f8046b212ed47e91ea4d55484b6b6995 animals_a2020v10n12p2233.pdf 1b7a913b50be2c0783d84edfa2ab75700c7e6ee7 animals_a2020v10n12p2233.pdf d5faf2989546c270130d17c60657fc5cacdcb86476a9b767d49ff665b4057aea animals_a2020v10n12p2233.pdf Title: The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the “Charolais de Cuba” Cattle Subject: Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population. Keywords: genomic inbreeding; effective population size; runs of homozygosity; candidate genes; tropical climate; adaptation Author: Yoel Rodríguez-Valera, Dominique Rocha, Michel Naves, Gilles Renand, Eliecer Pérez-Pineda, Yuliaxis Ramayo-Caldas and Sebastian E. Ramos-Onsins Creator: LaTeX with hyperref package Producer: pdfTeX-1.40.18 CreationDate: Mon Nov 30 03:17:59 2020 CET ModDate: Mon Nov 30 03:44:11 2020 CET Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 16 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 4736858 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- EHMLRX+URWPalladioL-Ital Type 1 Custom yes yes no 10 0 APVEBO+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 YKYICR+URWPalladioL-Roma Type 1 Custom yes yes no 19 0 OFLXAT+Rpxr Type 1 Builtin yes yes no 23 0 YSPQJI+VnURWPalladioL-Bold Type 1 Custom yes yes no 27 0 SZMRXJ+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 36 0 MCBCCI+SourceSansRoman-Regular Type 1C Custom yes yes no 58 0 MCBCCM+SourceSansRoman.613wght Type 1C Custom yes yes no 62 0 MCBCCO+SourceSansRoman-Bold Type 1C Custom yes yes no 66 0 FFGMKQ+VnURWPalladioL Type 1 Custom yes yes no 73 0 FBNTAM+Rpxi Type 1 Builtin yes yes no 83 0 ETKVOT+Pxsy Type 1 Builtin yes yes no 87 0 RLLWQT+Pxex Type 1 Builtin yes yes no 91 0 UGLOHL+PazoMath Type 1 Builtin yes yes no 95 0 CZKGAS+CMR10 Type 1 Builtin yes yes no 99 0 CKBPVA+EURM10 Type 1 Builtin yes yes no 103 0 PBEIHU+Rpxb Type 1 Builtin yes yes no 110 0 GEJNTL+VnURWPalladioL-Italic Type 1 Custom yes yes no 169 0 VSHNAE+Rpcxr Type 1 Builtin yes yes no 176 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2021-01-15 05:37:18 CET RepresentationInformation: animals_a2020v10n12p2233.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2021-01-11 10:42:07 CET Size: 4736858 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 426 FreeObjects: 7 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Children: Item: Title: Data Used and Marker Quality Controls Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Detection of Runs of Homozygosity (ROH) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: Estimation of Genomic Inbreeding Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: Estimation of Effective Population Size Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Candidate Regions Responsible of the CHCU Adaptation to Tropical Conditions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Children: Item: Title: Estimation of Runs of Homozygosity (ROH) and Genomic Inbreeding Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: Estimation of Effective Populations Size Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Item: Title: Candidate Regions Responsible of the CHCU Adaptation to Tropical Conditions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Children: Item: Title: Limitations and Trade-Offs of the Analysis Based on Genotype Datasets and Small Sample Sizes Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Item: Title: Estimation of Runs of Homozygosity (ROHs) and Genomic Inbreeding Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Item: Title: Estimation of Effective Populations Size Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Item: Title: Candidate Regions Responsible of the CHCU Adaptation to Tropical Conditions 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: The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the “Charolais de Cuba” Cattle Author: Yoel Rodríguez-Valera, Dominique Rocha, Michel Naves, Gilles Renand, Eliecer Pérez-Pineda, Yuliaxis Ramayo-Caldas and Sebastian E. Ramos-Onsins Subject: Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population. 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