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Genomic Variability in Autochthonous and Specialized Livestock Populations

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

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 34830

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Special Issue Editors

Dr. Maria Giuseppina Strillacci

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Guest Editor

Department of Veterinary Medicine, Università Degli Studi di Milano, Milan, Italy
Interests: animal breeding and genetics; biodiversity; animal genomics; genetic and disease

Prof. Dr. Alessandro Bagnato

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Guest Editor

Department of Veterinary Medicine, Università Degli Studi di Milano, Milan, Italy
Interests: animal genomics; genetic improvement; zootechnics; biodiversity

Special Issue Information

Dear Colleagues,

This special issue aims to collect studies that disclose the effect of natural selection and selective breeding on genomic variation in local and specialized livestock populations.

Many generations of natural selection and, in more recent time, of human controlled selective breeding generated a large number of livestock populations and breeds adapted to cope with a wide range of disease, parasite and environmental challenges including extreme climate conditions.

The value of the animal genetic diversity and the ability of autochthonous breeds to produce in challenging environmental conditions, as in rangeland, has been extensively recognized. On the other hand, in the last century specialized cosmopolitan livestock populations have been strongly selected to efficiently produce in artificial and controlled environments.

The increasing availability of structural genomic information in small autochthonous populations (i.e. SNP chip and WGS data) can be used to disclose the specificity and uniqueness of their genomic structural variation compared to the specialized cosmopolitan ones.

We believe that a collection of studies raising evidences on genomic peculiarities of autochthonous and specialized breeds can represent a value for the overall scientific and farming communities.

Dr. Maria Giuseppina Strillacci
Prof. Dr. Alessandro Bagnato
Guest Editors

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Keywords

Animal genetic resources
Autochthonous breeds
Specialized breeds
Genetic variability
Adaptation
Selective breeding
Biodiversity
SNP data
WGS data

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Published Papers (10 papers)

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Research

16 pages, 2028 KiB

Open AccessArticle

One Health and Cattle Genetic Resources: Mining More than 500 Cattle Genomes to Identify Variants in Candidate Genes Potentially Affecting Coronavirus Infections

by Samuele Bovo, Giuseppina Schiavo and Luca Fontanesi

Animals 2022, 12(7), 838; https://doi.org/10.3390/ani12070838 - 26 Mar 2022

Cited by 1 | Viewed by 2273

Abstract

Epidemiological and biological characteristics of coronaviruses and their ability to cross species barriers are a matter of increasing concerns for these zoonotic agents. To prevent their spread, One Health approaches should be designed to include the host (animal) genome variability as a potential risk factor that might confer genetic resistance or susceptibility to coronavirus infections. At present, there is no example that considers cattle genetic resources for this purpose. In this study, we investigated the variability of six genes (ACE2, ANPEP, CEACAM1 and DPP4 encoding for host receptors of coronaviruses; FURIN and TMPRSS2 encoding for host proteases involved in coronavirus infection) by mining whole genome sequencing datasets from more than 500 cattle of 34 Bos taurus breeds and three related species. We identified a total of 180 protein variants (44 already known from the ARS-UCD1.2 reference genome). Some of them determine altered protein functions or the virus–host interaction and the related virus entry processes. The results obtained in this study constitute a first step towards the definition of a One Health strategy that includes cattle genetic resources as reservoirs of host gene variability useful to design conservation and selection programs to increase resistance to coronavirus diseases. Full article

(This article belongs to the Special Issue Genomic Variability in Autochthonous and Specialized Livestock Populations)

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14 pages, 8860 KiB

Open AccessArticle

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

by Rosalia Di Gerlando, Salvatore Mastrangelo, Marco Tolone, Ilaria Rizzuto, Anna Maria Sutera, Angelo Moscarelli, Baldassare Portolano and Maria Teresa Sardina

Animals 2022, 12(2), 217; https://doi.org/10.3390/ani12020217 - 17 Jan 2022

Cited by 12 | Viewed by 2677

Abstract

Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome. Full article

(This article belongs to the Special Issue Genomic Variability in Autochthonous and Specialized Livestock Populations)

