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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
28/11/2018 |
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Data da última atualização: |
24/01/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
PERIPOLLI, E.; STAFUZZA, N. B.; MUNARI, D. P.; LIMA, A. L. F.; IRGANG, R.; MACHADO, M. A.; PANETTO, J. C. do C.; VENTURA, R. V.; BALDI, F.; SILVA, M. V. G. B. |
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Afiliação: |
ELISA PERIPOLLI, UNESP; NEDENIA BONVINO STAFUZZA, UNESP; DANÍSIO PRADO MUNARI, UNESP / CNPQ; ANDRÉ LUÍS FERREIRA LIMA, UFSC; RENATO IRGANG, UFSC; MARCO ANTONIO MACHADO, CNPGL; JOAO CLAUDIO DO CARMO PANETTO, CNPGL; RICARDO VIEIRA VENTURA, USP / Beef Improvement Opportunities, Canada / University of Guelph, Canada; FERNANDO BALDI, UNESP; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL. |
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Título: |
Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. |
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Ano de publicação: |
2018 |
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Fonte/Imprenta: |
BMC Genomics, v. 19, n. 34, 2018. |
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Páginas: |
13 p. |
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DOI: |
10.1186/s12864-017-4365-3 |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract BACKGROUND: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). RESULTS: ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1-2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from -0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length. CONCLUSIONS: Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. MenosAbstract BACKGROUND: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). RESULTS: ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1-2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficient... Mostrar Tudo |
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Palavras-Chave: |
Dairy traits; Inbreeding coefficients; ROH islands. |
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Thesagro: |
Bos Indicus. |
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Categoria do assunto: |
L Ciência Animal e Produtos de Origem Animal |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/187250/1/Cnpgl-2018-BMC-Gen-Machado-Assessment.pdf
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Marc: |
LEADER 03293naa a2200301 a 4500
001 2100275
005 2023-01-24
008 2018 bl uuuu u00u1 u #d
024 7 $a10.1186/s12864-017-4365-3$2DOI
100 1 $aPERIPOLLI, E.
245 $aAssessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle.$h[electronic resource]
260 $c2018
300 $a13 p.
520 $aAbstract BACKGROUND: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). RESULTS: ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1-2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from -0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length. CONCLUSIONS: Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records.
650 $aBos Indicus
653 $aDairy traits
653 $aInbreeding coefficients
653 $aROH islands
700 1 $aSTAFUZZA, N. B.
700 1 $aMUNARI, D. P.
700 1 $aLIMA, A. L. F.
700 1 $aIRGANG, R.
700 1 $aMACHADO, M. A.
700 1 $aPANETTO, J. C. do C.
700 1 $aVENTURA, R. V.
700 1 $aBALDI, F.
700 1 $aSILVA, M. V. G. B.
773 $tBMC Genomics$gv. 19, n. 34, 2018.
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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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Registro Completo
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Biblioteca(s): |
Embrapa Mandioca e Fruticultura. |
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Data corrente: |
11/02/2011 |
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Data da última atualização: |
06/04/2011 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
B - 2 |
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Autoria: |
EIRAS, M.; SILVA, S. R. da; STUCHI, E. S.; FLORES, R.; DARÓS, J. A. |
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Afiliação: |
Marcelo Eiras, CPDSV; Simone Rodrigues da Silva, ESALQ/USP; EDUARDO SANCHES STUCHI, CNPMF; Ricardo Flores, CSIC; José Antonio Daròs, CSIC. |
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Título: |
Viroid species associated with the bark-cracking phenotype of 'Tahiti' acid lime in the State of São Paulo, Brazil. |
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Ano de publicação: |
2010 |
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Fonte/Imprenta: |
Tropical Plant Pathology, Brasília, DF, v. 35, n. 5, p. 303-309, 2010. |
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Idioma: |
Português |
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Notas: |
Short communication |
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Conteúdo: |
Viroids have been used as "graft transmissible dwarfing agents" (GTDA) in several countries, mainly to reduce growth of citrus trees, thus increasing their density in orchards. In the State of São Paulo, Brazil, plants of the acid lime 'Tahiti' are usually grafted with a complex of GTDA, presumably viroids. The aim of the present work was the identification and molecular characterization of the viroids infecting trees of acid lime 'Tahiti' displaying "Quebra galho" (bark-cracking). Viroids were identified and characterized by biological indexing in 'Etrog' citron, Northern-blot hybridization, RT-PCR, cloning and complete sequencing of the RNA genomes. Citrus exocortis viroid (CEVd), Hop stunt viroid (HSVd) and Citrus dwarfing viroid (CDVd) were found in different combinations. Although we have not been able to infer a direct relationship between the agronomical performance and symptom severity with the presence of a specific viroid or viroid combination, the differences in the severity of "Quebra-galho" symptoms among different trees is probably associated with the presence (or absence) of CEVd, with its interaction with other viroids perhaps determining the different phenotypes observed in the field. |
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Palavras-Chave: |
Citrus dwarfing; Exocortis; Xyloporosis. |
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Thesaurus NAL: |
cachexia; Pospiviroid; Pospiviroidae. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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Marc: |
LEADER 01952naa a2200253 a 4500
001 1876907
005 2011-04-06
008 2010 bl uuuu u00u1 u #d
100 1 $aEIRAS, M.
245 $aViroid species associated with the bark-cracking phenotype of 'Tahiti' acid lime in the State of São Paulo, Brazil.
260 $c2010
500 $aShort communication
520 $aViroids have been used as "graft transmissible dwarfing agents" (GTDA) in several countries, mainly to reduce growth of citrus trees, thus increasing their density in orchards. In the State of São Paulo, Brazil, plants of the acid lime 'Tahiti' are usually grafted with a complex of GTDA, presumably viroids. The aim of the present work was the identification and molecular characterization of the viroids infecting trees of acid lime 'Tahiti' displaying "Quebra galho" (bark-cracking). Viroids were identified and characterized by biological indexing in 'Etrog' citron, Northern-blot hybridization, RT-PCR, cloning and complete sequencing of the RNA genomes. Citrus exocortis viroid (CEVd), Hop stunt viroid (HSVd) and Citrus dwarfing viroid (CDVd) were found in different combinations. Although we have not been able to infer a direct relationship between the agronomical performance and symptom severity with the presence of a specific viroid or viroid combination, the differences in the severity of "Quebra-galho" symptoms among different trees is probably associated with the presence (or absence) of CEVd, with its interaction with other viroids perhaps determining the different phenotypes observed in the field.
650 $acachexia
650 $aPospiviroid
650 $aPospiviroidae
653 $aCitrus dwarfing
653 $aExocortis
653 $aXyloporosis
700 1 $aSILVA, S. R. da
700 1 $aSTUCHI, E. S.
700 1 $aFLORES, R.
700 1 $aDARÓS, J. A.
773 $tTropical Plant Pathology, Brasília, DF$gv. 35, n. 5, p. 303-309, 2010.
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Embrapa Mandioca e Fruticultura (CNPMF) |
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