Inside the Genetics and Genomics of Variability and Functionality in Vertebrates: Current Applications and Perspectives

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 August 2021) | Viewed by 16696

Special Issue Editors


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Guest Editor
Animal Breeding and Genetics, Department of Veterinary Medicine, University of Bari "Aldo Moro", SP. 62 per Casamassima km. 3, 70010 Valenzano (BA), Italy
Interests: genomics; animal genetics; animal breeding

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Guest Editor
Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Italy
Interests: livestock population genetics and genomics; conservation genetics
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Special Issue Information

Dear Colleagues,

In the last years, applications of genetics and genomics have entered the study of vertebrates due not only to the availability of platforms that allow rapid and affordable study of the DNA sequence and its variation, with the possibility of generating amount of information that was unthinkable up to a few years ago, but also to the exponential growth of statistical and information technology (IT) applications that allow managing and maximizing the available information. The challenge in the post-genomic era is extracting functional or evolutionary inferences from DNA data. Simultaneously, tools such as microsatellites, although scaled down in use, continue to be used for the study of the structure and variability of animal populations, especially when updated technical and adequate economic means are not available.

In this Special Issue, we propose a collection of works on the possible applications of genetics and genomics to the various fields of the study of vertebrate populations (both domestic and wild), with particular attention to those applications aimed at current issues of climate change, conservation, and sustainable management and improvement of genetic resources.

Dr. Vincenzo Landi
Dr. Elena Ciani
Guest Editors

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Keywords

  • Single nucleotide polymorphisms (SNPs)
  • Microsatellites (short tandem repeats, STRs)
  • Copy number variations (CNVs)
  • Selection signatures
  • Functional genomics
  • Gene flow Admixture
  • Phylogeography

Published Papers (5 papers)

