Special Issue "Genomics Applied to Conservation of Farm Animal Genetic Diversity"

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 Editor

Dr. Kor Oldenbroek
E-Mail Website
Guest Editor
Animal Breeding and Genomics and Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands
Interests: animal breeding; farm animals; genetic resources; genetic diversity; inbreeding; in vivo and in vitro conservation

Special Issue Information

Dear Colleagues,

Genomic tools (e.g., SNP genotyping, whole-genome sequencing) and genomic analysis can be applied to improve the decisions made in the conservation of farm animal genetic diversity. Conservation of genetic diversity, both among and within breeds, is a costly process. Choices for conservation in vivo (keeping a small population alive) or in vitro (gene banks) of a breed and the animals within breeds require sound genetic research. In the past, this could only be based on the history of breeds and pedigree analysis. Nowadays, genomic information is the standard for the choices to be made in conservation. Genomics may accurately measure the genetic distances among breeds and the relationships among animals within breeds. In addition, genomics can be used to detect potentially valuable rare alleles and haplotypes and their carriers in these breeds. This Special Issue aims to present genomic research that answers the question of what we need to conserve now for possible utilization in the future.

Dr. Kor Oldenbroek
Guest Editor

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

  • SNP genotyping
  • whole-genome sequencing
  • decisions for conservation
  • in vivo and in vitro conservation
  • genetic distances among breeds
  • relationships among animals
  • rare alleles and haplotypes

Published Papers (2 papers)

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Research

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Article
Unraveling the Genetic Diversity and Population Structure of Bangladeshi Indigenous Cattle Populations Using 50K SNP Markers
Animals 2021, 11(8), 2381; https://doi.org/10.3390/ani11082381 - 12 Aug 2021
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Abstract
Understanding the genetic basis of locally adapted indigenous cattle populations is essential to design appropriate strategies and programs for their genetic improvement and conservation. Here, we report genetic diversity measures, population differentiation, and structure of 218 animals sampled from six indicine cattle populations [...] Read more.
Understanding the genetic basis of locally adapted indigenous cattle populations is essential to design appropriate strategies and programs for their genetic improvement and conservation. Here, we report genetic diversity measures, population differentiation, and structure of 218 animals sampled from six indicine cattle populations of Bangladesh. Animals were genotyped with Illumina Bovine SNP50K BeadChip along with genotyped data of 505 individuals included from 19 zebu and taurine breeds worldwide. The principal component analysis (PCA) showed clear geographic separation between taurine and indicine lineages where Bangladeshi indigenous cattle clustered with South Asian zebu populations. However, overlapped clusters in PCA, heterozygosity estimates, and Neighbor-Joining phylogenetic tree analysis revealed weak genetic differentiation among the indigenous cattle populations of Bangladesh. The admixture analysis at K = 5 and 9 suggests distinct genetic structure of the studied populations along with 1 to 4% of taurine ancestry. The effective population size suggested a limited pool of ancestors particularly for Sahiwal and North Bengal Grey cattle. In conclusion, these findings shed insights into the genetic architecture of six indigenous cattle populations of Bangladesh for the first time and suggested as distinct gene pools without potential admixture with zebu or taurine populations. Full article
(This article belongs to the Special Issue Genomics Applied to Conservation of Farm Animal Genetic Diversity)
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Review

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Review
An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds
Animals 2021, 11(7), 2016; https://doi.org/10.3390/ani11072016 - 06 Jul 2021
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Abstract
Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on [...] Read more.
Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds. Full article
(This article belongs to the Special Issue Genomics Applied to Conservation of Farm Animal Genetic Diversity)
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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.

