History of registered Gyr breed in Brazilian Northeast: population structure and genetic improvement of growth traits

This paper provides an evaluation of the population structure, phenotype and genetic trends of registered Gyr herd cattle in northeast Brazil. The study provides important baseline information for the management, conservation and potential population expansion of this economically and culturally important cattle breed. Pedigree data were analyzed for individuals born between 1964 and 2006. Body weight values were adjusted to 205 and 365 days of age for animals born between 1978 and 2006. Phenotypic change of zebu Gyr in northeast Brazil is solely due to environmental improvement. However, there is potential for artificial selection for weight gain in young cattle. Effective population size decreased during the 1990s and the average inbreeding coefficient increased during the studied period. An increase of the effective population size of Gyr in northeast Brazil is strongly recommended, along with an increase in the management of the mating process to prevent inbreeding and to maintain the genetic variability of the breed.Com o intuito de fornecer subsídios para programas de conservação, seleção e expansão da raça Gir no Nordeste do Brasil, objetivou-se avaliar o histórico do rebanho Gir registrado no nordeste brasileiro, com base na sua estrutura populacional e no progresso genético e fenotípico de características de desenvolvimento ponderal. Foram utilizadas informações de pedigree de animais nascidos no período de 1964 a 2006 e dados dos pesos ajustados aos 205 e 365 dias de idade de bovinos nascidos de 1978 a 2006. O progresso genético para a raça no Nordeste foi ocasionado exclusivamente pelo melhoramento ambiental. O tamanho efetivo da população reduziu a partir da década de 90, e o coeficiente de endogamia médio aumentou durante o período estudado. É imprescindível que o tamanho efetivo da raça Gir do nordeste seja ampliado e que haja maior controle de acasalamentos entre indivíduos aparentados, para prevenção da endogamia e conservação da variabilidade genética e viabilidade da raça

Endogamy and genetic variability in selective mating using distribution of extremes

The objective of this study was to evaluate selective mating using distribution of extremes, among other mating strategies, on its ability to decrease the endogamy and the loss of genetic variability. The genetic simulation system (Genesys) was used to simulate two genomes (each one with a single characteristic whose distinction was the value of heritability) and the base and original populations. Each initial population was submitted to assisted selection by markers for ten consecutive generations. For evaluation of strategies, the estimated parameters were phenotypic value, endogamy and additive genetic variance, in different family sizes, for both characteristics. In all scenarios combining heritability and family sizes, the selective mating was superior to the others, in the ability to decrease endogamy and maintain higher magnitudes of genetic variability. Consequently, superior phenotypic increments were obtained, pointing to a major detection of quantitative trait loci in the assisted selection by markers due to gradual decrease of the additive genetic variance over the generations

Processed pseudogenes acquired somatically during cancer development

Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5′ truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context

Population structure of Brazilian Gyr dairy cattle

The objective of the present study was to evaluate the genetic structure of Gyr cattle selected for milk production. Files of pedigree and production were composed of 27,610 animals. The ENDOG program was used for the calculation of individual inbreeding coefficient (F) and coefficient of average relatedness (AR), effective number of animals(Ne), effective number of founders (f e) and ancestors (f a), and generation interval (GI). Individual inbreeding coefficients and average relatedness in the population were 2.82% and 2.10%, respectively. It was observed a reduction in the effective number of animals, especially after publication of the results of the first progeny test. The estimated effective number of founders was 146 and 75 for the ancestrals. Out of those, only 28 ancestors accounted for the origin of 50% of the population genes. The average generation interval was 8.41 years and it was longer for males than for females. For maintaining genetic variability in future generations, it should be invested mating strategies that reduce inbreeding and which do not use massively only some high breeding value sires.O objetivo neste trabalho foi avaliar a estrutura genética da raça Gir selecionada para produção de leite. Os arquivos de pedigree e de produção eram compostos de 27.610 animais. Utilizou-se o programa ENDOG para cálculo dos coeficientes individuais de endogamia (F) e coeficiente de relação médio (AR), número efetivo de animais (Ne), de fundadores (fe) e de ancestrais (fa) e do intervalo de gerações (GI). Os coeficientes individuais de endogamia e de relação médios da população foram 2,82 e 2,10%, respectivamente. Foi observada redução do número efetivo de animais, especialmente após a publicação dos resultados do primeiro teste de progênie. O número efetivo de fundadores estimado foi de 146 e o de ancestrais, 75. Desses, apenas 28 ancestrais foram responsáveis pela origem de 50% dos genes da população. O intervalo médio de gerações foi 8,41 anos e foi maior para machos que para fêmeas. Para manutenção da variabilidade genética em futuras gerações, deve-se investir em estratégias de acasalamento que reduzam a endogamia e que não façam uso maciço de apenas alguns reprodutores de alto valor genético