, com Aeromonas hydrophila. Os peixes foram mantidos em caixas plásticas de 300L e, com o objetivo de reduzir as reservas vitamínicas, durante os primeiros 60 dias, foram alimentados com dietas isentas das vitaminas C e E. Após esse período, os peixes foram estocados na densidade inicial de 14 peixes/caixa e as dietas-teste foram oferecidas durante 60 dias. Ao final do experimento, todos os peixes foram infectados com 6×10(6) UFC de A. hydrophila/peixe, injetada intraperitonealmente. Não houve interação nível de vitamina C vs. nível de vitamina E quanto à mortalidade. A suplementação com as vitaminas C e E não reduziu a taxa de mortalidade dos peixes desafiados com A. hydrophila. Independentemente da suplementação vitamínica, após o desafio, os peixes menores apresentaram maior taxa de mortalidade que os maiores e o grupo mantido em ambiente com temperatura mais alta apresentou maior taxa de mortalidade após o desafio.

Growth, fat content and fatty acid profile of South American catfish, surubim (Pseudoplatystoma fasciatum) juveniles fed live, commercial and formulated diets

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Fuzzy modeling to predict chicken egg hatchability in commercial hatchery

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

Anaerobic biodigestion of pigs feces in the initial, growing and finishing stages fed with diets formulated with corn or sorghum

Objetivou-se avaliar a produção e a qualidade do biogás e do biofertilizante obtidos em biodigestores abastecidos com dejetos de suínos, nas fases inicial, crescimento e terminação, alimentados com dietas formuladas à base de milho ou sorgo. Foram utilizados 20 biodigestores de bancada, com tempo de retenção hidráulica de 30 dias, e cargas diárias que continham 4,0 a 6,0% de sólidos totais (ST) e 3,6 a 5,2% de sólidos voláteis (SV). Nos efluentes dos biodigestores, foram verificados teores médios de ST variando de 1,6 a 2,0% e de SV entre 1,2 e 1,6%. As reduções médias de ST foram de 57,7 a 64,7% e de SV de 61,7 a 69,0%, sendo que houve diferença somente na fase de terminação, na qual as maiores reduções médias foram para biodigestores abastecidos com dejetos de animais alimentados com dietas à base de milho. Nos biodigestores abastecidos com dejetos de animais em fase inicial e de crescimento, alimentados com dietas formuladas à base de milho, foram verificadas maiores produções médias de biogás e os maiores potenciais médios de produção de biogás. Os potenciais médios obtidos foram 0,033; 0,181; 0,685; 0,788 e 1,132 m³ por kg de afluente, estrume, ST adicionados, SV adicionados e SV reduzidos, respectivamente. Não foram verificadas diferenças quanto ao teor médio de metano no biogás entre dietas e fases. As concentrações médias dos nutrientes N, P, K, Ca, Mg, Na, Fe, Mn, Zn e Cu no afluente e efluente dos biodigestores variaram entre as dietas e fases.

Ingredient classification according to the digestible amino acid profile: an exploratory analysis

This study aimed: 1) to classify ingredients according to the digestible amino acid (AA) profile; 2) to determine ingredients with AA profile closer to the ideal for broiler chickens; and 3) to compare digestible AA profiles from simulated diets with the ideal protein profile. The digestible AA levels of 30 ingredients were compiled from the literature and presented as percentages of lysine according to the ideal protein concept. Cluster and principal component analyses (exploratory analyses) were used to compose and describe groups of ingredients according to AA profiles. Four ingredient groups were identified by cluster analysis, and the classification of the ingredients within each of these groups was obtained from a principal component analysis, showing 11 classes of ingredients with similar digestible AA profiles. The ingredients with AA profiles closer to the ideal protein were meat and bone meal 45, fish meal 60 and wheat germ meal, all of them constituting Class 1; the ingredients from the other classes gradually diverged from the ideal protein. Soybean meal, which is the main protein source for poultry, showed good AA balance since it was included in Class 3. on the contrary, corn, which is the main energy source in poultry diets, was classified in Class 8. Dietary AA profiles were improved when corn and/or soybean meal were partially or totally replaced in the simulations by ingredients with better AA balance.

Effect of crude protein levels and organic selenium supplementation in the diets fed during the breeding season on reproductive parameters of red-winged tinamous (Rhynchotus rufescens)

There is little information on the nutrition of red-winged tinamous (Rhynchotus rufescens) reared in captivity, and their nutritional requirements still need to be determined. This study aimed at determining dietary crude protein requirements and testing four organic selenium supplementation levels in the diet of red-winged tinamous during the breeding season. Birds were housed in a conventional broiler house divided in 16 boxes with one male and three females each. Iso-energy (2800kcal ME/kg) pelleted feeds, based on corn and soybean meal, were supplied in tube feeders. In the first experiment, treatments consisted of four different diets containing different crude protein (CP) contents (15, 18, 21, or 24%) and in the second experiment, the four diets contained equal protein level (22.5%) and four different organic selenium levels (0, 0.2, 0.4, or 0.8ppm). Data were analyzed by the least square method. The best egg weight and eggshell thickness were obtained with 22.5% dietary CP. Organic selenium did not influence the studied reproductive traits of red-winged tinamous (Rhynchotus rufescens) males or females.

Heritabilities and genetic correlations for reproductive traits in an F2 reciprocal cross chicken population

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

Comparison of micronized whole soybeans to common protein sources in dry dog and cat diets

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

Amylase utilization for the extrusion of dog diets

Effects of amylase addition on extruder parameters, cost of extrusion, kibble quality and digestibility of dog food were measured in two separate experiments. In experiment 1, 120 kilo-novo-alpha-amilase-unit (KNU)/kg of heat stable alpha-amylase produced by Bacillus licheniformis was added in liquid form during a preconditioning period. In experiment 23684 KNU/kg of heat stable alpha-amylase produced by Aspergillus oryzae was mixed with the ingredients before extrusion. The diets were processed in a single screw extruder and submitted to digestibility and on experiment 1 also to palatability tests. Digestibility was tested using 12 dogs, six per diet. Data were submitted to analysis of variance followed by F-test. Amylase addition altered extrusion parameters in both experiments (P<0.05), with higher output (kg of dry matter [DM]/h: 28% and 43% higher in experiments 1 and 2) and less electric energy consumption (kW to produce 100 kg DM: 22% and 29% lower in experiments 1 and 2). Kibble appearance and quality [density (g/L), cutting force (g), and starch gelatinization degree (%)] did not change with enzyme treatment (P>0.05). Likewise, enzyme addition did not change nutrient digestibility, fecal dry matter or food palatability (P<0.05). Taken together our results suggest that amylase promoted the breakdown of amylose chains, thereby reducing the dough viscosity and resistance inside the extruder which allowed for higher product flow and less electricity energy consumption without altering food quality. (C) 2012 Elsevier B.V. All rights reserved.