ArticleGenetics, selection, evolution : GSE2018
Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances.
Article in Genetics, selection, evolution : GSE, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 86 citations in OpenAlex.
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- Assessment of inbreeding coefficients and inbreeding depression on complex traits from genomic and pedigree data in Nelore cattle.BMC genomics · 2024Article
- Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data.BMC genomics · 2024Article
- Analysis of Runs of Homozygosity in Aberdeen Angus Cattle.Animals : an open access journal from MDPI · 2024Article
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- Integrating genomics and transcriptomics to identify candidate genes for high egg production in Wulong geese (Anser cygnoides orientalis).BMC genomics · 2023Article
- Selection, recombination and population history effects on runs of homozygosity (ROH) in wild red deer (Cervus elaphus).Heredity · 2023Article
- Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China.Frontiers in genetics · 2023Article
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- Genome-wide survey on three local horse populations with a focus on runs of homozygosity pattern.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2022Article
- Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs.BMC genomics · 2022Article
- Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals.BMC genomics · 2022Article
- Genomic inbreeding and runs of homozygosity analysis of indigenous cattle populations in southern China.PloS one · 2022Article
- Islands of runs of homozygosity indicate selection signatures inJDS communications · 2021Article
- The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events.Genetics, selection, evolution : GSE · 2021Article
- Impaired Reproductive Function in Equines: From Genetics to Genomics.Animals : an open access journal from MDPI · 2021Review
- Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data.BMC genomics · 2021Review
- Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data.BMC genomics · 2021Article
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Authors and funding
16 authors at 6 institutions in 6 countries.
Funding
Abstract
backgroundRuns 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.
methodsROH 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.
resultsIn 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.
conclusionsOur findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps.
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