Scaning of Selection Signatures in Dairy Buffalo (Bubalus bubalis)
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Data
2020-07-28
Autores
Nascimento, André Vieira do
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Universidade Estadual Paulista (Unesp)
Resumo
O objetivo do presente trabalho foi aperfeiçoar o mapa do painel Axiom Buffalo Genotyping (ABG) com mapeamento de SNPs com posição indefinida SNPs e predizer a localização genômica de QTL (Quantitative Trait Loci) bovinos no genoma bubalino por meio de alinhamento local. Além de identificar assinaturas de seleção em rebanho da raça Murrah, buscando genes e QTL relacionados a aspectos raciais e produtivos da espécie. Foram utilizados 865 animais genotipados com o painel ABG. Todas as sequências das sondas (123.040) foram realinhadas contra o genoma bubalino (UOA_WB_1) usando o BLAST, já as sequencias dos QTL bovinos foram alinhadas com o genoma do búfalo usando o Burrows-Wheeler Aligner. O controle de qualidade dos genótipos foi realizado com a remoção de marcadores não autossômicos, duplicados, com Call rateSNP e Call rateAmostra inferiores a 0,95 e 0,90 respectivamente. Para a identificação de assinaturas de seleção por ROH (Runs of homozygosity), os seguintes parâmetros foram utilizados: região genômica com comprimento homozigoto maior que 1Mb; mínimo de 30 SNP em homozigose; ao menos 1 SNP por 100 kb; intervalo máximo entre dois SNPs de até 500 kb; e no máximo 1 locus heterozigoto por segmento. A análise de iHS (Integrated Haplotype Score) foi realizada com o software SELSCAN. As médias de |iHS| foram estimadas em janelas de 500 kb, com 250 kb de sobreposição. Sendo consideradas assinaturas de seleção as janelas com valores médios de |iHS| superior a 2,36 (0,1% superior). Foram estimados os níveis de endogamia, onde os coeficientes de endogamia foram calculados a partir da matriz de parentesco genômico (FGRM), pedigree (FPED) e ROH (FROH). O número de SNP mapeados aumentou de 106.778 no mapa ABG para 116.708 em nosso mapa. As assinaturas de seleção foram identificadas usando o Novo mapa e o mapa ABG. Houve intensificação dos picos de autozigosidade e surgimento de novos no BBU5 e BBU11 quando todos os marcadores no novo mapa foram utilizados. Após alinhamento e controle de qualidade, 63.995 QTL bovinos foram mapeados com sucesso para o genoma do búfalo. Assim, o novo mapa de SNP pode melhorar os resultados das análises genômicas, por meio do aumento de 9.930 SNPs e redução do espaçamento médio do marcador em ~2kb. Devido a homologia entre bovinos e búfalos, as coordenadas dos QTL apresentados neste trabalho, podem ser consideradas potenciais QTL em búfalos, levando à apresentação do primeiro banco de dados de QTL de búfalos. Do total de animais, 350 tiveram ROHs superiores a 10 Mb e comprimento médio por animal de 4,28 ± 1,85 Mb. Coeficiente de endogamia utilizando informação de pedigree teve baixa correlação com estimativas genômicas. As estimativas de FGRM foram maiores que as obtidas por meio do FPED e FROH. Análises baseadas em ROH identificaram assinaturas de seleção nos cromossomos autossômicos 1, 2, 3, 5, 16 e 18, enquanto iHS identificou regiões em assinatura de seleção localizadas nos cromossomos 1, 6, 7, 9, 14 e 23. Ambas análises abrangeram genes e QTL previamente relacionados a características de produção de leite, reprodução, morfológica e resposta imune. Os níveis de endogamia nessa população ainda são baixos, mas devem ser gerenciados para evitar perdas futuras devido à depressão por endogamia.
