Special Issue "High Throughput Technique use in Animal Genetics and Genomics"

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 October 2021.

Special Issue Editors

Dr. Tomasz Szmatola
E-Mail Website1 Website2
Guest Editor
Center for Experimental and Innovative Medicine, University of Agriculture in Kraków, Rędzina 1C, 30-248 Kraków, Poland
Interests: genomics; bioinformatics; runs of homozygosity; microarray; NGS; transcriptomics
Dr. Artur Gurgul
E-Mail Website1 Website2
Guest Editor
Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland
Interests: genomics; microarray; NGS; population genetics; cattle
Dr. Ewa Ocłoń
E-Mail Website1 Website2
Guest Editor
Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland
Interests: genomics; recombinant proteins; cell cultures; miRNA; nutritional/metabolic diseases
Dr. Klaudia Pawlina-Tyszko
E-Mail Website
Guest Editor
Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083 Balice n., Kraków, Poland
Interests: genomics; miRNA; cell cultures; CNV; transcriptomics; sarcoids

Special Issue Information

Dear Colleagues,

Over the past few decades, there has been a rapid development of high-throughput genome analysis methods, including next-generation sequencing (NGS) and genotyping microarrays. These methods allow for genome- or population-scale screening of single nucleotide polymorphisms (SNPs), insertions or deletions (INDELs), and copy number variations (CNVs) as well as genome-scale gene expression analysis. Methods based on NGS can also be used for various de novo sequencing applications, including sequencing of unknown genomes or transcriptomes, and the discovery of unknown sequence variants and new splice sites that can be utilized, e.g., for more accurate gene expression analysis. All of these applications are particularly useful in animal genomics to explore animal genome functionality and diversity under difficult conditions of constant artificial selection, which strongly reduces genetic variation. Animal genomics receives much less attention than aspects of the human genome but seems to be more challenging as more dynamic changes in the population structure and living conditions are expected for breeding animals. The most interesting topics in animal genomics appear to be the ones revealing the structure of the genome (particularly in species without a known genome), analyzing a population’s genetic structure, mapping quantitative trait loci, and identifying disease-related variants and genome responses to inbreeding and artificial selection. Additionally, the use of animal models in understanding human diseases should not be forgotten, nor should all other functional studies that aim to elucidate genotype expression at the mRNA, protein, and general phenotype level.

The aim of this Special Issue is to present original research articles and reviews utilizing/concerned with various high-throughput techniques in regard to animal genomics and genetics, particularly research focused on population genetics, genome/transcriptome assembly, quantitative trait loci mapping, disease variant detection, and all aspects of genome functional annotation.

Dr. Tomasz Szmatola
Dr. Artur Gurgul
Dr. Ewa Ocłoń
Dr. Pawlina Klaudia
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • NGS
  • microarray
  • high-throughput techniques
  • selection
  • transcriptome
  • genome

Published Papers

This special issue is now open for submission, see below for planned papers.

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: The contribution of wssGBLUP method for genomic breeding values prediction for linear type traits in Holstein cattle
Authors: Michaela Brzáková; Jiří Bauer; Jiří Šplíchal; Josef Přibyl
Affiliation: Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 01 Prague, Czech Republic
Abstract: The forthcoming study compares the genomic breeding value predicted by ssGBLUP (single step GBLUP) and wssGBLUP (weighted single-step GBLUP). There is an assumption that the wssGBLUP method may increase the accuracy of GEBV. The validation test for genomic evaluation between GEBVs was made according to Mäntysaari, et al. (2010). The first results show that the GEPH prediction using the wssGBLUP provides higher accuracy of GEBV compared to ssGBLUP. The study will compare the contribution of the wssGBLUP method for GEBV for 25 exterior characteristics of Holstein cattle with different heritability coefficients (low to high). In this study, the 50K DNA chip was used. During the prediction of GEBV, the weights of individual SNPs are estimated. There are several approaches how to estimates SNPs weights. Based on current results, the most suitable is a nonlinear method that provides relatively stable SNP weights over many iterations. Depending on the length of study, it is also possible to include (if they will be found) significant SNPs for exterior traits. However, the main aim is to compare both method's suitability for 25 exterior traits with different heritability in Holstein cattle.

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