1ae5f36df43c12236012554bb3f29636 pmc_9778079.pdf 95a088f91c5334a3d48010731c77b273d64e14c3 pmc_9778079.pdf a25dd74bb6d5115457279af034cc5e89b82550b8e049a823b817c5e9482fce65 pmc_9778079.pdf Title: Deviations from Mendelian Inheritance on Bovine X-Chromosome Revealing Recombination, Sex-of-Offspring Effects and Fertility-Related Candidate Genes Subject: Transmission ratio distortion (TRD), or significant deviations from Mendelian inheritance, is a well-studied phenomenon on autosomal chromosomes, but has not yet received attention on sex chromosomes. TRD was analyzed on 3832 heterosomal single nucleotide polymorphisms (SNPs) and 400 pseudoautosomal SNPs spanning the length of the X-chromosome using 436,651 genotyped Holstein cattle. On the pseudoautosomal region, an opposite sire-TRD pattern between male and female offspring was identified for 149 SNPs. This finding revealed unique SNPs linked to a specific-sex (Y- or X-) chromosome and describes the accumulation of recombination events across the pseudoautosomal region. On the heterosomal region, 13 SNPs and 69 haplotype windows were identified with dam-TRD. Functional analyses for TRD regions highlighted relevant biological functions responsible to regulate spermatogenesis, development of Sertoli cells, homeostasis of endometrium tissue and embryonic development. This study uncovered the prevalence of different TRD patterns across both heterosomal and pseudoautosomal regions of the X-chromosome and revealed functional candidate genes for bovine reproduction. Keywords: transmission ratio distortion; chromosome X; recombination; bovine Author: Samir Id-Lahoucine, Joaquim Casellas, Pablo A. S. Fonseca, Aroa Suárez-Vega, Flavio S. Schenkel and Angela Cánovas Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Fri Dec 9 10:07:45 2022 CET ModDate: Fri Dec 9 10:11:00 2022 CET Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 23 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 2214312 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- AIQCCL+VnURWPalladioL-Bold Type 1 Custom yes yes no 10 0 HKBJPQ+VnURWPalladioL Type 1 Custom yes yes no 15 0 FBZHUA+URWPalladioL-Bold Type 1 Custom yes yes no 19 0 KSXGIW+URWPalladioL-Roma Type 1 Custom yes yes no 24 0 HCGNFC+URWPalladioL-Ital 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 RWBCRL+CMSY10 Type 1 Builtin yes yes no 71 0 YLNFLJ+EURM10 Type 1 Builtin yes yes no 75 0 MBCBTD+wasy8 Type 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yes yes no 194 0 BCDFEE+PalatinoLinotype-Roman TrueType WinAnsi yes yes no 198 0 BCDGEE+PalatinoLinotype-Italic TrueType WinAnsi yes yes no 202 0 BCDHEE+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 206 0 WBVKDJ+URWPalladioL-BoldItal Type 1 Custom yes yes no 232 0 BCDEEE+PalatinoLinotype-Bold TrueType WinAnsi yes yes no 247 0 BCDFEE+PalatinoLinotype-Roman TrueType WinAnsi yes yes no 251 0 BCDGEE+PalatinoLinotype-Italic TrueType WinAnsi yes yes no 255 0 BCDHEE+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 259 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-01-19 02:29:03 CET RepresentationInformation: pmc_9778079.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-01-13 02:16:43 CET Size: 2214312 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 556 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4923ab24 Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@44c8afef Children: Item: Title: Genotype Data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7b69c6ba Item: Title: Imputation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46daef40 Item: Title: Male- and Female-Offspring Specific-TRD Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: Statistical Analyses Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: Pseudoautosomal Characterization Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Item: Title: Functional Analyses Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Results and Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Children: Item: Title: Characterization of X-Chromosome Using Parent-Offspring Genotyped Trios Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: Deviations from Mendelian Inheritance on the Pseudoautosomal Part of the Sex Chromosomes Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Opposite Sire-TRD between Male- and Female-Offspring Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Item: Title: Specific Sex-Offspring Sire-TRD Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: Deviations from Mendelian Inheritance on the Heterosomal Part of the