Copy number variations and single-nucleotide polymorphisms associated with beef fatty acid profile in nellore cattle
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2017-05-05
Autores
Lemos, Marcos Vinícius Antunes de [UNESP]
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Universidade Estadual Paulista (Unesp)
Resumo
Objetivou-se identificar regiões no genôma de bovinos da raça Nelore que apresentam variações no número de cópias (CNV) e, associar estes CNV com o perfil de ácidos graxos da carne. Além disso, objetivou-se realizar associação genica ampla utilizando os método de single step (GWASss) a fim de detectar regiões genômicas associadas aos ácidos graxos dos grupos saturados, mono e poliinsaturados, assim como os omegas 3, 6 e sua relação. O estudo de caracterização e distribuição dos CNVs ao longo do genoma de bovinos Nelore, foi realizado através do software PennCNV utizando dados genotípicos de 3.794 aniamais, resultando em 399.361 CNVs identificados. Após controle de qualidade, 2.902 foram mantidos nas analises, resultando em 195.873 CNVs, com tamanho medio de 54,744 pb, maximo de 8.7 Mb e minimo 3 kb. As regiões de CNV foram geradas pela sobreposição dos CNVs através do software CNVRuler. Os cromossomos que mostraram maior incidencia de CNVR foram BTA19 (24,26%), BTA23 (18,68%) e BTA25 (18,05%). Ja os que mostraram menor incidencia foram BTA29 (1,63%), BTA13 (9,72%) and BTA8 (9,72%). As 9.805 regiões da CNV estimadas no presente estudo cobrem aproximadamente 13.05% do genoma bovino e sobrepõem-se a 5.495 genes conhecidos que envolvem processos biológicos que poderiam estar envolvidos na adaptação ambiental da subespécie a áreas tropicais. O estudo de GWASss identificou 115 janelas que explicaram mais de 1% da variação genética aditiva para os 22 ácidos graxos estudados. A identificação destas regiões e seus genes genes, tais qual ELOVL5, ESRRG, PCYT1A e os genes do grupo ABC (ABCA5, ABCA6 e ABCA10) são genes que estão relacionados direto e inderamente ao metabolismo lipídico. O GWAS entres os fenótipos de AG e os CNVs resultaram em um total de 186 CNVR siginificantivos para os grupos dos ácidos graxos saturados (43), monosaturados (42), poliinsaturados (66) e omegas (35), nas quais foram identificados 278 genes com funçao descrita. Estes resultados apontaram genes associados a AG de varias saturações, podendo ser destacados os genes SAMD8 e BSCL2, os quais estão relacionados ao metabolism lipidico; e o gene RAPGEF6, relacionado ao metabolism energetico. Assim os inúmeras regiões genômicas encontradas neste estudo, bem como os genes identificados nas mesmas, devem contribuir para a formação de uma base genética do perfil de ácidos graxos da carne de bovino Nelore (Bos indicus), podendo contribuir para uma melhor seleção das características associadas à melhora da saúde humana. saúde. O conhecimento desses CNVs deverá melhorar a compreensão dos mecanismos genéticos e fisiológicos que contribuem para as características produtivas, bem como na seleção de animais mais produtivos e eficientes, contribuindo para o melhoramento genético das características produtivas.
