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Molecular Markers in Wildlife and Livestock Animals in the Genomics...
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Molecular Markers in Wildlife and Livestock Animals in the Genomics Era

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

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 14269

Special Issue Editor

Prof. Dr. Zissis Mamuris

E-Mail Website
Guest Editor
Department of Biochemistry and Biotechnology, University of Thessaly, 41221 Larissa, Greece
Interests: population genetics; biodiversity; evolution; molecular markers; animal genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The development of molecular markers the last decades have paved the way in answering major questions in the field of genetics; unravelling the evolution patterns of lineages and allowing a more robust species’ delimitation; pinpointing genes implicated in local adaptation; describing in detail the population’s genetics and dynamics; revealing the genomic regions that are associated with phenotypic traits and enabling the development of more accurate selections schemas in livestock breeds; mapped the breadth of the genetic biodiversity that is present in animal populations.

The available “toolkit” for the selection of appropriate molecular markers has grown enormously big in the last twenty years, with the advent of Next Generation Sequencing methods coupled with advanced bioinformatics tools. As a result, every year, more and more genomes from non-model species are sequenced and deposited in public repositories, and scientists have the opportunity to select markers from a genome-wide perspective and genotype a massive number of them in large populations in a short period of time with the application of available techniques. These approaches have enabled a more granular characterization of animal genetic diversity to address even the most complex challenges in animal conservation. The climate change, a threatening factor and a major challenge for the majority of the animal species, imposes a new dimension in animal conservation that can only be tackled by identifying and harnessing the underlying genetic diversity.

Prof. Dr. Zissis Mamuris
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 submissions that pass pre-check are 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 semimonthly 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 2400 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

  • molecular markers
  • genomics
  • diversity
  • conservation
  • breeding

Published Papers (4 papers)

