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Biblioteca(s): |
Embrapa Pecuária Sudeste. |
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Data corrente: |
04/10/2010 |
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Data da última atualização: |
30/08/2013 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
LIU G. E.; HOU, Y. L.; ZHU, B.; CARDONE, M. F.; JIANG, L.; CELLAMARE, A.; MITRA, A.; ALEXANDER, L. J.; COUTINHO. L. L.; DELL'AQUILA, M. E.; GASBARRE, L. C.; LACALANDRA, G.; LI, R. W.; MATUKUMALLI, L. K.; NONNEMAN, D.; REGITANO, L. C. de A.; SMITH, T. P; SONG, J. Z.; SONSTEGARD, T. S.; Van TASSELL, C. P.; VENTURA, M.; EICHLER, E. E.; McDANELD, T. G.; KEELE, J. W. |
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Afiliação: |
GEORGE E. LIU; YALI HOU; BIN ZHU; MARIA FRANCESCA CARDONE; LU JIANG; ANGELO CELLAMARE; APRATIM MITRA; LEESON J. ALEXANDER; LUIZ L. COUTINHO; MARIA ELENA DELL'AQUILA; LOU C. GASBARRE; GIANNI LACALANDRA; ROBERT W. LI; LAKSHMI K. MATUKUMALLI; DAN NONNEMAN; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; TIM P. L. SMITH; JIUZHOU SONG; TAD S. SONSTEGARD; CURT P. Van TASSELL; MARIO VENTURA; EVAN E. EICHLER; TARA G. McDANELD; JOHN W. KEELE. |
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Título: |
Analysis of copy number variations among diverse cattle breeds. |
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Ano de publicação: |
2010 |
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Fonte/Imprenta: |
Genome Research, v. 20, n. 5, p. 693-703, 2010 |
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Idioma: |
Português |
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Conteúdo: |
Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, three Bos indicus, and three composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 megabases or similar to 1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research. MenosGenomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, three Bos indicus, and three composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 megabases or similar to 1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in t... Mostrar Tudo |
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Palavras-Chave: |
Gene-expression; Genome-wide association; Inbred mouse strains; Segmental duplications; Structural variation. |
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Categoria do assunto: |
G Melhoramento Genético |
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Marc: |
LEADER 03058naa a2200457 a 4500
001 1863542
005 2013-08-30
008 2010 bl --- 0-- u #d
100 1 $aLIU G. E.
245 $aAnalysis of copy number variations among diverse cattle breeds.
260 $c2010
520 $aGenomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, three Bos indicus, and three composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 megabases or similar to 1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.
653 $aGene-expression
653 $aGenome-wide association
653 $aInbred mouse strains
653 $aSegmental duplications
653 $aStructural variation
700 1 $aHOU, Y. L.
700 1 $aZHU, B.
700 1 $aCARDONE, M. F.
700 1 $aJIANG, L.
700 1 $aCELLAMARE, A.
700 1 $aMITRA, A.
700 1 $aALEXANDER, L. J.
700 1 $aCOUTINHO. L. L.
700 1 $aDELL'AQUILA, M. E.
700 1 $aGASBARRE, L. C.
700 1 $aLACALANDRA, G.
700 1 $aLI, R. W.
700 1 $aMATUKUMALLI, L. K.
700 1 $aNONNEMAN, D.
700 1 $aREGITANO, L. C. de A.
700 1 $aSMITH, T. P
700 1 $aSONG, J. Z.
700 1 $aSONSTEGARD, T. S.
700 1 $aVan TASSELL, C. P.
700 1 $aVENTURA, M.
700 1 $aEICHLER, E. E.
700 1 $aMcDANELD, T. G.
700 1 $aKEELE, J. W.
773 $tGenome Research$gv. 20, n. 5, p. 693-703, 2010
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Embrapa Pecuária Sudeste (CPPSE) |
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| 1. |  | LIU G. E.; HOU, Y. L.; ZHU, B.; CARDONE, M. F.; JIANG, L.; CELLAMARE, A.; MITRA, A.; ALEXANDER, L. J.; COUTINHO. L. L.; DELL'AQUILA, M. E.; GASBARRE, L. C.; LACALANDRA, G.; LI, R. W.; MATUKUMALLI, L. K.; NONNEMAN, D.; REGITANO, L. C. de A.; SMITH, T. P; SONG, J. Z.; SONSTEGARD, T. S.; Van TASSELL, C. P.; VENTURA, M.; EICHLER, E. E.; McDANELD, T. G.; KEELE, J. W. Analysis of copy number variations among diverse cattle breeds. Genome Research, v. 20, n. 5, p. 693-703, 2010| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
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