1. Title: An overview about the use of genotyping techniques for assessing genetic diversity in local farm animal breeds
Article type: Review
Author: Dr. Anna Olschewsky, Prof. Dr. Dirk Hinrichs
Abstract (Draft): The number of local farm animal breeds is declining worldwide. However, these breeds provide a high amount of genetic diversity that is worth being conserved to handle future challenges. For assessing genetic diversity, various genotyping techniques have been developed. Based on genomic information different parameters can be measured that shed light on between- and within-breed diversity. These two fields should be considered when prioritizing breeds for conservation. The aim of the present work was to determine which genotyping techniques have been used and which diversity parameters were analyzed using which programs. A total of 133 studies from the Asian, European, African and American continents were reviewed that examined genetic diversity in local sheep, goat, cattle, pig and chicken breeds. The results show that over time almost all available genotyping techniques were used. Based on this, many different parameters of genetic diversity were calculated with a large variety of different programs. Therefore, the present results provide for the first time a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds with high genetic diversity.

2. Author: Ina Hulsegge
   Abstarct: Genome-wide inbreeding as a consequence of a sharp reduction in numbers and selection in the DF cattle population Genetic diversity is an important characteristic of populations, as it is required to adapt a population to changing environments and human demands. Over the last century, genetic diversity in European cattle species has been affected by the replacement of many locally developed breeds with a few high-performance breeds. The predominant selection of cattle from specialized dairy breeds caused a sharp decline in the population size of locally developed breeds. In the Netherlands the local Dutch Friesian (DF) breed has gradually been replaced by Holstein Friesian (HF), between 1970 and 1990. The objective of this study is to determine the effect of the sharp reduction in population size and selection on genetic diversity and on the other hand the maintenance of genetic diversity by conservation of DF. Genetic material of 12 historic (1961-1989) and 12 recent (2003-2015) DF sires and 12 recent HF sires in the Netherlands (1998-2014) was sequenced. The latter were added to compare the diversity in DF groups with the diversity in the high productive HF breed. Genomic inbreeding coefficients were estimated based on runs of homozygosity (ROH) analysis using PLINK. Lower genomic diversity and more inbreeding were observed in recent DF than historic DF and recent HF, illustrating the effects if reduction in size and selection in the DF breed. The analysis by chromosome showed a higher level of genomic inbreeding (Froh) in recent DF in 19 chromosomes. HF showed at chromosome 25 the highest Froh. The results are of importance because they will help design and implement breeding programs and conservation strategies.

3. Title: SNPs in sheep: Characterization of Lithuanian sheep populations
   Authors: Rūta Šveistienė, Miika Tapio 
   Abstarct: In Lithuania there are two recognized native sheep breeds: old native Lithuanian Coarsewooled and Lithuanian Blackface. In addition, 2005 a primitive Heidschnucke type Skudden sheep has been imported to Lithuania and argued to possibly represent a lost Lithuanian sheep type. The aim of the study was to investigate the genetic variation in the two Lithuanian native sheep breeds, compare them with the imported and theoretically close by origin Skudden sheep and establish the historical patterns of admixture and genetic relatedness of Lithuanian sheep breeds with British, Central European and Nordic sheep breeds included in the SheepHapMap study. A total of 72 individuals, representing old Lithuanian Native Coarsewooled sheep breed, modern Lithuanian Blackface and imported Skudde sheep breed, were genotyped using Neogen 12K Illumina Infinium chip. The population analysis was carried out by including only the mapped markers also available in SheepHapMap SNP data to enable comparison. Model-based clustering, principal component analysis and neighbor net analysis show similar patterns for the Lithuanian sheep populations.  Lithuanian Coarsewooled and Skudden in Lithuania both have unique divergence and possibly some shared ancestry with exotic heritage breeds, while the Lithuanian Blackface conforms a modern synthetic breed. Compared to the earlier microsatellite based analyses of a different sample of the Lithuanian Coarsewooled, the breed appeared more unique and less variable. The study showed clearly that the Coarsewooled and the Skudde are distinct from each other. Historical data strongly suggests the Coarsewooled to present a local breed, while the Skudde orgin is less directly linked to the geographical area of modern-day Lithuania. The absence of clear genetic similarity suggest the possible Lithuanian Heidschnucke type sheep contribution to the Skudde might not have been significant. Therefore, within the modern-day Lithuanian context, the Lithuanian Coarsewooled Sheep is the more important historical sheep type for conservation.


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