X-Chromosome Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Children: Item: Title: SNP-by-SNP Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Item: Title: Haplotype Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Item: Title: Recessive TRD Pattern Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Item: Title: Functional Impact around the Pseudoautosomal Boundaries Identified Using Opposite TRD Patterns between Male and Female Offspring Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Item: Title: Enriched Metabolic Pathways, Diseases and Biological Functions Associated with the Positional Candidate Genes Displaying Deviations from Mendelian Inheritance on the X-Chromosome Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Item: Title: Functional Candidate Genes Identified in the Candidate Regions with Deviations from Mendelian Expectations Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Item: Title: Validation of Functional Candidate Genes Previously Identified in Independent Populations Using Genome-Wide Association Studies’ Meta-Analysis for Fertility Traits in Cattle Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@87f383f Info: Title: Deviations from Mendelian Inheritance on Bovine X-Chromosome Revealing Recombination, Sex-of-Offspring Effects and Fertility-Related Candidate Genes Author: Samir Id-Lahoucine, Joaquim Casellas, Pablo A. S. Fonseca, Aroa Suárez-Vega, Flavio S. Schenkel and Angela Cánovas Subject: Transmission ratio distortion (TRD), or significant deviations from Mendelian inheritance, is a well-studied phenomenon on autosomal chromosomes, but has not yet received attention on sex chromosomes. TRD was analyzed on 3832 heterosomal single nucleotide polymorphisms (SNPs) and 400 pseudoautosomal SNPs spanning the length of the X-chromosome using 436,651 genotyped Holstein cattle. On the pseudoautosomal region, an opposite sire-TRD pattern between male and female offspring was identified for 149 SNPs. This finding revealed unique SNPs linked to a specific-sex (Y- or X-) chromosome and describes the accumulation of recombination events across the pseudoautosomal region. On the heterosomal region, 13 SNPs and 69 haplotype windows were identified with dam-TRD. Functional analyses for TRD regions highlighted relevant biological functions responsible to regulate spermatogenesis, development of Sertoli cells, homeostasis of endometrium tissue and embryonic development. This study uncovered the prevalence of different TRD patterns across both heterosomal and pseudoautosomal regions of the X-chromosome and revealed functional candidate genes for bovine reproduction. 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174, 563, 210, 573 Annotation: Subtype: Link Rect: 519, 539, 557, 550 Annotation: Subtype: Link Rect: 59, 529, 95, 539 Annotation: Subtype: Link Rect: 176, 506, 214, 516 Annotation: Subtype: Link Rect: 220, 506, 256, 516 Annotation: Subtype: Link Rect: 395, 482, 432, 493 Annotation: Subtype: Link Rect: 196, 460, 234, 470 Annotation: Subtype: Link Rect: 59, 425, 96, 435 Annotation: Subtype: Link Rect: 205, 391, 242, 401 Annotation: Subtype: Link Rect: 412, 355, 449, 366 Annotation: Subtype: Link Rect: 517, 344, 555, 355 Annotation: Subtype: Link Rect: 286, 310, 323, 320 Annotation: Subtype: Link Rect: 329, 310, 365, 320 Annotation: Subtype: Link Rect: 396, 286, 434, 297 Annotation: Subtype: Link Rect: 440, 286, 476, 297 Annotation: Subtype: Link Rect: 478, 263, 515, 274 Annotation: Subtype: Link Rect: 521, 263, 557, 274 Annotation: Subtype: Link Rect: 519, 240, 557, 251 Annotation: Subtype: Link Rect: 59, 230, 95, 240 Annotation: Subtype: Link Rect: 256, 206, 293, 217 Annotation: Subtype: Link Rect: 246, 183, 283, 194 Annotation: Subtype: Link Rect: 415, 160, 453, 171 Annotation: Subtype: Link Rect: 434, 137, 472, 148 Annotation: Subtype: Link Rect: 280, 102, 317, 113 Annotation: Subtype: Link Rect: 319, 79, 356, 90 Page: Sequence: 23 Annotations: Annotation: Subtype: Link Rect: 436, 689, 474, 700 Annotation: Subtype: Link Rect: 480, 689, 516, 700 Annotation: Subtype: Link Rect: 186, 655, 224, 665 Annotation: Subtype: Link Rect: 230, 655, 266, 665 Annotation: Subtype: Link Rect: 397, 631, 435, 642 Annotation: Subtype: Link Rect: 441, 631, 477, 642 Annotation: Subtype: Link Rect: 104, 598, 142, 608 Annotation: Subtype: Link Rect: 148, 598, 184, 608 Annotation: Subtype: Link Rect: 166, 563, 203, 573 Checksum: 8388b4d7 Type: CRC32 Checksum: 1ae5f36df43c12236012554bb3f29636 Type: MD5 Checksum: 95a088f91c5334a3d48010731c77b273d64e14c3 Type: SHA-1