The objective of this study was to identify genomic regions of Nellore cattle that present variations in the number of copies (CNV) and to associate these CNV with the fatty acid profile of the meat. In addition, the objective of this study was to carry out a genome-wid association using the single step method (GWASss) to detect genomic regions associated with saturated, mono and polyunsaturated fatty acids, as well as omega 3, 6 and their relationship. The study of the characterization and distribution of CNVs along the Nellore genome was performed by PennCNV software using genotypic data of 3,794 animals, resulting in 399,361 CNVs identified. After quality control, 2,902 were maintained in the analyzes, resulting in 195,873 CNVs, with an average size of 54,744 pb, maximum of 8.7 Mb and minimum 3 kb. The CNV regions were generated by the overlap of the CNVs by CNVRuler software. The chromosomes that showed the highest incidence of CNVR were BTA19 (24.26%), BTA23 (18.68%) and BTA25 (18.05%). Those with the lowest incidence were BTA29 (1.63%), BTA13 (9.72%) and BTA8 (9.72%). The 9,805 CNV regions estimated in the present study covered approximately 13.05% of the bovine genome and overlaped 5,495 genes known to envolve in biological processes that could be involved in the environmental adaptation of the subspecies to tropical areas. The GWASss study showed 115 windows that explained more than 1% of the additive genetic variation for the 22 fatty acids studied. The identification of these regions and their genes, such as ELOVL5, ESRRG, PCYT1A and the ABC group genes (ABCA5, ABCA6 and ABCA10) are genes directly and indirectly related to lipid metabolism. The GWAS between AG phenotypes and CNVs resulted in a total of 186 CNVRs that were significant for the saturated (43), monosaturated (42), polyunsaturated (66) and omegas (35) fatty acids groups, in which 278 genes with described function. These results pointed genes associated to AG of various saturations, and the genes SAMD8 and BSCL2, which are related to lipid metabolism; and the RAPGEF6 gene, related to energetic metabolism. Thus, the numerous genomic regions found in this study, as well as the genes identified in them, should contribute to the formation of a genetic basis of the Nellore beef (Bos indicus) fatty acid profile, contributing to a better selection of the traits associated with improvement of human health. The knowledge of these CNVs could improve the understanding of the genetic and physiological mechanisms that contribute to the productive traits, as well as the selection of more productive and efficient animals.
The objective of this study was to identify genomic regions of Nellore cattle that present variations in the number of copies (CNV) and to associate these CNV with the fatty acid profile of the meat. In addition, the objective of this study was to carry out a genome-wid association using the single step method (GWASss) to detect genomic regions associated with saturated, mono and polyunsaturated fatty acids, as well as omega 3, 6 and their relationship. The study of the characterization and distribution of CNVs along the Nellore genome was performed by PennCNV software using genotypic data of 3,794 animals, resulting in 399,361 CNVs identified. After quality control, 2,902 were maintained in the analyzes, resulting in 195,873 CNVs, with an average size of 54,744 pb, maximum of 8.7 Mb and minimum 3 kb. The CNV regions were generated by the overlap of the CNVs by CNVRuler software. The chromosomes that showed the highest incidence of CNVR were BTA19 (24.26%), BTA23 (18.68%) and BTA25 (18.05%). Those with the lowest incidence were BTA29 (1.63%), BTA13 (9.72%) and BTA8 (9.72%). The 9,805 CNV regions estimated in the present study covered approximately 13.05% of the bovine genome and overlaped 5,495 genes known to envolve in biological processes that could be involved in the environmental adaptation of the subspecies to tropical areas. The GWASss study showed 115 windows that explained more than 1% of the additive genetic variation for the 22 fatty acids studied. The identification of these regions and their genes, such as ELOVL5, ESRRG, PCYT1A and the ABC group genes (ABCA5, ABCA6 and ABCA10) are genes directly and indirectly related to lipid metabolism. The GWAS between AG phenotypes and CNVs resulted in a total of 186 CNVRs that were significant for the saturated (43), monosaturated (42), polyunsaturated (66) and omegas (35) fatty acids groups, in which 278 genes with described function. These results pointed genes associated to AG of various saturations, and the genes SAMD8 and BSCL2, which are related to lipid metabolism; and the RAPGEF6 gene, related to energetic metabolism. Thus, the numerous genomic regions found in this study, as well as the genes identified in them, should contribute to the formation of a genetic basis of the Nellore beef (Bos indicus) fatty acid profile, contributing to a better selection of the traits associated with improvement of human health. The knowledge of these CNVs could improve the understanding of the genetic and physiological mechanisms that contribute to the productive traits, as well as the selection of more productive and efficient animals.
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Palavras-chave
Variações no numero de cópias, Ácidos graxos, SNP, Seleção genômica, Nelore, Copy number variation, Fatty acid, Nellore, Genomic selection