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Research

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12 pages, 974 KiB  
Article
Molecular Assessments, Statistical Effectiveness Parameters and Genetic Structure of Captive Populations of Tursiops truncatus Using 15 STRs
by Rocío Gómez, Rocío M. Neri-Bazán, Araceli Posadas-Mondragon, Pablo A. Vizcaíno-Dorado, Jonathan J. Magaña and José Leopoldo Aguilar-Faisal
Animals 2022, 12(14), 1857; https://doi.org/10.3390/ani12141857 - 21 Jul 2022
Viewed by 1469
Abstract
Genetic analysis is a conventional way of identifying and monitoring captive and wildlife species. Knowledge of statistical parameters reinforcing their usefulness and effectiveness as powerful tools for preserving diversity is crucial. Although several studies have reported the diversity of cetaceans such as Tursiops [...] Read more.
Genetic analysis is a conventional way of identifying and monitoring captive and wildlife species. Knowledge of statistical parameters reinforcing their usefulness and effectiveness as powerful tools for preserving diversity is crucial. Although several studies have reported the diversity of cetaceans such as Tursiops truncatus using microsatellites, its informative degree has been poorly reported. Furthermore, the genetic structure of this cetacean has not been fully studied. In the present study, we selected 15 microsatellites with which 210 dolphins were genetically characterized using capillary electrophoresis. The genetic assertiveness of this set of hypervariable markers identified one individual in the range of 6.927e13 to 1.806e16, demonstrating its substantial capability in kinship relationships. The genetic structure of these 210 dolphins was also determined regarding the putative capture origin; a genetic stratification (k = 2) was found. An additional dolphin group of undetermined origin was also characterized to challenge the proficiency of our chosen markers. The set of markers proposed herein could be a helpful tool to guarantee the maintenance of the genetic diversity rates in conservation programs both in Tursiops truncatus and across other odontocetes, Mysticeti and several genera of endangered and vulnerable species. Full article
(This article belongs to the Special Issue Molecular Markers in Wildlife and Livestock Animals in the Genomics Era)
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11 pages, 864 KiB  
Article
A 20-SNP Panel as a Tool for Genetic Authentication and Traceability of Pig Breeds
by Riccardo Moretti, Andrea Criscione, Federica Turri, Salvatore Bordonaro, Donata Marletta, Bianca Castiglioni and Stefania Chessa
Animals 2022, 12(11), 1335; https://doi.org/10.3390/ani12111335 - 24 May 2022
Cited by 3 | Viewed by 1722
Abstract
Food authentication in local breeds has important implications from both an economic and a qualitative point of view. Meat products from autochthonous breeds are of premium value, but can easily incur fraudulent or accidental substitution or mislabeling. The aim of this study was [...] Read more.
Food authentication in local breeds has important implications from both an economic and a qualitative point of view. Meat products from autochthonous breeds are of premium value, but can easily incur fraudulent or accidental substitution or mislabeling. The aim of this study was to identify a small number of SNPs using the Illumina PorcineSNP60 BeadChip for breed traceability, in particular of the Italian Nero Siciliano pig and its derived products. A panel of 12 SNPs was sufficient to discriminate Nero Siciliano pig from cosmopolitan breeds and wild boars. After adding 8 SNPs, the final panel of 20 SNPs allowed us to discriminate all the breeds involved in the study, to correctly assign each individual to its breed, and, moreover, to discriminate Nero Siciliano from first-generation hybrids. Almost all livestock breeds are being genotyped with medium- or high-density SNP panels, providing a large amount of information for many applications. Here, we proposed a method to select a reduced SNP panel to be used for the traceability of pig breeds. Full article
(This article belongs to the Special Issue Molecular Markers in Wildlife and Livestock Animals in the Genomics Era)
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16 pages, 4613 KiB  
Article
Comparative Expression Profiling and Sequence Characterization of ATP1A1 Gene Associated with Heat Tolerance in Tropically Adapted Cattle
by Muhammed Elayadeth-Meethal, Aravindakshan Thazhathu Veettil, Muhasin Asaf, Sathiamoorthy Pramod, Shane K. Maloney, Graeme B. Martin, M. Jordana Rivero, Veerasamy Sejian, Punnoth Poonkuzhi Naseef, Mohamed Saheer Kuruniyan and Michael R. F. Lee
Animals 2021, 11(8), 2368; https://doi.org/10.3390/ani11082368 - 11 Aug 2021
Cited by 10 | Viewed by 4593
Abstract
Climate change is an imminent threat to livestock production. One adaptation strategy is selection for heat tolerance. While it is established that the ATP1A1 gene and its product play an important role in the response to many stressors, there has been no attempt [...] Read more.
Climate change is an imminent threat to livestock production. One adaptation strategy is selection for heat tolerance. While it is established that the ATP1A1 gene and its product play an important role in the response to many stressors, there has been no attempt to characterize the sequence or to perform expression profiling of the gene in production animals. We undertook a field experiment to compare the expression profiles of ATP1A1 in heat-tolerant Vechur and Kasaragod cattle (Bos taurus indicus) with the profile of a heat-susceptible crossbreed (B. t. taurus × B. t. indicus). The cattle were exposed to heat stress while on pasture in the hot summer season. The environmental stress was quantified using the temperature humidity index (THI), while the heat tolerance of each breed was assessed using a heat tolerance coefficient (HTC). The ATP1A1 mRNA of Vechur cattle was amplified from cDNA and sequenced. The HTC varied significantly between the breeds and with time-of-day (p < 0.01). The breed–time-of-day interaction was also significant (p < 0.01). The relative expression of ATP1A1 differed between heat-tolerant and heat-susceptible breeds (p = 0.02). The expression of ATP1A1 at 08:00, 10:00 and 12:00, and the breed–time-of-day interaction, were not significant. The nucleotide sequence of Vechur ATP1A1 showed 99% homology with the B. t. taurus sequence. The protein sequence showed 98% homology with B. t. taurus cattle and with B. grunniens (yak) and 97.7% homology with Ovis aries (sheep). A molecular clock analysis revealed evidence of divergent adaptive evolution of the ATP1A1 gene favoring climate resilience in Vechur cattle. These findings further our knowledge of the relationship between the ATP1A1 gene and heat tolerance in phenotypically incongruent animals. We propose that ATP1A1 could be used in marker assisted selection (MAS) for heat tolerance. Full article
(This article belongs to the Special Issue Molecular Markers in Wildlife and Livestock Animals in the Genomics Era)
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Review

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20 pages, 784 KiB  
Review
Genomics of Adaptations in Ungulates
by Vivien J. Chebii, Emmanuel A. Mpolya, Farai C. Muchadeyi and Jean-Baka Domelevo Entfellner
Animals 2021, 11(6), 1617; https://doi.org/10.3390/ani11061617 - 29 May 2021
Cited by 2 | Viewed by 4408
Abstract
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and [...] Read more.
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats. Full article
(This article belongs to the Special Issue Molecular Markers in Wildlife and Livestock Animals in the Genomics Era)
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