Estudo do desequilíbrio de ligação e estimativa do tamanho efetivo em uma população da raça gir selecionada para crescimento pós-desmama
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Data
2017-02-24
Autores
Toro Ospina, Alejandra Maria [UNESP]
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Universidade Estadual Paulista (Unesp)
Resumo
O objetivo deste estudo foi estimar o desequilíbrio de ligação (r2) nas distâncias de 25-50kb, 50-100kb, 100-500kb, 0,5-1Mb e o tamanho efetivo (Ne) nas gerações 0, 5, 10, 15, 20 em população da raça Gir selecionada para crescimento pós-desmama. Os animais utilizados no presente estudo foram provenientes do rebanho fechado do Instituto de Zootecnia, Sertãozinho, SP. Foram obtidos os genótipos de 155 animais com o painel BovineDL 33kb e 18 com painel HD imputado onde realizou-se controle de qualidade (CQ) para alelo de menor frequência (MAF) < 0,02 e call rate < 0,1. Depois do CQ permaneceram 27.236 SNPs e 155 animais do painel de 33 kb e 732.962 SNPs e 173 animais do painel HD Imputado. As análises de r2 foram realizadas pelo programa Plink e programa estatístico R Studio e o Ne por meio do DL. Os resultados das distâncias 25-50kb, 50-100kb, 100-500kb e 0,5-1Mb do r2 para o painel 33kb foram iguais a 0,29, 0,25, 0,16 e 0,032 respectivamente, e 0,35, 0,29, 0,18, 0,032 para o painel HD imputado demostrando que o DL permaneceu nas distâncias menores a 100kb, decaindo com o aumento das distâncias. Estes resultados foram maiores aos descritos na literatura para animais zebuínos, sugerindo como causa os segmentos longos de haplótipos que compartilham os animais aparentados. O Ne foi igual a 9, 17, 24, 30 e 30 animais nas gerações 0, 5, 10, 15, 20, observa-se que o Ne é maior na geração 20, com 30 animais, e decai drasticamente a partir da 5 geração com 17 animais, e sendo de 9 animais a última geração, um tamanho pequeno para uma população. Os valores encontrados neste estudo mostram alto DL e baixo Ne, provavelmente pelo sistema de seleção e a estrutura da população da raça Gir avaliada, que apresenta alto nível de endogamia, perda da variabilidade genética, uso intensivo de pequeno número de reprodutores, conduzindo a diminuição da deriva genética da população, ocasionando dificuldades na seleção dos animais.
The aim of this study was to estimate the linkage disequilibrium (r2) at distances of 25-50kb, 50-100kb, 100-500kb, 0,5-1Mb and the effective population size (Ne) in generations 0, 5, 10, 15, 20 in population of the selected Gir for yearling growth. The animals used in this study were from the closed herd Animal Science Institute, Sertãozinho, SP. the genotypes of 155 animals were obtained with BovineDL 33kb and 18 animals of panel HD, where quality control was held (QC) for minor allele frequency (MAF) <0.02 and call rate <0.1. After QC remained 27,236 SNPs and 155 animals to panel 33 kb, 732.962 SNPs and 173 the panel HD imputation. The r2 analyzes were performed by Plink program and R Studio statistical program and Ne through the DL. The results of r2 for distances 25-50kb, 50-100kb, 100-500kb and 0,5-1Mb were equal to 0.29, 0.25, 0.16 and 0.032, respectively, showing that the DL remained in smaller distances 100kb, decreasing with increasing distances. These results were higher than those reported in the literature for Zebu animals, suggesting a cause to long haplotype segments that share the related animals. Ne is equal to 9, 17, 24, 30 and 30 in the generations 0, 5, 10, 15, 20, it is observed that Ne is higher in generation 20 with 30 animals and decays sharply from 5 Generation 17 animals, and with 9 animals the latest generation, small size for a population. The values found in this study to DL and Ne, explain the selection system and the structure of the population of Gir evaluated, which has a high level of inbreeding, loss of genetic variability, intensive small number of players, leading to decreased drift population genetics, causing difficulties in the selection of the next generations.
The aim of this study was to estimate the linkage disequilibrium (r2) at distances of 25-50kb, 50-100kb, 100-500kb, 0,5-1Mb and the effective population size (Ne) in generations 0, 5, 10, 15, 20 in population of the selected Gir for yearling growth. The animals used in this study were from the closed herd Animal Science Institute, Sertãozinho, SP. the genotypes of 155 animals were obtained with BovineDL 33kb and 18 animals of panel HD, where quality control was held (QC) for minor allele frequency (MAF) <0.02 and call rate <0.1. After QC remained 27,236 SNPs and 155 animals to panel 33 kb, 732.962 SNPs and 173 the panel HD imputation. The r2 analyzes were performed by Plink program and R Studio statistical program and Ne through the DL. The results of r2 for distances 25-50kb, 50-100kb, 100-500kb and 0,5-1Mb were equal to 0.29, 0.25, 0.16 and 0.032, respectively, showing that the DL remained in smaller distances 100kb, decreasing with increasing distances. These results were higher than those reported in the literature for Zebu animals, suggesting a cause to long haplotype segments that share the related animals. Ne is equal to 9, 17, 24, 30 and 30 in the generations 0, 5, 10, 15, 20, it is observed that Ne is higher in generation 20 with 30 animals and decays sharply from 5 Generation 17 animals, and with 9 animals the latest generation, small size for a population. The values found in this study to DL and Ne, explain the selection system and the structure of the population of Gir evaluated, which has a high level of inbreeding, loss of genetic variability, intensive small number of players, leading to decreased drift population genetics, causing difficulties in the selection of the next generations.
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Palavras-chave
Seleção genômica, Haplótipos, Deriva genética, Endogamia, Genomic selection, Haplotypes, Genetic drift, Inbreeding