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11 pages, 3779 KiB

Open AccessArticle

Genetic Variation in the Prion Protein Gene (PRNP) of Two Tunisian Goat Populations

by Samia Kdidi, Mohamed Habib Yahyaoui, Michela Conte, Barbara Chiappini, Mohamed Hammadi, Touhami Khorchani and Gabriele Vaccari

Animals 2021, 11(6), 1635; https://doi.org/10.3390/ani11061635 - 31 May 2021

Cited by 5 | Viewed by 4648

Abstract

Scrapie is a fatal prion disease. It belongs to transmissible spongiform encephalopathies (TSEs), and occurs in sheep and goats. Similarly, to ovine species, the prion protein gene (PRNP) plays a major role in conferring resistance or susceptibility to TSE in goats. This study assesses the variability of PRNP in native and crossed-breed goat populations raised in the Southeast of Tunisia and provides information on the distribution of PRNP haplotypes and genotypes in these goat populations. A total of 116 unrelated goats including 82 native and 34 crossed-breed goats were screened for PRNP polymorphisms using Sanger sequencing. Sequence analysis revealed 10 non-synonymous polymorphisms (G37V, M137I, R139S, I142M, H143R, N146D, R154H, R211Q, Q222K, and S240P), giving rise to 12 haplotypes and 23 genotypes. Moreover, four silent mutations were detected at codons 30, 42, 138, and 179; the former was reported for the first time in goat (nucleotide 60 c→t). Interestingly, the PrP variants associated with resistance (D146 and K222) or with a prolonged incubation time of goat to scrapie (M142, R143, H154, Q211) were absent or detected with low frequencies except for H154 variant, which is present with high frequency (1%, 1%, 4%, 0%, 88%, and 6%, respectively, for native goats, and 0%, 1%, 0%, 1%, 78%, and 1%, respectively, for crossed goats). The analysis of PRNP polymorphisms of goats raised in other regions of the country will be useful in getting a global view of PRNP genetic variability and the feasibility of goat breeding programs in Tunisia. Full article

(This article belongs to the Special Issue Genomic Variability in Autochthonous and Specialized Livestock Populations)

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11 pages, 1013 KiB

Open AccessArticle

Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

by Salvatore Mastrangelo, Rosalia Di Gerlando, Maria Teresa Sardina, Anna Maria Sutera, Angelo Moscarelli, Marco Tolone, Matteo Cortellari, Donata Marletta, Paola Crepaldi and Baldassare Portolano

Animals 2021, 11(6), 1510; https://doi.org/10.3390/ani11061510 - 23 May 2021

Cited by 17 | Viewed by 3066

Abstract

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource. Full article

(This article belongs to the Special Issue Genomic Variability in Autochthonous and Specialized Livestock Populations)

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15 pages, 11104 KiB

Open AccessArticle

Redefinition of the Mora Romagnola Pig Breed Herd Book Standard Based on DNA Markers Useful to Authenticate Its “Mono-Breed” Products: An Example of Sustainable Conservation of a Livestock Genetic Resource

by Silvia Tinarelli, Anisa Ribani, Valerio Joe Utzeri, Valeria Taurisano, Claudio Bovo, Stefania Dall’Olio, Francesco Nen, Samuele Bovo, Giuseppina Schiavo, Maurizio Gallo and Luca Fontanesi

Animals 2021, 11(2), 526; https://doi.org/10.3390/ani11020526 - 18 Feb 2021

Cited by 16 | Viewed by 3565

Abstract

Mora Romagnola is an autochthonous pig breed, raised in the north of Italy. Mono-breed pork products of this breed are part of important niche value chain that is intrinsically linked to the conservation of this local genetic resources that can only survive due to the premium price that these products can obtain on the market. However, the added value attracts fraudsters that unscrupulously sell mis-labelled Mora Romagnola products, causing consumer distrust that, in turn, undermines the conservation strategy of this breed. To monitor and better characterise this local breed, we phenotyped 826 Mora Romagnola pigs for three breed-specific traits. Then, we genotyped almost all living sows and boars registered to the Herd Book (n. = 357 animals) for polymorphisms in the MC1R and NR6A1 genes (affecting coat colour and vertebral number, respectively). The results were used to re-define the breed descriptors of the Mora Romagnala breed that included information on the allowed genotypes at these two genes. A few pigs that did not carry the allowed genotypes were excluded from its Herd Book. Finally, we evaluated the usefulness of these DNA markers to authenticate Mora Romagnola meat against meat derived from other 11 pig breeds and wild boars. To our knowledge, the Mora Romagnola Herd Book is one of the first examples that established a direct link between a genetic standard of a breed with the possibility to authenticate mono-breed products using DNA markers with the specific purpose to combat frauds and, indirectly, support the conservation of a livestock genetic resource. Full article

