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      Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences

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          Abstract

          Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2–71.3 Mb), BTA5 (10.0–19.7 Mb), BTA20 (10.0–19.9 and 20.0–22.7 Mb), and BTA25 (0.5–9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviole t protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            The Sequence Alignment/Map format and SAMtools

            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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              fastp: an ultra-fast all-in-one FASTQ preprocessor

              Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: MethodologyRole: ResourcesRole: Writing – review & editing
                Role: Writing – review & editing
                Role: Writing – review & editing
                Role: Writing – review & editing
                Role: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: ResourcesRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLOS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                26 October 2022
                2022
                : 17
                : 10
                : e0276309
                Affiliations
                [1 ] Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
                [2 ] BIOPOLIS/CIBIO/ InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
                [3 ] Natural Resources Institute Finland, Jokioinen, Finland
                [4 ] Animal Production Department, Faculty of Agriculture, Cairo University, Giza, Egypt
                [5 ] Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
                [6 ] Agricultural Research Council-Animal Production Institute, Irene, South Africa
                [7 ] Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
                University of Iceland, ICELAND
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0003-3679-4685
                https://orcid.org/0000-0001-6350-6373
                https://orcid.org/0000-0002-0480-0959
                https://orcid.org/0000-0002-4873-6637
                https://orcid.org/0000-0003-0484-4545
                Article
                PONE-D-21-24693
                10.1371/journal.pone.0276309
                9605288
                36288367
                c4cf3df7-ed7e-4809-a427-31d738a912c1
                © 2022 Gonzalez-Prendes et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 4 August 2021
                : 4 October 2022
                Page count
                Figures: 5, Tables: 2, Pages: 19
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100007601, Horizon 2020;
                Award ID: 727715
                The research presented in this publication was funded by the Long-term EU-Africa research and innovation Partnership on food and nutrition security and sustainable Agriculture (LEAP-Agri) as part of the OPTIBOV project (LEAP-Agri-326) and co-founded by the European Union’s Horizon 2020 research and innovation program under grant agreement No 727715. The funding bodies had no role in the design of the study, the collection, analysis, interpretation of data, or the writing of the manuscript.
                Categories
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                Custom metadata
                The VCF files with variant from all breeds will be available at https://zenodo.org/deposit/6616286. Raw reads will be accessed on https://www.ebi.ac.uk with the Accession number PRJEB56301 before publication.

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