Estudo genômico populacional e de associação ampla com características de eficiência alimentar e crescimento em frangos de corte
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Data
2016-11-30
Autores
Marchesi, Jorge Augusto Petroli [UNESP]
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Universidade Estadual Paulista (Unesp)
Resumo
Galinhas são responsáveis por significativa parcela da produção de proteína para o consumo humano no mundo, movimentando a economia de diversos países. Com desenvolvimento de tecnologias de genotipagem de polimorfismos com painéis de alta densidade tornou-se possível a realização de estudos de associação ampla do genoma (GWAS) com características de importância econômica para a indústria avícola e também sua incorporação como ferramenta em estudos de conservação genética e de estrutura populacional em frangos de corte. No presente estudo objetivou-se avaliar a estrutura populacional de uma linhagem de frangos de corte por meio da análise conjunta de informações do desequilíbrio de ligação (DL), tamanho efetivo populacional (Ne), coeficiente de endogamia e segmentos de homozigose (ROH) e realizar GWAS com características de eficiência alimentar e crescimento. Para isso foram utilizadas 1.433 aves provenientes da expansão de uma linha paterna de frangos de corte genotipadas com o painel 600K Affymetrix® Axiom® HD (Affymetrix®). No controle de qualidade, foram excluídos SNPs com “call rate” abaixo de 98%, desvio do equilíbrio de Hardy-Weinberg (p-valor ≤ 10-6) e cuja frequência do alelo raro foi inferior a 2%, utilizando-se apenas os cromossomos GGA1 ao GGA28 para o estudo da estrutura populacional. Para o estudo de GWAS foram utilizados os cromossomos autossômicos e grupos de ligação (programas SNP1101 e QxPak) e cromossomo sexual Z (programa QxPak). O controle de qualidade de amostras considerou a exclusão de indivíduos que apresentaram “call rate” de SNPs inferiores a 90%. O DL foi calculado com o programa Plink v.1.9 utilizando a correlação entre dois SNPs (r²). A partir dos dados de DL foi calculado o Ne para até 200 gerações passadas utilizando o programa SNP1101 v.1.0. ROH foram identificados utilizando o programa Plink v.1.9, onde foram considerados segmentos de no mínimo 100 SNPs com tamanho mínimo de 1.000 Kb, sendo permitida a presença de um SNP heterozigoto e a ausência de um SNP em uma janela de 100 SNPs. O limite de significância estatística para a associação foi inferido pelo teste de Bonferroni a 5%, utilizando o número de marcadores independentes. O DL médio entre SNPs adjacentes em todos os autossomos foi de 0,37 e variou de 0,38 a 0,43, 0,36 a 0,40 e 0,29 a 0,41 em macrocromossomos, cromossomos intermediários e microcromossomos, respectivamente. O Ne, a partir de dados de DL, sugere que a população ancestral de 200 gerações passadas era muito maior (548 animais) do que a recente população de 5 gerações passadas (157 animais). Nesta população, 1.279 dos indivíduos apresentaram segmentos ROH. O número total de segmentos genômicos em homozigose observados neste estudo foi de 9.414, dos quais 5.462 estão presentes em mais de 1% da população. Apenas uma região, a do microcromossomo GGA15, com tamanho de 2,81 Mb (entre 2.214.888 e 5.022.515 pb), apresentou ROH que correspondeu a 52,41% da população (738 aves). Esta região abriga dois genes de miRNAs e 41 genes codificadores de proteínas, dos quais, 10 genes apresentam função relacionada com a formação e maturação de células germinativas. Na análise de GWAS, 48 regiões genômicas foram associadas sugestivamente (p < 5 x 10-5) com as características de eficiência alimentar, e 33 com as características de crescimento. Apenas duas regiões genômicas foram significativamente associadas (p < 2 x 10-6) à duas características de crescimento (peso aos 41 e 42 dias de idade). Alguns dos SNPs significativos estão localizados dentro ou próximos de genes que são conhecidos por influenciar as características estudadas em populações de frangos de corte, mas grande parte dos marcadores significativos estão associados a genes com funções pouco claras ou não descritas na expressão destas características. Como conclusão, foi evidenciada a importância da utilização de painéis de genotipagem de SNPs em alta densidade para fornecer conhecimentos sobre a estrutura genética de populações de frangos de corte e estudos de associação do genoma mais eficientes. Diversas foram as regiões genômicas encontradas, algumas ainda não descritas como associadas às características estudadas. Os resultados também fornecem valiosas informações sobre genes e SNPs candidatos envolvidos na determinação destas características e suas informações podem ser incorporadas em programas de seleção genômica em frangos de corte.
