Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances
Abstract Background Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incor...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | deu |
| Published: |
BMC
2018-08-01
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| Series: | Genetics Selection Evolution |
| Online Access: | http://link.springer.com/article/10.1186/s12711-018-0414-x |
| _version_ | 1819133177603555328 |
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| author | Wilson Nandolo Yuri T. Utsunomiya Gábor Mészáros Maria Wurzinger Negar Khayadzadeh Rafaela B. P. Torrecilha Henry A. Mulindwa Timothy N. Gondwe Patrik Waldmann Maja Ferenčaković José F. Garcia Benjamin D. Rosen Derek Bickhart Curt P. van Tassell Ino Curik Johann Sölkner |
| author_facet | Wilson Nandolo Yuri T. Utsunomiya Gábor Mészáros Maria Wurzinger Negar Khayadzadeh Rafaela B. P. Torrecilha Henry A. Mulindwa Timothy N. Gondwe Patrik Waldmann Maja Ferenčaković José F. Garcia Benjamin D. Rosen Derek Bickhart Curt P. van Tassell Ino Curik Johann Sölkner |
| author_sort | Wilson Nandolo |
| collection | DOAJ |
| description | Abstract Background Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle. Methods ROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses. Results In Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR. Conclusions Our findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps. |
| first_indexed | 2024-12-22T09:43:09Z |
| format | Article |
| id | doaj.art-1887fe8e9fa8416e8007d4700fb6bc85 |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-12-22T09:43:09Z |
| publishDate | 2018-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-1887fe8e9fa8416e8007d4700fb6bc852022-12-21T18:30:36ZdeuBMCGenetics Selection Evolution1297-96862018-08-0150111310.1186/s12711-018-0414-xMisidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distancesWilson Nandolo0Yuri T. Utsunomiya1Gábor Mészáros2Maria Wurzinger3Negar Khayadzadeh4Rafaela B. P. Torrecilha5Henry A. Mulindwa6Timothy N. Gondwe7Patrik Waldmann8Maja Ferenčaković9José F. Garcia10Benjamin D. Rosen11Derek Bickhart12Curt P. van Tassell13Ino Curik14Johann Sölkner15Division of Livestock Sciences (NUWI), University of Natural Resources and Life SciencesSchool of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP)Division of Livestock Sciences (NUWI), University of Natural Resources and Life SciencesDivision of Livestock Sciences (NUWI), University of Natural Resources and Life SciencesDivision of Livestock Sciences (NUWI), University of Natural Resources and Life SciencesSchool of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP)National Livestock Resources Research InstituteLilongwe University of Agriculture and Natural ResourcesDepartment of Animal Breeding and Genetics, Swedish University of Agricultural SciencesDepartment of Animal Science, Faculty of Agriculture, University of ZagrebSchool of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP)Animal Genomics and Improvement LaboratoryAnimal Genomics and Improvement LaboratoryAnimal Genomics and Improvement LaboratoryDepartment of Animal Science, Faculty of Agriculture, University of ZagrebDivision of Livestock Sciences (NUWI), University of Natural Resources and Life SciencesAbstract Background Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle. Methods ROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses. Results In Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR. Conclusions Our findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps.http://link.springer.com/article/10.1186/s12711-018-0414-x |
| spellingShingle | Wilson Nandolo Yuri T. Utsunomiya Gábor Mészáros Maria Wurzinger Negar Khayadzadeh Rafaela B. P. Torrecilha Henry A. Mulindwa Timothy N. Gondwe Patrik Waldmann Maja Ferenčaković José F. Garcia Benjamin D. Rosen Derek Bickhart Curt P. van Tassell Ino Curik Johann Sölkner Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances Genetics Selection Evolution |
| title | Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances |
| title_full | Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances |
| title_fullStr | Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances |
| title_full_unstemmed | Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances |
| title_short | Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances |
| title_sort | misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances |
| url | http://link.springer.com/article/10.1186/s12711-018-0414-x |
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