1e8ac0cfb627ed9fded9efc252b4a417 pmc_10606707.pdf b38251e01493269d2d509559eacb2576ef280574 pmc_10606707.pdf fe9e061e4691fb80fbcf05004f1c40cd8d6c37983a6394609f5fc475b61703d8 pmc_10606707.pdf Title: Genomic Scanning of Inbreeding Depression for Litter Size in Two Varieties of Iberian Pigs Subject: Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120. Keywords: Iberian pig; litter size; inbreeding depression Author: Carlos Hervás-Rivero, Houssemeddine Srihi, David López-Carbonell, Joaquim Casellas, Noelia Ibáñez-Escriche, Sara Negro and Luis Varona Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Sun Oct 15 08:59:37 2023 CEST ModDate: Sun Oct 15 09:03:48 2023 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 11 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 2857690 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- ARIQJE+VnURWPalladioL Type 1 Custom yes yes no 10 0 LETDKQ+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 WAOWKH+URWPalladioL-Roma Type 1 Custom yes yes no 20 0 OMVQMK+URWPalladioL-Ital Type 1 Custom yes yes no 24 0 ENXZUH+VnURWPalladioL-Bold Type 1 Custom yes yes no 28 0 KONDUX+EuphemiaUCAS-Bold Type 1C WinAnsi yes yes no 46 0 HIZBRM+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 49 0 JYUNWZ+CMSY10 Type 1 Builtin yes yes no 71 0 EYCCMB+URWPalladioL-BoldItal Type 1 Custom yes yes no 78 0 RFLZJB+CMR10 Type 1 Builtin yes yes no 82 0 EFSUMO+PazoMath-Italic Type 1 Builtin yes yes no 86 0 IMCNIN+PalatinoLinotype,Italic TrueType MacRoman yes yes no 100 0 IMCLMP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 103 0 IMCLOA+PalatinoLinotype CID TrueType Identity-H yes yes yes 106 0 IMCLOB+PalatinoLinotype TrueType WinAnsi yes yes no 112 0 IMCLOD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 115 0 IMCMHA+PalatinoLinotype TrueType MacRoman yes yes no 118 0 IMCNIN+PalatinoLinotype,Italic TrueType MacRoman yes yes no 130 0 IMCLMP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 133 0 IMCLOA+PalatinoLinotype CID TrueType Identity-H yes yes yes 136 0 IMCLOB+PalatinoLinotype TrueType WinAnsi yes yes no 142 0 IMCLOD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 145 0 IMCMHA+PalatinoLinotype TrueType MacRoman yes yes no 148 0 IMCLMP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 163 0 IMCLOA+PalatinoLinotype CID TrueType Identity-H yes yes yes 166 0 IMCLOB+PalatinoLinotype TrueType WinAnsi yes yes no 172 0 IMCLOD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 175 0 IMCMHA+PalatinoLinotype TrueType MacRoman yes yes no 178 0 IMCNCP+PalatinoLinotype,BoldItalic TrueType WinAnsi yes yes no 192 0 IMCLMP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 195 0 IMCLOA+PalatinoLinotype CID TrueType Identity-H yes yes yes 198 0 IMCLOB+PalatinoLinotype TrueType WinAnsi yes yes no 204 0 IMCLOD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 207 0 IMCNCP+PalatinoLinotype,BoldItalic TrueType WinAnsi yes yes no 219 0 IMCLMP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 222 0 IMCLOA+PalatinoLinotype CID TrueType Identity-H yes yes yes 225 0 IMCLOB+PalatinoLinotype TrueType WinAnsi yes yes no 231 0 IMCLOD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 234 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2024-02-02 02:32:44 CET RepresentationInformation: pmc_10606707.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2024-02-01 02:44:56 CET Size: 2857690 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 410 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: section.1 Item: Title: Materials and Methods Destination: section.2 Item: Title: Results and Discussion Destination: section.3 Children: Item: Title: Variance Component Estimation Destination: subsection.3.1 Item: Title: Runs of Homozygosity (ROH) Identification Destination: subsection.3.2 Item: Title: ROH Segments and Inbreeding Depression Destination: subsection.3.3 Item: Title: Conclusions Destination: section.4 Item: Title: References Destination: section.5 Info: Title: Genomic Scanning of Inbreeding Depression for Litter Size in Two Varieties of Iberian Pigs Author: Carlos Hervás-Rivero, Houssemeddine Srihi, David López-Carbonell, Joaquim Casellas, Noelia Ibáñez-Escriche, Sara Negro and Luis Varona Subject: Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120. 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