Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken.

Excessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat production and is a health concern for consumers. We genotyped 497 birds from a Brazilian F2 Chicken Resource Population, using a high-density SNP array (600 K), to estimate the genomic heritability of fat deposition related traits and to identify genomic regions and positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks and SNP data from a previous whole genome sequencing study in the founders of this chicken F2 population were used to refine the list of PCGs and to identify potential causative SNPs. We obtained high genomic heritabilities (0.43-0.56) and identified 22 unique QTLs for abdominal fat and carcass fat content traits. These QTLs harbored 26 PCGs involved in biological processes such as fat cell differentiation, insulin and triglyceride levels, and lipid biosynthetic process. Three of these 26 PCGs were located within haplotype blocks there were associated with fat traits, five overlapped with selection signature regions, and 12 contained predicted deleterious variants. The identified QTLs, PCGs and potentially causative SNPs provide new insights into the genetic control of fat deposition and can lead to improved accuracy of selection to reduce excessive fat deposition in chickens.

A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens.

BACKGROUND: Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) that might regulate fat deposition and be useful for selection against excess fat content in chicken's carcass. This study aimed to estimate genomic heritability coefficients and to identify QTLs and PCGs for abdominal fat (ABF) and skin (SKIN) traits in a broiler chicken population, originated from the White Plymouth Rock and White Cornish breeds. RESULTS: ABF and SKIN are moderately heritable traits in our broiler population with estimates ranging from 0.23 to 0.33. Using a high density SNP panel (355,027 informative SNPs), we detected nine unique QTLs that were associated with these fat traits. Among these, four QTL were novel, while five have been previously reported in the literature. Thirteen PCGs were identified that might regulate fat deposition in these QTL regions: JDP2, PLCG1, HNF4A, FITM2, ADIPOR1, PTPN11, MVK, APOA1, APOA4, APOA5, ENSGALG00000000477, ENSGALG00000000483, and ENSGALG00000005043. We used sequence information from founder animals to detect 4843 SNPs in the 13 PCGs. Among those, two were classified as potentially deleterious and two as high impact SNPs. CONCLUSIONS: This study generated novel results that can contribute to a better understanding of fat deposition in chickens. The use of high density array of SNPs increases genome coverage and improves QTL resolution than would have been achieved with low density. The identified PCGs were involved in many biological processes that regulate lipid storage. The SNPs identified in the PCGs, especially those predicted as potentially deleterious and high impact, may affect fat deposition. Validation should be undertaken before using these SNPs for selection against carcass fat accumulation and to improve feed efficiency in broiler chicken production.

Produtividade de ratos Wistar em diferentes sistemas de acasalamento / Productivity of Wistar rats in different mating systems

O objetivo foi avaliar a produtividade e uniformidade da produção de ratos Wistar (Rattus norvegicus) em três sistemas de acasalamento: monogâmico permanente, com um casal mantido permanentemente em cada gaiola; poligâmico permanente, com duas matrizes e um macho, mantidos permanentemente em cada gaiola; e poligâmico temporário, em que o macho foi mantido na gaiola com duas matrizes até a certificação de cada cópula e, em seguida, foi retirado, retornando após o desmame das ninhadas. Para isso, 69 fêmeas de 90 dias de idade (matrizes) foram aleatoriamente distribuídas nos três grupos. As avaliações compreenderam cinco ciclos reprodutivos por matriz. Foram obtidas ninhadas mais pesadas a desmama no sistema poligâmico temporário. Além disso, não houve mortalidade de matrizes neste sistema, o que é um indicador importante de bem estar animal. No sistema monogâmico permanente, o intervalo de tempo necessário para produzir um filhote desmamado por matriz foi menor que nos sistemas poligâmicos. Deve-se considerar, no entanto, que este sistema requer o dobro do número de gaiolas e de machos reprodutores que os poligâmicos. Portanto, o sistema poligâmico temporário pode ser recomendado nas colônias de expansão e produção de ratos Wistar, com a ressalva de que necessita de mão de obra qualificada para identificação de cópula nas matrizes e manejo de rotação dos machos.