(This article belongs to the Special Issue Genomic Variability in Autochthonous and Specialized Livestock Populations)

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13 pages, 1215 KiB

Open AccessArticle

Copy Number Variants in Four Italian Turkey Breeds

by Maria Giuseppina Strillacci, Stefano Paolo Marelli, Raffaella Milanesi, Luisa Zaniboni, Chiara Punturiero and Silvia Cerolini

Animals 2021, 11(2), 391; https://doi.org/10.3390/ani11020391 - 3 Feb 2021

Cited by 9 | Viewed by 2423

Abstract

Heritage breeds can be considered a genetic reservoir of genetic variability to be conserved and valorized considering their historical, cultural, and adaptive characteristics and possibly for their high potential in commercial hybrid genetic improvement by gene introgression. The aim of the present research is to investigate via Copy Number Variant (CNVs) the genomic makeup of 4 Italian autochthonous turkey breeds (Bronzato Comune—BrCI, 24; Ermellinato di Rovigo—ErRo, 24; Parma e Piacenza—PrPc, 25; Romagnolo—RoMa, 29). CNVs detection was performed using two different software and an interbreed CNVs comparison was carried out. A total of 1077 CNVs were identified in 102 turkeys, summarized into 519 CNV regions (CNVRs), which resulted after merging in 101 and 18 breed and shared regions. Biodiversity was analyzed using the effective information supplied by CNVs analysis, and BrCI and ErRo were characterized by a low mapped CNV number. Differences were described at a genomic level related to physiological, reproductive, and behavioral traits. The comparison with other three Italian turkey breeds (Brianzolo, Colle Euganei, and Nero Italiano) using a CNV data set available in the literature showed high clustering properties at the genomic level, and their relationships are strictly linked to the geographical origin and to the history of the rural structure of their native regions. Full article

(This article belongs to the Special Issue Genomic Variability in Autochthonous and Specialized Livestock Populations)

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14 pages, 2345 KiB

Open AccessArticle

Population Structure Assessed Using Microsatellite and SNP Data: An Empirical Comparison in West African Cattle

by Isabel Álvarez, Iván Fernández, Amadou Traoré, Nuria A. Menéndez-Arias and Félix Goyache

Animals 2021, 11(1), 151; https://doi.org/10.3390/ani11010151 - 11 Jan 2021

Cited by 9 | Viewed by 2537

Abstract

A sample of 185 West African cattle belonging to nine different taurine, sanga, and zebu populations was typed using a set of 33 microsatellites and the BovineHD BeadChip of Illumina. The information provided by each type of marker was summarized via clustering methods and principal component analyses (PCA). The aim was to assess differences in performance between both marker types for the identification of population structure and the projection of genetic variability on geographical maps. In general, both microsatellites and Single Nucleotide Polymorphism (SNP) allowed us to differentiate taurine cattle from zebu and sanga cattle, which, in turn, would form a single population. Pearson and Spearman correlation coefficients computed among the admixture coefficients (fitting K = 2) and the eigenvectors corresponding to the first two factors identified using PCA on both microsatellite and SNP data were statistically significant (most of them having p < 0.0001) and high. However, SNP data allowed for a better fine-scale identification of population structure within taurine cattle: Lagunaire cattle from Benin were separated from two different N’Dama cattle samples. Furthermore, when clustering analyses assumed the existence of two parental populations only (K = 2), the SNPs could differentiate a different genetic background in Lagunaire and N’Dama cattle. Although the two N’Dama cattle populations had very different breeding histories, the microsatellite set could not separate the two N’Dama cattle populations. Classic bidimensional dispersion plots constructed using factors identified via PCA gave different shapes for microsatellites and SNPs: plots constructed using microsatellite polymorphism would suggest the existence of weakly differentiated, highly intermingled, subpopulations. However, the projection of the factors identified on synthetic maps gave comparable images. This would suggest that results on population structuring must be interpreted with caution. The geographic projection of genetic variation on synthetic maps avoids interpretations that go beyond the results obtained, particularly when previous information on the analyzed populations is scant. Factors influencing the performance of the projection of genetic parameters on geographic maps, together with restrictions that may affect the election of a given type of markers, are discussed. Full article