The aim of the present work was to improve the map of Axiom Buffalo Genotyping array with determining the positions of ~10 thousand SNPs and to predict the genomic location of QTL (Quantitative Trait Loci) cattle in the buffalo genome using local alignment. In addition to identifying signature of selection in a Murrah breed herd, looking for genes and QTL related to racial and productive aspects of the specie. A population of 865 animals genotyped with the Axiom Buffalo Genotyping (ABG) panel was used. All probe sequences (123,040) have been realigned with buffalo genome (UOA_WB_1) using BLAST, however the sequences of bovine QTL were aligned with the buffalo genome using the Burrows-Wheeler Aligner. The quality control of the genotypes was carried out with the removal of duplicate non-autosomal markers, with call rateSNP and call rateSample less than 0.95 and 0.90 respectively. For the detection of signature of selection by ROH (Runs of homozygosity), the following parameters were used: genomic region with homozygous length greater than 1Mb; minimum of 30 SNP in homozygosis; at least 1 SNP per 100 kb; maximum interval between two SNPs up to 500 kb; and no more than 1 heterozygous locus per segment. Integrated Haplotype Score (iHS) analysis was performed with the SELSCAN software. The averages of |iHS| were estimated in 500 kb windows, with 250 kb of overlap allowed. Where selection signatures were the windows with mean values of |iHS| greater than 2.36 (top 0.1%). The inbreeding of coefficients were calculated from the genomic relationship matrix (FGRM), pedigree (FPED) and ROH (FROH). The number of SNP mapped increased from 106,778 in ABG map to 116,708 in our map. We identified signatures of selection using the new map and the ABG map. There was an intensification of peaks of autozygosity and the appearance of new ones in the BBU5 and BBU11 when we used all the markers on the new map were. After alignment and quality control, 63,995 cattle QTL were successfully mapped to the buffalo genome. Thus, the new SNP map can improve the results of genomic analyzes, by increasing 9,930 SNPs and reducing the average marker spacing by ~ 2kb. Due to the homology between cattle and buffaloes, the coordinates of the QTL presented in this work can be considered potential buffalo QTLs, leading to the presentation of the first buffalo QTL database. Of the total animals, 350 had ROHs greater than 10 Mb and average length per animal of 4.28 ± 1.85 Mb. Inbreeding estimates of the pedigree had a low correlation with genomic estimates. The estimates of FGRM were higher compared to FPED and FROH. Analysis of selection signatures based on ROH highlighted regions on autosomal chromosomes 1, 2, 3, 5, 16 and 18, while iHS identified regions located on chromosomes 1, 6, 7, 9, 14 and 23. The regions of both analyzes were in overlap with genes and QTL previously related to traits of milk production, reproduction, morphology and immune response. Inbreeding levels in this population are still low, but must be managed to avoid future losses due to inbreeding depression.
The aim of the present work was to improve the map of Axiom Buffalo Genotyping array with determining the positions of ~10 thousand SNPs and to predict the genomic location of QTL (Quantitative Trait Loci) cattle in the buffalo genome using local alignment. In addition to identifying signature of selection in a Murrah breed herd, looking for genes and QTL related to racial and productive aspects of the specie. A population of 865 animals genotyped with the Axiom Buffalo Genotyping (ABG) panel was used. All probe sequences (123,040) have been realigned with buffalo genome (UOA_WB_1) using BLAST, however the sequences of bovine QTL were aligned with the buffalo genome using the Burrows-Wheeler Aligner. The quality control of the genotypes was carried out with the removal of duplicate non-autosomal markers, with call rateSNP and call rateSample less than 0.95 and 0.90 respectively. For the detection of signature of selection by ROH (Runs of homozygosity), the following parameters were used: genomic region with homozygous length greater than 1Mb; minimum of 30 SNP in homozygosis; at least 1 SNP per 100 kb; maximum interval between two SNPs up to 500 kb; and no more than 1 heterozygous locus per segment. Integrated Haplotype Score (iHS) analysis was performed with the SELSCAN software. The averages of |iHS| were estimated in 500 kb windows, with 250 kb of overlap allowed. Where selection signatures were the windows with mean values of |iHS| greater than 2.36 (top 0.1%). The inbreeding of coefficients were calculated from the genomic relationship matrix (FGRM), pedigree (FPED) and ROH (FROH). The number of SNP mapped increased from 106,778 in ABG map to 116,708 in our map. We identified signatures of selection using the new map and the ABG map. There was an intensification of peaks of autozygosity and the appearance of new ones in the BBU5 and BBU11 when we used all the markers on the new map were. After alignment and quality control, 63,995 cattle QTL were successfully mapped to the buffalo genome. Thus, the new SNP map can improve the results of genomic analyzes, by increasing 9,930 SNPs and reducing the average marker spacing by ~ 2kb. Due to the homology between cattle and buffaloes, the coordinates of the QTL presented in this work can be considered potential buffalo QTLs, leading to the presentation of the first buffalo QTL database. Of the total animals, 350 had ROHs greater than 10 Mb and average length per animal of 4.28 ± 1.85 Mb. Inbreeding estimates of the pedigree had a low correlation with genomic estimates. The estimates of FGRM were higher compared to FPED and FROH. Analysis of selection signatures based on ROH highlighted regions on autosomal chromosomes 1, 2, 3, 5, 16 and 18, while iHS identified regions located on chromosomes 1, 6, 7, 9, 14 and 23. The regions of both analyzes were in overlap with genes and QTL previously related to traits of milk production, reproduction, morphology and immune response. Inbreeding levels in this population are still low, but must be managed to avoid future losses due to inbreeding depression.
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Palavras-chave
Autozigosidade, Murrah, Endogamia, Autozygosity, Inbreeding