838d7f8aaa09cbecdb39f86f32de47a2 pmc_11593383.pdf a4f4ddce0b5d8b9d2e6abcbfd407df4047d60928 pmc_11593383.pdf 5a0d5626d00068ac0b77fd02bee39451c66f64cedf9f3c0735d49456d2ec1750 pmc_11593383.pdf Title: Runs of Homozygosity Islands in Autochthonous Spanish Cattle Breeds Subject: Background/Objectives: Understanding the genetic architecture of autochthonous European cattle breeds is important for developing effective conservation strategies and sustainable breeding programs. Spanish beef cattle, which trace their origins to ancient migrations from the Near East with later admixture from African populations, exhibit a rich genetic diversity shaped by environmental adaptation and selective breeding. Runs of Homozygosity (ROH) are extended stretches of identical genetic material inherited from both parents. They serve as indicators of inbreeding and selection signatures within populations. ROH islands, or regions of the genome where ROH segments are highly concentrated across individuals within a breed, indicate genomic regions under selective pressure. Methods: This study explores the distribution of ROH islands across seven Spanish beef cattle breeds (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Retinta, Pirenaica, and Rubia Gallega). By analyzing high-density SNP data, we characterized ROH patterns and identified genomic regions with high levels of homozygosity, which may indicate selection pressures or common ancestry. Results: Our findings revealed breed-specific ROH patterns as well as shared ROH islands, underscoring genetic relationships and differentiation among the breeds. Notably, Morucha displayed the highest number of ROH, while Asturiana de los Valles had the fewest. FROH values, which indicate genomic inbreeding, varied among the breeds, with Morucha and Retinta being associated with higher values. We identified 57 ROH islands, with shared regions among populations that suggest common ancestral selection pressures. Key genes within these regions, like MSTN, are associated with muscle growth, body weight, and fertility. Conclusions: This study offers valuable insights for breeding strategies and conservation efforts, highlighting the genetic diversity and historical background of Spanish cattle breeds. Keywords: autochthonous cattle; runs of homozygosity (ROH); ROH islands; selection signatures Author: C. Hervás-Rivero, N. Mejuto-Vázquez, D. López-Carbonell, J. Altarriba, C. Diaz, A. Molina, R. Rodríguez-Bermúdez, J. Piedrafita, J. A. Baro and L. Varona Creator: LaTeX with hyperref Producer: pdfTeX-1.40.25 CreationDate: Mon Nov 18 08:04:35 2024 CET ModDate: Mon Nov 18 08:26:54 2024 CET Custom Metadata: no Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 12 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 794062 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- JCYIDT+VnURWPalladioL-Bold Type 1 Custom yes yes yes 10 0 YBIUPV+URWPalladioL-Bold Type 1 Custom yes yes yes 16 0 HWLYGT+URWPalladioL-Roma Type 1 Custom yes yes yes 22 0 DQKGOD+URWPalladioL-Ital Type 1 Custom yes yes yes 27 0 ARIQJE+VnURWPalladioL Type 1 Custom yes yes yes 32 0 EAHJEB+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 77 0 EAHJED+PalatinoLinotype TrueType WinAnsi yes yes no 80 0 EAHJEF+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 83 0 EAHJKF+PalatinoLinotype TrueType MacRoman yes yes no 86 0 EAHJEB+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 99 0 EAHJEC+PalatinoLinotype CID TrueType Identity-H yes yes yes 102 0 EAHJED+PalatinoLinotype TrueType WinAnsi yes yes no 108 0 EAHJEF+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 111 0 EAHJKF+PalatinoLinotype TrueType MacRoman yes yes no 114 0 LGTZLE+CMSY10 Type 1 Builtin yes yes yes 122 0 EAHJEB+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 136 0 EAHJEC+PalatinoLinotype CID TrueType Identity-H yes yes yes 139 0 EAHJED+PalatinoLinotype TrueType WinAnsi yes yes no 145 0 EAHJEF+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 148 0 EAHJKF+PalatinoLinotype TrueType MacRoman yes yes no 151 0 IOLAWT+PazoMath-Italic Type 1 Builtin yes yes yes 162 0 LWLIVD+EURM10 Type 1 Builtin yes yes yes 176 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2025-02-20 02:13:03 CET RepresentationInformation: pmc_11593383.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2025-02-19 04:53:55 CET Size: 794062 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 420 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: section.1 Item: Title: Materials and Methods Destination: section.2 Children: Item: Title: Data and Data Preparation Destination: subsection.2.1 Item: Title: ROH Calculation Destination: subsection.2.2 Item: Title: FROH Calculation Destination: subsection.2.3 Item: Title: Identification of ROH Islands Destination: subsection.2.4 Item: Title: Identification of Candidate Genes Destination: subsection.2.5 Item: Title: Results Destination: section.3 Children: Item: Title: ROH Analysis Destination: subsection.3.1 Item: Title: FROH Results Destination: subsection.3.2 Item: Title: ROH Islands Destination: subsection.3.3 Item: Title: Discussion Destination: section.4 Item: Title: Conclusions Destination: section.5 Item: Title: References Destination: appendix.A. Info: Title: Runs of Homozygosity Islands in Autochthonous Spanish Cattle Breeds Author: C. Hervás-Rivero, N. Mejuto-Vázquez, D. López-Carbonell, J. Altarriba, C. Diaz, A. Molina, R. Rodríguez-Bermúdez, J. Piedrafita, J. A. Baro and L. Varona Subject: Background/Objectives: Understanding the genetic architecture of autochthonous European cattle breeds is important for developing effective conservation strategies and sustainable breeding programs. Spanish beef cattle, which trace their origins to ancient migrations from the Near East with later admixture from African populations, exhibit a rich genetic diversity shaped by environmental adaptation and selective breeding. Runs of Homozygosity (ROH) are extended stretches of identical genetic material inherited from both parents. They serve as indicators of inbreeding and selection signatures within populations. ROH islands, or regions of the genome where ROH segments are highly concentrated across individuals within a breed, indicate genomic regions under selective pressure. Methods: This study explores the distribution of ROH islands across seven Spanish beef cattle breeds (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Retinta, Pirenaica, and Rubia Gallega). By analyzing high-density SNP data, we characterized ROH patterns and identified genomic regions with high levels of homozygosity, which may indicate selection pressures or common ancestry. Results: Our findings revealed breed-specific ROH patterns as well as shared ROH islands, underscoring genetic relationships and differentiation among the breeds. Notably, Morucha displayed the highest number of ROH, while Asturiana de los Valles had the fewest. FROH values, which indicate genomic inbreeding, varied among the breeds, with Morucha and Retinta being associated with higher values. We identified 57 ROH islands, with shared regions among populations that suggest common ancestral selection pressures. Key genes within these regions, like MSTN, are associated with muscle growth, body weight, and fertility. Conclusions: This study offers valuable insights for breeding strategies and conservation efforts, highlighting the genetic diversity and historical background of Spanish cattle breeds. 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