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Research

15 pages, 2437 KiB  
Article
Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland
by Angelika Podbielska, Katarzyna Piórkowska and Tomasz Szmatoła
Animals 2021, 11(8), 2193; https://doi.org/10.3390/ani11082193 - 23 Jul 2021
Cited by 3 | Viewed by 5239
Abstract
This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult [...] Read more.
This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999. Full article
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9 pages, 257 KiB  
Article
Genetic Association Analysis for Relative Growths of Body Compositions and Metabolic Traits to Body Weights in Broilers
by Ying Zhang, Hengyu Zhang, Yunfeng Zhao, Xiaojing Zhou, Jie Du and Runqing Yang
Animals 2021, 11(2), 469; https://doi.org/10.3390/ani11020469 - 10 Feb 2021
Cited by 1 | Viewed by 1775
Abstract
In animal breeding, body components and metabolic traits always fall behind body weights in genetic improvement, which leads to the decline in standards and qualities of animal products. Phenotypically, the relative growth of multiple body components and metabolic traits relative to body weights [...] Read more.
In animal breeding, body components and metabolic traits always fall behind body weights in genetic improvement, which leads to the decline in standards and qualities of animal products. Phenotypically, the relative growth of multiple body components and metabolic traits relative to body weights are characterized by using joint allometric scaling models, and then random regression models (RRMs) are constructed to map quantitative trait loci (QTLs) for relative grwoth allometries of body compositions and metabolic traits in chicken. Referred to as real joint allometric scaling models, statistical utility of the so-called LASSO-RRM mapping method is given a demonstration by computer simulation analysis. Using the F2 population by crossing broiler × Fayoumi, we formulated optimal joint allometric scaling models of fat, shank weight (shank-w) and liver as well as thyroxine (T4) and glucose (GLC) to body weights. For body compositions, a total of 9 QTLs, including 4 additive and 5 dominant QTLs, were detected to control the allometric scalings of fat, shank-w, and liver to body weights; while a total of 10 QTLs of which 6 were dominant, were mapped to govern the allometries of T4 and GLC to body weights. We characterized relative growths of body compositions and metabolic traits to body weights in broilers with joint allometric scaling models and detected QTLs for the allometry scalings of the relative growths by using RRMs. The identified QTLs, including their highly linked genetic markers, could be used to order relative growths of the body components or metabolic traits to body weights in marker-assisted breeding programs for improving the standard and quality of broiler meat products. Full article
12 pages, 3680 KiB  
Article
Study on the Function and Mechanism of Lin28B in the Formation of Chicken Primordial Germ Cells
by Qisheng Zuo, Jing Zhou, Man Wang, Yani Zhang, Guohong Chen and Bichun Li
Animals 2021, 11(1), 43; https://doi.org/10.3390/ani11010043 - 28 Dec 2020
Cited by 2 | Viewed by 1939
Abstract
Lin28A and Lin28B are two homologues of the same family of RNA binding proteins (RBPs). The function and molecular mechanism of Lin28A in the formation of primordial germ cells (PGCs) are very clear, but the related research on Lin28B is rarely reported. Here, [...] Read more.
Lin28A and Lin28B are two homologues of the same family of RNA binding proteins (RBPs). The function and molecular mechanism of Lin28A in the formation of primordial germ cells (PGCs) are very clear, but the related research on Lin28B is rarely reported. Here, we found that the overexpression of Lin28B can promote the formation of PGC in vivo. Furthermore, the overexpression of Lin28B also resulted in the inhibition of totipotency gene expression and upregulated the PGCs marker genes, and a significant increase in the number of PGCs in genital ridge, as detected by Periodic Acid-Schiff(PAS) staining. However, the inhibited Lin28B expression showed completely opposite results, which were confirmed on the PGC induction model in vitro. Mechanistically, we found that the overexpression of Lin28B can inhibit the maturation of let-7a-3p, and the results of high-throughput sequencing indicated that let-7a-3p was a negative regulator of the formation process of PGCs. Therefore, we conclude that our results determine that Lin28B participates in the formation of PGCs through let-7a-3p, which set a theoretical foundation for improving the function and mechanism of Lin28 family in the formation of PGCs. Full article
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15 pages, 2089 KiB  
Article
Mitochondrial DNA Variations in Colombian Creole Sheep Confirm an Iberian Origin and Shed Light on the Dynamics of Introduction Events of African Genotypes
by Herman Alberto Revelo, Diana López-Alvarez, Vincenzo Landi, Lauden Rizzo and Luz Angela Alvarez
Animals 2020, 10(9), 1594; https://doi.org/10.3390/ani10091594 - 8 Sep 2020
Cited by 9 | Viewed by 2742
Abstract
The genetic origins and diversity of Creole sheep from five regions of Colombia were investigated based on mitochondrial DNA (mtDNA) variations across 89 sequences from five breeds: one wool Creole sheep (CL) and four hair Creole sheep, including Ethiopian (OPCE), Sudan [...] Read more.
The genetic origins and diversity of Creole sheep from five regions of Colombia were investigated based on mitochondrial DNA (mtDNA) variations across 89 sequences from five breeds: one wool Creole sheep (CL) and four hair Creole sheep, including Ethiopian (OPCE), Sudan (OPCS), Pelibuey (OPCP) and Wayúu (OPCW). A global comparison was done using 62 haplotypes from Iberian, African, Indian, Caribbean, Mexican, Caucasian and European sheep based on sequences retrieved from GenBank. This study aimed to identify the maternal origin of Colombian Creole sheep and their genetic relationships at a global level. The results showed 31 different haplotypes from Colombian Creole sheep, which can be assigned to maternal lineage B, the most common lineage found in European sheep breeds and the only one found in several Iberian breed (e.g., Churra, Spanish Merino) that most likely participated in the Creole formation. Additional analyses showed that wool and hair sheep retained a broad genetic identity despite being geographically separated. The global-level phylogenetic analysis revealed that Colombian Creole sheep belong to a distinct and defined genetic lineage that is likely the result of a founder effect with ecotypes of Iberian descent and the subsequent introduction of foreign breeds. This is consistent with historical reports on the presence of sheep in South America and, particularly, Colombia. Full article
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20 pages, 5013 KiB  
Article
Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores
by Andreia J. Amaral, Ana L. Pavão and Luis T. Gama
Animals 2020, 10(6), 1089; https://doi.org/10.3390/ani10061089 - 24 Jun 2020
Cited by 5 | Viewed by 3440
Abstract
Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions [...] Read more.
Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions harboring contiguous homozygous genotypes named runs of homozygosity (ROH), and to estimate past effective population size by analysis of linkage disequilibrium (LD). Genetic markers associated with production traits were also investigated, exploiting the unique genetic and adaptation features of this breed. A total of 639 ROH with length >4 Mb were identified, with mean length of 14.96 Mb. The mean genomic inbreeding was 0.09, and long segments of ROH were common, indicating recent inbred matings. The LD pattern indicates a large effective population size, suggesting the inflow of exotic germplasm in the past. The genome-wide association study identified novel markers significantly affecting longevity, age at first calving and direct genetic effects on calf weight. These results provide the first evidence of the association of longevity with genes related with DNA recognition and repair, and the association of age at first calving with aquaporin proteins, which are known to have a crucial role in reproduction. Full article
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