Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits
Abstract Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from R...
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BMC
2018-09-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5060-8 |
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| author | Elisa Peripolli Julia Metzger Marcos Vinícius Antunes de Lemos Nedenia Bonvino Stafuzza Sabrina Kluska Bianca Ferreira Olivieri Fabieli Louise Braga Feitosa Mariana Piatto Berton Fernando Brito Lopes Danísio Prado Munari Raysildo Barbosa Lôbo Cláudio de Ulhoa Magnabosco Fernando Di Croce Jason Osterstock Sue Denise Angélica Simone Cravo Pereira Fernando Baldi |
| author_facet | Elisa Peripolli Julia Metzger Marcos Vinícius Antunes de Lemos Nedenia Bonvino Stafuzza Sabrina Kluska Bianca Ferreira Olivieri Fabieli Louise Braga Feitosa Mariana Piatto Berton Fernando Brito Lopes Danísio Prado Munari Raysildo Barbosa Lôbo Cláudio de Ulhoa Magnabosco Fernando Di Croce Jason Osterstock Sue Denise Angélica Simone Cravo Pereira Fernando Baldi |
| author_sort | Elisa Peripolli |
| collection | DOAJ |
| description | Abstract Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. |
| first_indexed | 2024-12-13T13:20:32Z |
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| id | doaj.art-7cb9cc2059844600957de523b2ba12e0 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T13:20:32Z |
| publishDate | 2018-09-01 |
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| series | BMC Genomics |
| spelling | doaj.art-7cb9cc2059844600957de523b2ba12e02022-12-21T23:44:25ZengBMCBMC Genomics1471-21642018-09-0119111410.1186/s12864-018-5060-8Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traitsElisa Peripolli0Julia Metzger1Marcos Vinícius Antunes de Lemos2Nedenia Bonvino Stafuzza3Sabrina Kluska4Bianca Ferreira Olivieri5Fabieli Louise Braga Feitosa6Mariana Piatto Berton7Fernando Brito Lopes8Danísio Prado Munari9Raysildo Barbosa Lôbo10Cláudio de Ulhoa Magnabosco11Fernando Di Croce12Jason Osterstock13Sue Denise14Angélica Simone Cravo Pereira15Fernando Baldi16Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita FilhoInstitute for Animal Breeding and Genetics, University of Veterinary Medicine HannoverDepartamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita FilhoDepartamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita FilhoDepartamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita FilhoDepartamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita FilhoDepartamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita FilhoDepartamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita FilhoDepartamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita FilhoDepartamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita FilhoAssociação Nacional de Criadores e Pesquisadores (ANCP)Embrapa CerradosZoetisZoetisZoetisUniversidade de São Paulo, Departamento de Nutrição e Produção AnimalDepartamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita FilhoAbstract Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle.http://link.springer.com/article/10.1186/s12864-018-5060-8Bos indicusIndicineGenomic inbreedingGene ontology |
| spellingShingle | Elisa Peripolli Julia Metzger Marcos Vinícius Antunes de Lemos Nedenia Bonvino Stafuzza Sabrina Kluska Bianca Ferreira Olivieri Fabieli Louise Braga Feitosa Mariana Piatto Berton Fernando Brito Lopes Danísio Prado Munari Raysildo Barbosa Lôbo Cláudio de Ulhoa Magnabosco Fernando Di Croce Jason Osterstock Sue Denise Angélica Simone Cravo Pereira Fernando Baldi Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits BMC Genomics Bos indicus Indicine Genomic inbreeding Gene ontology |
| title | Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits |
| title_full | Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits |
| title_fullStr | Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits |
| title_full_unstemmed | Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits |
| title_short | Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits |
| title_sort | autozygosity islands and roh patterns in nellore lineages evidence of selection for functionally important traits |
| topic | Bos indicus Indicine Genomic inbreeding Gene ontology |
| url | http://link.springer.com/article/10.1186/s12864-018-5060-8 |
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