(This article belongs to the Special Issue Genomic Variability in Autochthonous and Specialized Livestock Populations)

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18 pages, 2599 KiB

Open AccessArticle

The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System

by Maria Giuseppina Strillacci, Mario Vevey, Veruska Blanchet, Roberto Mantovani, Cristina Sartori and Alessandro Bagnato

Animals 2020, 10(12), 2385; https://doi.org/10.3390/ani10122385 - 12 Dec 2020

Cited by 13 | Viewed by 3519

Abstract

The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler® (GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the F_ST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and F_ST parameters. The mean F_ROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were −0.003, −0.01 and −0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed. Full article

(This article belongs to the Special Issue Genomic Variability in Autochthonous and Specialized Livestock Populations)

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17 pages, 3246 KiB

Open AccessArticle

Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data

by Filippo Biscarini, Salvatore Mastrangelo, Gennaro Catillo, Gabriele Senczuk and Roberta Ciampolini

Animals 2020, 10(12), 2285; https://doi.org/10.3390/ani10122285 - 3 Dec 2020

Cited by 38 | Viewed by 4708

Abstract

Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in [...] Read more.

F_{I S}

and

F_{R O H}

), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (

H_{E} = 0.261

H_{O} = 0.274

). Pedigree-based average inbreeding (F) was estimated at

4.9 %

. The correlation was low between F and genomic-based approaches (

r = 0.03

with

F_{I S}

r = 0.21

with

F_{R O H}

), while it was higher between

F_{I S}

and

F_{R O H}

(

r = 0.78

). The low correlation between F and

F_{R O H}

coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like

F_{R O H}

may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals’ pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity. Full article

(This article belongs to the Special Issue Genomic Variability in Autochthonous and Specialized Livestock Populations)

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14 pages, 3433 KiB

Open AccessArticle

Hybrid Versus Autochthonous Turkey Populations: Homozygous Genomic Regions Occurrences Due to Artificial and Natural Selection

by Maria Giuseppina Strillacci, Stefano Paolo Marelli and Guillermo Martinez-Velazquez

Animals 2020, 10(8), 1318; https://doi.org/10.3390/ani10081318 - 30 Jul 2020

Cited by 8 | Viewed by 3139

Abstract

The Mexican turkey population is considered to be the descendant of the original domesticated wild turkey and it is distinct from hybrid strains obtained by the intense artificial selection activity that has occurred during the last 40 years. In this study 30 Mexican turkeys were genomically compared to 38 commercial hybrids using 327,342 SNP markers in order to elucidate the differences in genome variability resulting from different types of selection, i.e., only adaptive for Mexican turkey, and strongly directional for hybrids. Runs of homozygosity (ROH) were detected and the two inbreeding coefficients (F and F_ROH) based on genomic information were calculated. Principal component and admixture analyses revealed two different clusters for Mexican turkeys (MEX_cl_1 and MEX_cl_2) showing genetic differentiation from hybrids (HYB) (F_ST equal 0.168 and 0.167, respectively). A total of 3602 ROH were found in the genome of the all turkeys populations. ROH resulted mainly short in length and the ROH_island identified in HYB (n = 9), MEX_cl_1 (n = 1), and MEX_cl_2 (n = 2) include annotated genes related to production traits: abdominal fat (percentage and weight) and egg characteristics (egg shell color and yolk weight). F and F_ROH resulted correlated to each other only for Mexican populations. Mexican turkey genomic variability allows us to separate the birds into two subgroups according to the geographical origin of samples, while the genomic homogeneity of hybrid birds reflected the strong directional selection occurring in this population. Full article

(This article belongs to the Special Issue Genomic Variability in Autochthonous and Specialized Livestock Populations)

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