The objective was to evaluate the productivity and production uniformity of Wistar female rats (Rattus norvegicus) submitted to three mating systems: permanent monogamous, with a couple permanently maintained in each cage, permanent polygamous, with two females and one male permanently maintained in each cage, and temporary polygamous in which a male was maintained in a cage with two females until each mating was verified and was removed afterwards, returning after both litters were weaned. For that, 69 90-days-old females were randomly assigned to three groups. The evaluations comprised five reproduction cycles per dam. Litters that were heavier at weaning were obtained in the temporary polygamous systems. In addition, dam mortality was null in this system, which is an important animal welfare indicator. In the permanent monogamous system, the interval of time required to produce one weaned pup per dam was shorter than in the polygamous systems. One should consider, however that this system requires twice as many cages and sires than the polygamous systems. Therefore, the temporary polygamous mating system may be recommended for the expansion and production Wistar rats colonies, provided that qualified personnel is available to identify copulation in breeding females and to perform male rotation.

Temperatura e enriquecimento ambiental sobre o bem-estar de coelhos em crescimento / Temperature and environmental enrichment on the welfare of growing rabbits

O efeito da temperatura e o efeito do enriquecimento do piso de gaiola sobre o bem-estar de coelhos em crescimento foram avaliados. Quarenta e oito coelhos do grupo genético Botucatu, desmamados aos 35 dias de idade, foram alojados em Câmara Climática, quatro por gaiola (1,00 x 0,60 x 0,40m), em 12 gaiolas que tinham (ou não) metade do piso coberto com cama de palha. As gaiolas foram instaladas metade em sala com temperatura ambiente e metade em sala resfriada. Os animais tiveram livre acesso à ração balanceada e à água nos dois tipos de piso. Para se avaliar o bem-estar, foram realizadas cinco observações de 24 horas cada, uma por semana, sendo registradas as freqüências dos comportamentos: lúdico, estereotipado, exploratório, cuidados corporais e interação e comparadas entre gaiolas enriquecidas ou não nas duas salas. A média de temperatura e a média de umidade relativa do ar foram: 23,6°C e 78,7 por cento na sala natural e 20,6°C e 71,0 por cento na sala resfriada. O comportamento lúdico foi mais freqüente nas gaiolas enriquecidas (7,6 vs 4,3 por cento sala natural e 7,8 vs 3,8 por cento sala resfriada, P<0,01) e as estereotipias foram mais freqüentes nas gaiolas sem enriquecimento (4,4 vs. 2,7 por cento sala natural e 2,1 vs 1,1 por cento sala resfriada, P>0,01). Coelhos mantidos em temperatura natural preferiram a grade à cama de palha (77,9 vs. 22,1 por cento, P>0,01), enquanto na sala resfriada eles não mostraram preferência em relação ao piso (45,9 vs 54,1 por cento, P=0,41). Em sala resfriada, o enriquecimento com palha favoreceu o bem-estar animal.

The effects of temperature and cage floor enrichment on the welfare of growing rabbits were evaluated. Forty-eight rabbits from the Botucatu genetic group, weaned at 35 days of age were housed in an Environmental Chamber, four per cage (1.00 x 0.60 x 0.40m), in 12 cages that had (or not) half of the floor covered with litter straw. The cages were housed half in a room temperature chamber and half in a refrigerated chamber. Animals had free access to a balanced feed and water in the two types of floor. In order to evaluate welfare, five 24-hour observations were carried out, one per week, to register the frequencies of the following behaviors: ludic, stereotypic, exploratory, self-grooming and interactions, and to compare them between enriched and non-enriched cages from the two chambers. The average temperatures and relative humidities were 23.6°C and 78.7 percent in the room temperature chamber and 20.6°C and 71.0 percent in the refrigerated chamber. The ludic behavior was more frequent in the enriched cages (7.6 vs. 4.3 percent Room Temperature Chamber and 7.8 vs. 3.8 percent Refrigerated Chamber, P<0.01) and the stereotypies in the non-enriched cages (4.4 vs. 2.7 percent Room Temperature Chamber and 2.1 vs 1.1 percent Refrigerated Chamber, P<0.01). Rabbits kept at room temperature preferred the wire net floor over the litter straw (77.9 vs. 22.1 percent, P<0.01), whereas in the refrigerated chamber they did not show preference regarding floor types (45.9 vs. 54.1 percent, P=0.41). In the refrigerated chamber, cage floor enrichment favored animal welfare.