Chickens are responsible for a significant portion of protein production for human consumption in the world, moving the economy of many countries. The development of high-density arrays made possible the genome-wide association study (GWAS) for economic important traits to the poultry industry as well as its incorporation as a tool for genetic conservation and population structure studies in broilers. The present study aimed to evaluate the population structure of a broiler line of through the joint analysis of linkage disequilibrium (LD), effective population size (Ne), inbreeding coefficient and runs of homozygosity (ROH), and performing GWAS with growth and feed efficiency traits in a population from a male broilers line. A total of 1,433 birds were used from an expansion population of a paternal broiler line genotyped with 600K Affymetrix® Axiom® HD array (Affymetrix®). The genotype quality control considered the exclusion of single nucleotide polymorphisms (SNPs) with call rate below 98%, based on the deviations from Hardy-Weinberg equilibrium (p ≤ 1x10-6), and minor allele frequency was lower than 2%, using only Gallus gallus autosomes (GGA1 to GGA28) for the population structure study, and all autosomes, linkage groups and Z chromosome sex for GWAS. Quality control samples considered the exclusion of individuals who had SNPs call rate below 90%. The LD was calculated by Plink v.1.9 software using the correlation between two consecutive SNPs (r²). From the LD data was calculated Ne up to 200 generations ago using SNP1101 v.1.0 software. The ROH were identified using Plink v.1.9 software, which considered segments of at least 100 SNPs with a minimum length of 1,000 kb, and allowed the presence of a heterozygous SNP and the absence of one SNP in a window 100 SNPs. The GWAS analysis was performed using SNP1101 v.1.0 and QxPak 5.0 softwares. The statistical significance threshold for the association was inferred by the Bonferroni test at 5% using the number of independent markers. The average LD between adjacent SNPs in all autosomes was 0.37 and ranged from 0.38 to 0.43, 0.36 to 40, and 0.29 to 0.41 in macrochromosomes, intermediates chromosomes and microchromosomes, respectively. Ne from LD data showed that the ancestral population of 200 generations ago was much larger (548 animals) than the recent past generations population of 5 (157 animals). In this population, 1,279 individuals had ROH. The total number of genomic homozygous segments observed in this study was 9,414, of which 5,462 were present in more than 1% of the population. Only one region, in GGA15 microchromosome, with a length of 2.81 Mb (between 2,214,888 and 5,022,515 bp) showed ROH corresponding to 52.41% of the population (738 birds). This region includes two miRNAs genes, and 41 proteincoding genes. In this region, 10 genes have function related to the formation and maturation of germ cells. In GWAS analysis, 48 genomic regions were associated suggestively (p-value <5 x 10-5) with the feed efficiency traits, and 33 with growth traits. Only two genomic regions were significantly associated (p <2 x 10-6) to the two growth traits (body weight at 41 and 42 days of age). Some of the significant SNPs are located inside or near to genes that are known to influence the analyzed traits in broilers population, but most of the identified significant markers are associated with genes having unclear functions, or not described on the traits expression. In conclusion, the importance of using high-density genotyping arrays of SNPs could be highlighted in order to provide knowledge about the population structure and genome association studies. Several genomic regions not yet described were found as associated with the studied traits. These results also provide valuable information about candidate genes and SNPs that are involved in determining these traits and this information could be incorporated into marker assisted selection or genomic selection programs in broilers.
Chickens are responsible for a significant portion of protein production for human consumption in the world, moving the economy of many countries. The development of high-density arrays made possible the genome-wide association study (GWAS) for economic important traits to the poultry industry as well as its incorporation as a tool for genetic conservation and population structure studies in broilers. The present study aimed to evaluate the population structure of a broiler line of through the joint analysis of linkage disequilibrium (LD), effective population size (Ne), inbreeding coefficient and runs of homozygosity (ROH), and performing GWAS with growth and feed efficiency traits in a population from a male broilers line. A total of 1,433 birds were used from an expansion population of a paternal broiler line genotyped with 600K Affymetrix® Axiom® HD array (Affymetrix®). The genotype quality control considered the exclusion of single nucleotide polymorphisms (SNPs) with call rate below 98%, based on the deviations from Hardy-Weinberg equilibrium (p ≤ 1x10-6), and minor allele frequency was lower than 2%, using only Gallus gallus autosomes (GGA1 to GGA28) for the population structure study, and all autosomes, linkage groups and Z chromosome sex for GWAS. Quality control samples considered the exclusion of individuals who had SNPs call rate below 90%. The LD was calculated by Plink v.1.9 software using the correlation between two consecutive SNPs (r²). From the LD data was calculated Ne up to 200 generations ago using SNP1101 v.1.0 software. The ROH were identified using Plink v.1.9 software, which considered segments of at least 100 SNPs with a minimum length of 1,000 kb, and allowed the presence of a heterozygous SNP and the absence of one SNP in a window 100 SNPs. The GWAS analysis was performed using SNP1101 v.1.0 and QxPak 5.0 softwares. The statistical significance threshold for the association was inferred by the Bonferroni test at 5% using the number of independent markers. The average LD between adjacent SNPs in all autosomes was 0.37 and ranged from 0.38 to 0.43, 0.36 to 40, and 0.29 to 0.41 in macrochromosomes, intermediates chromosomes and microchromosomes, respectively. Ne from LD data showed that the ancestral population of 200 generations ago was much larger (548 animals) than the recent past generations population of 5 (157 animals). In this population, 1,279 individuals had ROH. The total number of genomic homozygous segments observed in this study was 9,414, of which 5,462 were present in more than 1% of the population. Only one region, in GGA15 microchromosome, with a length of 2.81 Mb (between 2,214,888 and 5,022,515 bp) showed ROH corresponding to 52.41% of the population (738 birds). This region includes two miRNAs genes, and 41 proteincoding genes. In this region, 10 genes have function related to the formation and maturation of germ cells. In GWAS analysis, 48 genomic regions were associated suggestively (p-value <5 x 10-5) with the feed efficiency traits, and 33 with growth traits. Only two genomic regions were significantly associated (p <2 x 10-6) to the two growth traits (body weight at 41 and 42 days of age). Some of the significant SNPs are located inside or near to genes that are known to influence the analyzed traits in broilers population, but most of the identified significant markers are associated with genes having unclear functions, or not described on the traits expression. In conclusion, the importance of using high-density genotyping arrays of SNPs could be highlighted in order to provide knowledge about the population structure and genome association studies. Several genomic regions not yet described were found as associated with the studied traits. These results also provide valuable information about candidate genes and SNPs that are involved in determining these traits and this information could be incorporated into marker assisted selection or genomic selection programs in broilers.
Descrição
Palavras-chave
Avicultura, Endogamia, Gallus gallus, Marcadores moleculares, Melhoramento genético, Animal breeding, Inbreeding, Molecular markers, Poultry