Genotypic characterization of microsatellite markers in broiler and layer selected chicken lines and their reciprocal F1s

Populações experimentais de frangos tem sido desenvolvidas pelo mundo para mapeamento de QTLs, mas a caracterização genotípica delas não é normalmente apresentada. O objetivo deste estudo foi caracterizar genotipicamente duas gerações F1 recíprocas e suas linhagens parentais com base na estimação de parâmetros genotípicos. Estas gerações F1 originaram duas populações brasileiras referências para mapear QTLs. Os parâmetros avaliados foram: conteúdo de informação polimórfica (PIC), heterozigosidades observada e esperada e número de alelos por loco nos cromossomos 1, 3 e 4. Todos os animais parentais e F1 de ambas as populações foram usados, em um total de 83 animais: 14 de uma linhagem de corte (TT) e 14 de uma linhagem de postura (CC), e 55 de suas gerações recíprocas F1. Tanto as linhagens como as populações referências foram desenvolvidas no Centro Nacional de Pesquisa de Suínos e Aves (EMBRAPA), Brasil. Os genótipos de todos os animais foram obtidos a partir de 34 marcadores microssatélites localizados nos cromossomos 1 (13), 3 (12) e 4 (9). Com base na amostragem realizada, as duas linhagens exibiram um total de 163 alelos, dos quais 31 (31,1%) e 44 (33,0%) foram oriundos exclusivamente de CC e TT, respectivamente, com freqüências alélicas que variaram de 0,03 a 0,82. A heterozigosidade observada foi maior (0,68-0,71) em ambas as gerações F1 do que em suas linhagens fundadoras devido ao desequilíbrio de ligação. Finalmente, as duas linhagens parentais possibilitaram a obtenção de gerações recíprocas F1 com valores elevados de PIC (0,50-0,52) e heterozigosidade observada, bem como com um número satisfatório de alelos por loco (4,06-4,32). Estes resultados permitirão comparar e selecionar famílias e marcadores microssatélites mais informativos em estudos de QTLs, reduzindo os custos de genotipagem.Chicken experimental populations have been developed worldwide for QTL mapping, but their genotypic characterizations are not usually discussed. The objective of this study was to characterize genotypically two F1 reciprocal generations and their parental lines based on the estimation of genotypic parameters. These F1 generations originated two Brazilian reference populations to map QTL. The evaluated parameters were polymorphic information content (PIC), observed and expected heterozygosities and number of alleles at microsatellite loci on chromosomes 1, 3 and 4. All parental and F1 chickens from both populations were used totalling of 83 chickens: 14 from a broiler (TT) and 14 from a layer line (CC) and 55 from their reciprocal F1 generations. The chicken lines and the resource populations were developed at the National Research Center for Swine and Poultry (EMBRAPA), Brazil. Genotypes from all animals were obtained from 34 loci on chromosomes 1 (13), 3 (12) and 4 (9). Based on the sampling, we found that the two lines exhibited a total of 163 different alleles, of which 31 (31.1%) and 44 (33.0%) alleles were unique in CC and TT lines, respectively, with allelic frequencies ranging from 0.03 to 0.82. The observed heterozygosity was higher (0.68-0.71) in both F1 generations than in their founder lines due to linkage disequilibrium. Finally, the two chicken lines used as founders created two F1 reciprocal generations with high levels of PIC (0.50-0.52) and observed heterozygosity, as well as satisfactory number of alleles per locus (4.06-4.32). Our results will allow to compare and select families with highly informative microsatellite markers for QTL studies, reducing genotyping costs

Caracterização genotípica de linhagens selecionadas de galinha de corte e postura e seus F1s recíprocos usando marcadores microssatélites

Chicken experimental populations have been developed worldwide for QTL mapping, but their genotypic characterizations are not usually discussed. The objective of this study was to characterize genotypically two F1 reciprocal generations and their parental lines based on the estimation of genotypic parameters. These F1 generations originated two Brazilian reference populations to map QTL. The evaluated parameters were polymorphic information content (PIC), observed and expected heterozygosities and number of alleles at microsatellite loci on chromosomes 1, 3 and 4. All parental and F1 chickens from both populations were used totalling of 83 chickens: 14 from a broiler (TT) and 14 from a layer line (CC) and 55 from their reciprocal F1 generations. The chicken lines and the resource populations were developed at the National Research Center for Swine and Poultry (EMBRAPA), Brazil. Genotypes from all animals were obtained from 34 loci on chromosomes 1 (13), 3 (12) and 4 (9). Based on the sampling, we found that the two lines exhibited a total of 163 different alleles, of which 31 (31.1%) and 44 (33.0%) alleles were unique in CC and TT lines, respectively, with allelic frequencies ranging from 0.03 to 0.82. The observed heterozygosity was higher (0.68-0.71) in both F1 generations than in their founder lines due to linkage disequilibrium. Finally, the two chicken lines used as founders created two F1 reciprocal generations with high levels of PIC (0.50-0.52) and observed heterozygosity, as well as satisfactory number of alleles per locus (4.06-4.32). Our results will allow to compare and select families with highly informative microsatellite markers for QTL studies, reducing genotyping costs.Populações experimentais de frangos tem sido desenvolvidas pelo mundo para mapeamento de QTLs, mas a caracterização genotípica delas não é normalmente apresentada. O objetivo deste estudo foi caracterizar genotipicamente duas gerações F1 recíprocas e suas linhagens parentais com base na estimação de parâmetros genotípicos. Estas gerações F1 originaram duas populações brasileiras referências para mapear QTLs. Os parâmetros avaliados foram: conteúdo de informação polimórfica (PIC), heterozigosidades observada e esperada e número de alelos por loco nos cromossomos 1, 3 e 4. Todos os animais parentais e F1 de ambas as populações foram usados, em um total de 83 animais: 14 de uma linhagem de corte (TT) e 14 de uma linhagem de postura (CC), e 55 de suas gerações recíprocas F1. Tanto as linhagens como as populações referências foram desenvolvidas no Centro Nacional de Pesquisa de Suínos e Aves (EMBRAPA), Brasil. Os genótipos de todos os animais foram obtidos a partir de 34 marcadores microssatélites localizados nos cromossomos 1 (13), 3 (12) e 4 (9). Com base na amostragem realizada, as duas linhagens exibiram um total de 163 alelos, dos quais 31 (31,1%) e 44 (33,0%) foram oriundos exclusivamente de CC e TT, respectivamente, com freqüências alélicas que variaram de 0,03 a 0,82. A heterozigosidade observada foi maior (0,68-0,71) em ambas as gerações F1 do que em suas linhagens fundadoras devido ao desequilíbrio de ligação. Finalmente, as duas linhagens parentais possibilitaram a obtenção de gerações recíprocas F1 com valores elevados de PIC (0,50-0,52) e heterozigosidade observada, bem como com um número satisfatório de alelos por loco (4,06-4,32). Estes resultados permitirão comparar e selecionar famílias e marcadores microssatélites mais informativos em estudos de QTLs, reduzindo os custos de genotipagem.EMBRAPA - PRODETA

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

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Produtividade de ratos Wistar em diferentes sistemas de acasalamento

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.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq