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Morpho-Functional and Genetic Characterization of Local Breeds
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Morpho-Functional and Genetic Characterization of Local Breeds

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

Deadline for manuscript submissions: closed (30 September 2020) | Viewed by 68362

Special Issue Editor

Prof. Dr. Juan Vicente Delgado Bermejo

E-Mail Website
Guest Editor
Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain
Interests: conservation and characterization of zoogenetic resources; exemplary genetic evaluation; real genetic evaluation; preparation of breeding catalogs and reports; control of yields in the field - Meat, milk, fiber, behavior, sports and eggs; information; storage and data preparation; artificial insemination; seminal collection and freezing
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Special Issue Information

Dear Colleagues,

Hunting and harvesting humans became farmers during the Neolithic period, when they started growing plants and tending animals. New Neolithic societies flourished and succeeded, starting the colonization of the world accompanied by their genetic resources. These genetic resources became adapted to a wide scope of environments, by means of genetic processes such as genetic drift, mutation, migration, and natural or induced selection. This diversification produced thousands of locally adapted breeds in several species, becoming the protagonist for food production until the arrival of the industrial revolution, when extensive farming was progressively substituted by intensive systems. At this point, hundreds of local breeds became endangered, and many of them disappeared. The second half of the 20th century was characterized by a general growing concern for the survival of these populations, especially in occidental countries, and many conservation programs were implemented. However, currently, many breeds are close to extinction, even if some of them are still to be discovered. The first step toward conservation is the definition and characterization of the breeds, and in the present issue, we offer a platform for the dissemination of the important findings obtained in the world through high-level research regarding the morphological (multivariate analysis involving quantitative and qualitative traits), productive (milk, meat, wool and fibers, eggs, sport and work, behavior, etc.), and genetic characterization (DNA markers, demography) of domestic species’ local breeds. International studies involving several local breeds in the aforementioned areas will be welcomed.

Dr. Juan Vicente Delgado Bermejo
Guest Editor

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Keywords

  • conservation
  • zoometry
  • multivariate analysis
  • milk
  • meat
  • wool and fiber
  • eggs
  • sport and work
  • microsatellites
  • SNPs
  • pedigree
  • demography

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Published Papers (19 papers)

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Research

13 pages, 451 KiB  
Article
PRNP Polymorphisms in Eight Local Goat Populations/Breeds from Central and Southern Italy
by Martina Torricelli, Carla Sebastiani, Marcella Ciullo, Simone Ceccobelli, Barbara Chiappini, Gabriele Vaccari, Antonio Capocefalo, Michela Conte, Samira Giovannini, Emiliano Lasagna, Francesca Maria Sarti and Massimo Biagetti
Animals 2021, 11(2), 333; https://doi.org/10.3390/ani11020333 - 28 Jan 2021
Cited by 12 | Viewed by 2752
Abstract
In goats, as in sheep, genotypes of the prion protein gene (PRNP) can influence animals’ susceptibility to scrapie. Since the polymorphic codons in sheep are well known, a genetic selection plan has been implemented in Europe, in order to reduce the [...] Read more.
In goats, as in sheep, genotypes of the prion protein gene (PRNP) can influence animals’ susceptibility to scrapie. Since the polymorphic codons in sheep are well known, a genetic selection plan has been implemented in Europe, in order to reduce the prevalence of susceptible genotypes to scrapie. In Italy, no breeding plan for scrapie resistance in goats has been adopted, yet. Likewise, according to the most recent modification of Regulation EU 999/2001 (Regulation EU 772/2020) of the European Commission (EU), based on all the available experimental and in field data, K222, D146 and S146 polymorphisms could be used as scrapie resistance alleles in genetic management both in scrapie outbreaks and in disease prevention. In order to collect data on the variability of PRNP, the present study aimed to analyze the sequence of the PRNP gene in eight Italian local goat populations/breeds reared in central and southern Italy (Bianca Monticellana, Capestrina, Facciuta della Valnerina, Fulva del Lazio, Garganica, Grigia Ciociara, Grigia Molisana, and Teramana), some of which were investigated for the first time; moreover, two cosmopolitan breeds (Alpine and Saanen) were included. Blood samples were collected from 219 goats. Genomic DNA was extracted from whole blood. DNA was used as template in PCR amplification of the entire PRNP open reading frame (ORF). Purified amplicons have been sequenced and aligned to Capra hircus PRNP. Particularly, the alleles carrying the resistance-related 222 K polymorphism occurred in all populations with a frequency between 2.5% and 12.5%. An additional resistance allele carrying the S146 variant was observed with a frequency of 3.7% only in the Alpine breed. For three of the estimated alleles, we could not establish if the found double polymorphisms in heterozygosis were in phase, due to technical limitations. In this context, in addition to selective culling in scrapie outbreaks according to the European regulation in force, in the future, selection plans could be adopted to deal with scrapie and to control its diffusion, meanwhile paying attention to preserve a high variability of PRNP. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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16 pages, 1922 KiB  
Article
Conditioning Factors of Linearized Wood’s Function Lactation Curve Shape Parameters, Milk Yield, Fat and Protein Content in Murciano-Granadina Primiparous Does
by Juan Vicente Delgado Bermejo, Francisco Antonio Limón Pérez, Francisco Javier Navas González, Jose Manuel León Jurado, Javier Fernández Álvarez and Luis Telo da Gama
Animals 2020, 10(11), 2115; https://doi.org/10.3390/ani10112115 - 15 Nov 2020
Cited by 4 | Viewed by 2457
Abstract
A total of 137,927 controls of 22,932 Murciano-Granadina first lactation goats (measured between 1996–2016) were evaluated to determine the influence of the number of kids, season, year and farm on total milk yield, daily milk yield, lactation length, total production of fat and [...] Read more.
A total of 137,927 controls of 22,932 Murciano-Granadina first lactation goats (measured between 1996–2016) were evaluated to determine the influence of the number of kids, season, year and farm on total milk yield, daily milk yield, lactation length, total production of fat and protein and percentages of fat and protein. All factors analyzed had a significant effect on the variables studied, except for the influence of the number of kids on the percentages of fat and protein, where the variation was very small. Goats with two offspring produced nearly 15% more milk, fat and protein per lactation compared to goats with simple kids. Kiddings occurring in summer–autumn resulted in average milk, fat and protein yields nearly 14, 19 and 23% higher when compared to winter–spring kiddings. Lactation curves were evaluated to determine the effects of the number of kids and season, using the linearized version of the model of Wood in random regression analyses. Peak Yield increased by about 0.3 kg per additional offspring at kidding, but persistence was higher in goats with single offspring. The kidding season significantly influenced the lactation curve shape. Hence summer-kidding goats were more productive, and peak occurred earlier, while a higher persistence was observed in goats kidding during autumn. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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10 pages, 840 KiB  
Communication
Exploring the Genotype at CSN3 Gene, Milk Composition, Coagulation and Cheese-Yield Traits of the Sardo-Modicana, an Autochthonous Cattle Breed from the Sardinia Region, Italy
by Michele Pazzola, Giuseppe Massimo Vacca, Antonia Noce, Marta Porcedda, Maria Onnis, Nicola Manca and Maria Luisa Dettori
Animals 2020, 10(11), 1995; https://doi.org/10.3390/ani10111995 - 30 Oct 2020
Cited by 7 | Viewed by 2465
Abstract
The Sardo-Modicana is a local cattle breed from Sardinia, Italy. No information about its dairy potential is available in the literature. This study investigated the genotype at the CSN3 gene and milk traits of the Sardo-Modicana cattle breed. Fifty-four cows were sampled for [...] Read more.
The Sardo-Modicana is a local cattle breed from Sardinia, Italy. No information about its dairy potential is available in the literature. This study investigated the genotype at the CSN3 gene and milk traits of the Sardo-Modicana cattle breed. Fifty-four cows were sampled for DNA extraction and genotyping at the κ-casein gene locus, CSN3. Forty individual milk samples were analyzed for milk composition, milk coagulation properties and cheese yield (CY%). All the Sardo-Modicana cows were BB homozygotes at CSN3. Hence, the results were compared with the other two local Sardinian breeds. Eighty-three Sarda and 21 Sardo-Bruna cows were genotyped, and the A allele was found (at frequencies of 0.416 and 0.405, respectively). As regards milk traits, the mean protein value was 3.74 g/100 mL, and the mean casein value was 2.98 g/100 mL. Total bacterial and somatic cell counts showed excellent levels of hygiene considering the extensive farming and hand milking. In addition, milk produced by Sardo-Modicana cows was characterized by favorable values of coagulation properties and cheese yield. This information may represent a starting point for the conservation and enhancement of this breed. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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23 pages, 4900 KiB  
Article
Genetic Diversity in the Portuguese Mertolenga Cattle Breed Assessed by Pedigree Analysis
by Nuno Carolino, Andreia Vitorino, Inês Carolino, José Pais, Nuno Henriques, Manuel Silveira and António Vicente
Animals 2020, 10(11), 1990; https://doi.org/10.3390/ani10111990 - 29 Oct 2020
Cited by 14 | Viewed by 4348
Abstract
The Mertolenga beef cattle, currently with 27,000 breeding females in Portugal, is the largest Portuguese native breed, despite some variation in the breeding stock over the last years. The purpose of this study was to estimate parameters related to the population structure and [...] Read more.
The Mertolenga beef cattle, currently with 27,000 breeding females in Portugal, is the largest Portuguese native breed, despite some variation in the breeding stock over the last years. The purpose of this study was to estimate parameters related to the population structure and genetic diversity and to investigate the major factors affecting genetic erosion in the breed, based on the pedigree herdbook information collected since the 1950s, including records on 221,567 animals from 425 herds. The mean generation intervals were 6.4 years for sires and 7.1 years for dams, respectively. The rate of inbreeding per year was 0.183% ± 0.020% and the correspondent effective population size was 38.83. In the reference population (35,017 calves born between 2015 and 2019), the average inbreeding and relatedness were 8.82% ± 10% and 2.05% ± 1.26%, respectively. The mean relationship among animals from the same and from different herds was 29.25% ± 9.36% and 1.87% ± 1.53%, respectively. The estimates for the effective number of founders, ancestors, founding herds and herds supplying sires were 87.9, 59.4, 21.4 and 73.5, respectively. Although the situation of the Mertolenga breed is not alarming, these results indicate the need to adopt measures to maintain the genetic variability of the population. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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12 pages, 2687 KiB  
Article
Genomic Characterization of a Set of Iberian Peninsula Bovine Local Breeds at Risk of Extinction: Morenas Gallegas
by María Asunción García-Atance, Carlos Carleos, Susana Dunner, Paulina G. Eusebi, Castor José Rivero, José Ramón Justo, Miguel Fernández, Javier Cañón and Óscar Cortés
Animals 2020, 10(11), 1956; https://doi.org/10.3390/ani10111956 - 23 Oct 2020
Cited by 2 | Viewed by 2905
Abstract
A set of five local bovine breeds in danger of extinction named Cachena, Caldelá, Limiá, Frieiresa, and Vianesa and included in the group of Morenas Gallegas are located in the Autonomous Community of Galicia at the Northwest of Spain. Local authorities launched a [...] Read more.
A set of five local bovine breeds in danger of extinction named Cachena, Caldelá, Limiá, Frieiresa, and Vianesa and included in the group of Morenas Gallegas are located in the Autonomous Community of Galicia at the Northwest of Spain. Local authorities launched a conservation plan at the end of the 21th century in order to preserve this important genetic reservoir. However, Morenas Gallegas bovine breeds never have been analyzed with genomic tools and this information may be crucial to develop conservation plans. The aim of the study was to analyze their genetic diversity and genetic relationships with a set of local and cosmopolitan European bovine breeds using single nucleotide polymorphisms. Our results show own genetic signatures for the Morenas Gallegas breeds which form a separate cluster when compared to the Spanish breeds analyzed, with the exception of the Cachena breed. The genetic diversity levels of the Morenas Gallegas were intermediate or high, and low inbreeding coefficients can be found except for the Frieiresa breed (11%). Vianesa breed evidenced two lineages depending on the Frieiresa component influence. The Morenas Gallegas bovine breeds group represent an important Spanish bovine genetic reservoir and despite their classification within a single generic group, the five breeds show their own genetic uniqueness. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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9 pages, 1298 KiB  
Communication
Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity
by Natalia V. Dementieva, Andrei A. Kudinov, Tatiana A. Larkina, Olga V. Mitrofanova, Artyom P. Dysin, Valeriy P. Terletsky, Valentina I. Tyshchenko, Darren K. Griffin and Michael N. Romanov
Animals 2020, 10(10), 1887; https://doi.org/10.3390/ani10101887 - 15 Oct 2020
Cited by 18 | Viewed by 2538
Abstract
Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred [...] Read more.
Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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14 pages, 1966 KiB  
Article
Diversity and Genetic Relationship of Free-Range Chickens from the Northeast Region of Brazil
by Débora Araújo de Carvalho, Amparo Martínez Martínez, Inês Carolino, Maria Claudene Barros, María Esperanza Camacho Vallejo, Fátima Santos-Silva, Marcos Jacob de Oliveira Almeida, Nuno Carolino, Juan Vicente Delgado Bermejo and José Lindenberg Rocha Sarmento
Animals 2020, 10(10), 1857; https://doi.org/10.3390/ani10101857 - 12 Oct 2020
Cited by 8 | Viewed by 3299
Abstract
In this study, we aimed to evaluate the genetic diversity within and among chicken breeds from the northeast region of Brazil (states of Bahia and Piauí) using microsatellite markers. In addition, we assessed the identity and genetic relationships of chickens from Europe, Africa, [...] Read more.
In this study, we aimed to evaluate the genetic diversity within and among chicken breeds from the northeast region of Brazil (states of Bahia and Piauí) using microsatellite markers. In addition, we assessed the identity and genetic relationships of chickens from Europe, Africa, and South America, as well as their influence on the formation of the Brazilian breeds. A total of 25 microsatellite markers and a panel containing 886 samples from 20 breeds (including the Brazilian chickens) were used in this study. Different statistical parameters were used to estimate the genetic diversity and relationship among the genetic groups studied. Our study indicates that the Brazilian Creole chickens have high genetic variability. The results show that chickens reared in the states of Bahia and Piauí could have originated from different ancestors. The Brazilian breeds studied have an evolutionary relationship with chickens from Portugal, Nigeria, Chile, and Spain. Our results will contribute directly to the conservation and recognition of Brazilian Creole chicken breeds and provide a solid basis for the demonstration of their genetic identity and genetic conservation of American Creole chicken populations. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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8 pages, 934 KiB  
Article
Diversity Analysis and Genetic Relationships among Local Brazilian Goat Breeds Using SSR Markers
by Marcos Paulo Carrera Menezes, Amparo Martinez Martinez, Edgard Cavalcanti Pimenta Filho, Jose Luis Vega-Pla, Juan Vicente Delgado, Janaina Kelli Gomes Arandas, Laura Leandro da Rocha and Maria Norma Ribeiro
Animals 2020, 10(10), 1842; https://doi.org/10.3390/ani10101842 - 10 Oct 2020
Cited by 10 | Viewed by 3303
Abstract
The genetic diversity of six Brazilian native goats was reported using molecular markers. Hair samples of 332 animals were collected from different goat breeds (Moxotó, Canindé, Serrana Azul, Marota, Repartida, and Graúna) from five states of Northeast Brazil (Paraíba, Pernambuco, Rio Grande do [...] Read more.
The genetic diversity of six Brazilian native goats was reported using molecular markers. Hair samples of 332 animals were collected from different goat breeds (Moxotó, Canindé, Serrana Azul, Marota, Repartida, and Graúna) from five states of Northeast Brazil (Paraíba, Pernambuco, Rio Grande do Norte, Bahia, and Piauí). A panel of 27 microsatellites or single sequence repeats (SSRs) were selected and amplified using a polymerase chain reaction (PCR) technique. All populations showed an average allele number of over six. The mean observed heterozygosity for Brazilian breeds was superior to 0.50. These results demonstrated the high genetic diversity in the studied populations with values ranging from 0.53 (Serrana Azul) to 0.62 (Repartida). The expected average heterozygosity followed the same trend ranging from 0.58 (Serrana Azul) to 0.65 (Repartida), and the values obtained are very similar for all six breeds. The fixation index (Fis) had values under 10% except for the Moxotó breed (13%). The mean expected heterozygosity of all Brazilian populations was over 0.50. Results indicated a within-breed genetic variability in the Brazilian breeds based on the average number of alleles and the average observed heterozygosity. The interbreed genetic diversity values showed proper genetic differentiation among local Brazilian goat breeds. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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7 pages, 1370 KiB  
Communication
Sexual Allometric Monomorphism in Araucan Pig from Colombia: Preliminary Results
by Arcesio Salamanca-Carreño, Jordi Jordana-Vidal, René Alejandro Crosby-Granados, José Norberto Arias-Landazábal and Pere M. Parés-Casanova
Animals 2020, 10(10), 1763; https://doi.org/10.3390/ani10101763 - 28 Sep 2020
Cited by 2 | Viewed by 2782
Abstract
This study aimed to evaluate the allometric growth of the Araucan pig breed, a creole breed from Arauca, East Colombia, locally known as “Sabaneros”, in relation to different quantitative traits and considering genders separately. To do this, a total of 31 male and [...] Read more.
This study aimed to evaluate the allometric growth of the Araucan pig breed, a creole breed from Arauca, East Colombia, locally known as “Sabaneros”, in relation to different quantitative traits and considering genders separately. To do this, a total of 31 male and 27 female Araucan pigs, ranging from 4 to 48 months of age, were studied in order to evaluate their growth patterns, using a multivariate approach. Animals belonged to different farms (“fincas”) of the Department of Arauca, Colombia. From each individual, 10 quantitative traits were obtained: face width, croup height, croup length, croup width, tail base height, hock height, loin height, cannon length, and length and width of ear. Our results, which must be interpreted as preliminary, showed that the Araucan pig is allometrically monomorphic as sexual differences do not increase with body size. We suggest that although males and females have evidently different reproductive roles, during growth they shift the allocation of energy to structures linked to environmental adaptation rather than those linked to reproduction. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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12 pages, 1868 KiB  
Article
Population Genetic Analysis of Ten Geographically Isolated Tibetan Pig Populations
by Peng Shang, Wenting Li, Zhankun Tan, Jian Zhang, Shixiong Dong, Kejun Wang and Yangzom Chamba
Animals 2020, 10(8), 1297; https://doi.org/10.3390/ani10081297 - 29 Jul 2020
Cited by 19 | Viewed by 3182
Abstract
Several geographically isolated populations of Tibetan pigs inhabit the high-altitude environment of the Tibetan Plateau. Their genetic relationships, contribution to the pool of genetic diversity, and their origin of domestication are unclear. In this study, whole-genome re-sequencing data from 10 geographically isolated Tibetan [...] Read more.
Several geographically isolated populations of Tibetan pigs inhabit the high-altitude environment of the Tibetan Plateau. Their genetic relationships, contribution to the pool of genetic diversity, and their origin of domestication are unclear. In this study, whole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed. Population genetic analyses revealed limited genetic differentiation among the Tibetan pig populations. Evidence from deleterious variant analysis indicated that population-specific deleterious variants were the major component of all mutational loci. Contribution to the meta-population was largest in the TT (Qinghai-Tibet Plateau) population, based on gene diversity or allelic diversity. Selective sweep analysis revealed numerous genes, including RXFP1, FZD1, OR1F1, TBX19, MSTN, ESR1, MC1R, HIF3A, and EGLN2 which are involved in lung development, hard palate development, coat color, hormone metabolism, facial appearance, and perception of smell. These findings increase our understanding of the origins and domestication of the Tibetan pig, and help optimize the strategy for their conservation. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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9 pages, 245 KiB  
Article
Milk Potential of Pantaneira Cows, a Local Breed, at Organic System
by Willian Biazolli, Marcus Vinicius Morais de Oliveira, Dirce Ferreira Luz, Leonardo de Oliveira Seno, Alysson Martins Wanderley, Pedro Gustavo Loesia Lima, Tatiane Fernandes and Fernando Miranda de Vargas Junior
Animals 2020, 10(6), 1079; https://doi.org/10.3390/ani10061079 - 23 Jun 2020
Cited by 1 | Viewed by 2646
Abstract
Pantaneiro cattle (Bos taurus taurus) is a breed locally adapted to the Brazilian Pantanal. Local breeds are essential for the quality production of organic systems based on planned grazing practices, because of their results in resilient and productive ecosystems, enhancing biodiversity. [...] Read more.
Pantaneiro cattle (Bos taurus taurus) is a breed locally adapted to the Brazilian Pantanal. Local breeds are essential for the quality production of organic systems based on planned grazing practices, because of their results in resilient and productive ecosystems, enhancing biodiversity. This study aimed to evaluate the performance of Pantaneira primiparous cows, and systems with reduced use of concentrate, simulating organic production conditions. Five animals, with an average body weight of 396.2 ± 43.5 kg, were kept in individual continuous grazing regimes and supplemented with different concentrate levels (1.2%, 0.9%, 0.6%, 0.3%, and 0.0% of body weight). The animals were allocated at random in a 5 × 5 Latin square design repeated twice during the study time. The cows had a low dry matter and nutrient intake with a reduction in concentrate level, with improvement in neutral detergent fiber digestibility and a reduction in total nutrient digestibility. No changes were observed in plasma glucose levels or urea excretion, but the plasma urea nitrogen decreased with reductions in concentrate levels. There was a reduction in milk yield, but the energy-corrected milk was not affected by the reduction in concentrate levels; furthermore, the milk yield efficiency was not affected. The milk fat content improved with the reduction in concentrate levels. The Pantaneira breed has the genetic potential for the maintenance of competitive production and quality in organic systems. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
11 pages, 3325 KiB  
Article
Genetic Characterization of the “Chusca Lojana”, a Creole Goat Reared in Ecuador, and Its Relationship with Other Goat Breeds
by Lenin Aguirre-Riofrio, Teddy Maza-Tandazo, Manuel Quezada-Padilla, Oscar Albito-Balcazar, Alex Flores-Gonzalez, Osvaldo Camacho-Enriquez, Amparo Martinez-Martinez, BioGoat Consortium and Juan Vicente Delgado-Bermejo
Animals 2020, 10(6), 1026; https://doi.org/10.3390/ani10061026 - 12 Jun 2020
Cited by 4 | Viewed by 3381
Abstract
The largest population of goats (62%) in Ecuador is in the dry forest region in the south of the country. A Creole goat, named “Chusca Lojana”, has adapted to the dry forest region where environmental conditions are warm-dry, with sparse vegetation. Knowledge of [...] Read more.
The largest population of goats (62%) in Ecuador is in the dry forest region in the south of the country. A Creole goat, named “Chusca Lojana”, has adapted to the dry forest region where environmental conditions are warm-dry, with sparse vegetation. Knowledge of the genetic information of the Creole goat is important to determine intra-racial diversity, the degree of genetic distance among other breeds of goats, and the possible substructure of the population, which is valuable for the conservation of such a species’ genetic resources. A total of 145 samples of the Creole goat was taken from the four biotypes previously identified. Genetic analyses were performed using 38 microsatellites recommended for studies of goat genetic diversity (FAO-ISAG). The results of within-breed genetic diversity showed a mean number of alleles per locus (MNA) of 8, an effective number of alleles (Ae) of 4.3, an expected heterozygosity (He) of 0.71, an observed heterozygosity (Ho) of 0.63, polymorphic information content (PIC) of 0.67, and an FIS value of 0.11. Between-breed genetic diversity among 43 goat populations (native of Spain, American Creole, Europeans, and Africans) showed the following values: FIS = 0.087, FIT = 0.176, and FST = 0.098. Regarding the analysis of the population structure, the results showed that the Creole Chusca Lojana goat population is homogeneous and no genetic separation was observed between the different biotypes (FST = 0.0073). In conclusion, the Chusca Lojana goat has a high genetic diversity, without exhibiting a genetic substructure. Therefore, it should be considered as a distinct population because crossbreeding with other breeds was not detected. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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6 pages, 659 KiB  
Article
Lineal Discrimination of Horses and Mules. A Sympatric Case from Arauca, Colombia
by Arcesio Salamanca-Carreño, Jordi Jordana, Rene Alejandro Crosby-Granados, Jannet Bentez-Molano and Pere M. Parés-Casanova
Animals 2020, 10(4), 679; https://doi.org/10.3390/ani10040679 - 13 Apr 2020
Cited by 4 | Viewed by 2189
Abstract
This is the first morphological comparative study between local horses and mules from Arauca, Colombia. It was realized to compare morphological traits between both species by analysing 15 adult mules (7 males and 8 females) and 150 adult horses (137 males and 13 [...] Read more.
This is the first morphological comparative study between local horses and mules from Arauca, Colombia. It was realized to compare morphological traits between both species by analysing 15 adult mules (7 males and 8 females) and 150 adult horses (137 males and 13 females), with an age interval from 2 to 22 years. Data consisted of 24 different body quantitative traits which can explain the body conformation: thoracic circumference, body length (BL), thoracic depth and width, withers height (WH), sternum height, shoulders width, chest width, forelimb cannon perimeter and length, head length and width, skull length and width, face length and width, ear length and width, loin height, croup height (CrH), width and length, dock height (DoH), and hock height. Heart girth circumference, body length, withers height, croup height, and dock height were the most discriminative traits, showing statistical differences between species. The formula is X = (BL × 0.402) + (WH × 0.323) + (CrH × 0.352) + (DoH × 0.384). A value of X > 184.5 assigns with total certainty that a skeleton belongs to a horse, and if X < 174.0, it is a mule. The proposed formula has a 100% specificity but a 71.4% sensibility for mules and an 84.4% for horses into the rank of 174.0–184.5. Therefore, results demonstrate that some postcranial anatomical elements of Equus could give enough information for a bone differentiation between horses and mules, at least in animals from the Araucan region, but the main interest is that it reflects the possibility to differentiate morphometrically both species from bone remains when horses and mules were sympatric. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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9 pages, 1369 KiB  
Communication
Molecular Identification of the “Facciuta Della Valnerina” Local Goat Population Reared in the Umbria Region, Italy
by Simone Ceccobelli, Emiliano Lasagna, Eymen Demir, Giacomo Rovelli, Emidio Albertini, Fabio Veronesi, Francesca Maria Sarti and Daniele Rosellini
Animals 2020, 10(4), 601; https://doi.org/10.3390/ani10040601 - 1 Apr 2020
Cited by 8 | Viewed by 2564
Abstract
Italy holds important genetic resources of small ruminant breeds. By distinguishing goat breeds at the DNA level, certification of products from specific breeds can be valorized. The aim of this study was to establish the genetic identity of Facciuta della Valnerina, a local [...] Read more.
Italy holds important genetic resources of small ruminant breeds. By distinguishing goat breeds at the DNA level, certification of products from specific breeds can be valorized. The aim of this study was to establish the genetic identity of Facciuta della Valnerina, a local goat population of Italy, compared with the cosmopolitan breeds, Saanen and Camosciata delle Alpi, reared in the same geographic area. A total of 116 microsatellite alleles ranging from 4 to 13 were detected at 16 loci in the three goat populations/breeds. A total of 23 private alleles with frequencies lower than 0.3 were detected in the Facciuta della Valnerina population. The mean numbers of alleles were 6.67, 4.58, and 4.92 in Facciuta della Valnerina, Camosciata delle Alpi, and Saanen, respectively. The expected heterozygosity ranged from 0.20 to 0.86. Most loci were highly polymorphic and informative (polymorphic information content ≥0.50). Factorial correspondence analysis and principal components analysis revealed very clear separation between Facciuta della Valnerina and the two reference goat breeds. Reducing the number of markers from 16 to 12 (on the basis of polymorphic information content and the number of alleles) still allowed us to distinguish the local population, indicating that microsatellite markers are capable of discriminating local livestock breeds at a low cost. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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12 pages, 978 KiB  
Article
Genetic Variability and Management in Nero di Parma Swine Breed to Preserve Local Diversity
by Elena Mariani, Andrea Summer, Michela Ablondi and Alberto Sabbioni
Animals 2020, 10(3), 538; https://doi.org/10.3390/ani10030538 - 24 Mar 2020
Cited by 8 | Viewed by 4023
Abstract
Nero di Parma is an endangered swine breed reared in the North of Italy which nowadays counts 1603 alive pigs. The aims of this study were (i) to explore the genetic diversity of the breed at pedigree level to determine the actual genetic [...] Read more.
Nero di Parma is an endangered swine breed reared in the North of Italy which nowadays counts 1603 alive pigs. The aims of this study were (i) to explore the genetic diversity of the breed at pedigree level to determine the actual genetic structure, (ii) to evaluate the effectiveness of the breeding recovery project and (iii) to potentially propose breeding strategies for the coming generations. The pedigree dataset contained 14,485 animals and was used to estimate demographic and genetic parameters. The mean equivalent complete generations was equal to 6.47 in the whole population, and it reached a mean value of 7.94 in the live animals, highlighting the quality of the available data. Average inbreeding was 0.28 in the total population, whereas it reached 0.31 in the alive animals and it decreased to 0.27 if only breeding animals were considered. The rate of inbreeding based on the individual increase in inbreeding was equal to 7%. This study showed the effectiveness of the recovery project of the breed. Nevertheless, we found that inbreeding and genetic diversity have reached alarming levels, therefore novel breeding strategies must be applied to ensure long-term survival of this breed. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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6 pages, 740 KiB  
Article
A Comparison of Traditional and Geometric Morphometric Techniques for the Study of Basicranial Morphology in Horses: A Case Study of the Araucanian Horse from Colombia
by Pere Miquel Parés-Casanova, Arcesio Salamanca-Carreño, René Alejandro Crosby-Granados and Jannet Bentez-Molano
Animals 2020, 10(1), 118; https://doi.org/10.3390/ani10010118 - 10 Jan 2020
Cited by 17 | Viewed by 4471
Abstract
Skull size and shape have been widely used to study domestic animal populations and breeds. Although several techniques have been proposed to quantify cranial form, few attempts have been made to compare the results obtained by different techniques. While linear morphometrics has traditionally [...] Read more.
Skull size and shape have been widely used to study domestic animal populations and breeds. Although several techniques have been proposed to quantify cranial form, few attempts have been made to compare the results obtained by different techniques. While linear morphometrics has traditionally been used in breed characterization, recent advances in geometric morphometrics have created new techniques for specifically quantifying shape and size. The objective of this study was to compare two morphometric methods for their ability to describe external morphology. For this purpose, 20 skull specimens of adult male Araucanian horses were examined. Two age categories were established (the “mature group”, M3 not fully erupted to moderately worn, n = 7; and the “senile group”, M3 totally erupted and highly worn, n = 13). Both methods showed that there were statistical differences between generations, but discrimination rates were different between methods with the geometric morphometric analysis obtaining a rate of 97.5%. Although linear morphometrics was found to be compatible with geometric morphometrics, the latter was better able to discriminate the two groups and it also provides more information on shape. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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24 pages, 2913 KiB  
Article
Sexual Dimorphism and Breed Characterization of Creole Hens through Biometric Canonical Discriminant Analysis across Ecuadorian Agroecological Areas
by Paula Alexandra Toalombo Vargas, Francisco Javier Navas González, Vincenzo Landi, José Manuel León Jurado and Juan Vicente Delgado Bermejo
Animals 2020, 10(1), 32; https://doi.org/10.3390/ani10010032 - 22 Dec 2019
Cited by 24 | Viewed by 3748
Abstract
Despite Ecuador having a wide biodiversity of zootechnical species, characterization studies of these genetic resources are scarce. The objective of this research was to perform the biometric characterization of the Creole hen population through 14 quantitative zoometric measures. We evaluated 207 hens and [...] Read more.
Despite Ecuador having a wide biodiversity of zootechnical species, characterization studies of these genetic resources are scarce. The objective of this research was to perform the biometric characterization of the Creole hen population through 14 quantitative zoometric measures. We evaluated 207 hens and 37 roosters from Ecuador’s three agro-ecological regions: the Sierra (highlands) region (Bolivar, Chimborazo, Tungurahua and Cotopaxi provinces); the Costa (coastal) region (Guayas); and the Oriente Amazonian region (Morona Santiago). Sexual dimorphism was assessed using one-way analysis of variance (ANOVA). Body dimensions were generally significantly higher for males (p < 0.05), especially for length of head, beak, neck, dorsum, tarsus, thigh, leg, and middle finger. Then, individuals were biometrically clustered into populations after a stepwise canonical discriminant analysis (CDA) computing interpopulation Mahalanobis distances. Agroecologically-based structured populations were identified when zoometrical criteria were used to classify the animals. Cotopaxi and Tungurahua provinces were reported to be the most distant from the rest, with a slight differentiation of the Morona Santiago province population from those in Guayas, Chimborazo and Bolívar. Conclusively, Ecuadorian Creole hens were higher than longer contrasting light hen breeds, which favors their dual-purpose aptitude. Hence, the development of selection programs aimed at Ecuadorian differentiated entity of production of eggs and meat across agro-ecological areas is feasible. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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10 pages, 990 KiB  
Article
GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds
by Imen Baazaoui, John McEwan, Rayna Anderson, Rudiger Brauning, Alan McCulloch, Tracey Van Stijn and Sonia Bedhiaf-Romdhani
Animals 2020, 10(1), 5; https://doi.org/10.3390/ani10010005 - 18 Dec 2019
Cited by 10 | Viewed by 3474
Abstract
The Tunisian Noire de Thibar sheep breed is a composite breed, recently selected to create animals that are uniformly black in order to avoid skin photosensitization after the ingestion of toxic “hypericum perforatum” weeds, which causes a major economic loss to [...] Read more.
The Tunisian Noire de Thibar sheep breed is a composite breed, recently selected to create animals that are uniformly black in order to avoid skin photosensitization after the ingestion of toxic “hypericum perforatum” weeds, which causes a major economic loss to sheep farmers. We assessed genetic differentiation and estimated marker FST using genotyping-by-sequencing (GBS) data in black (Noire de Thibar) and related white-coated (Queue fine de l’ouest) sheep breeds to identify signals of artificial selection. The results revealed the selection signatures within candidate genes related to coat color, which are assumed to be indirectly involved in the mechanism of photosensitization in sheep. The identified genes could provide important information for molecular breeding. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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19 pages, 3427 KiB  
Article
Sexual Dimorphism for Coping Styles Complements Traditional Methods for Sex Determination in a Multivariety Endangered Hen Breed
by Carlos Iglesias Pastrana, Francisco Javier Navas González, Carmen Marín Navas, Ander Arando Arbulu, Antonio González Ariza, José Manuel León Jurado, María Gabriela Pizarro Inostroza and Maria Esperanza Camacho Vallejo
Animals 2019, 9(12), 1165; https://doi.org/10.3390/ani9121165 - 17 Dec 2019
Cited by 2 | Viewed by 10428
Abstract
Sex determination is key to designing endangered poultry population conservation and breeding programs when sex distribution departs from Hardy–Weinberg equilibrium. A total of 112 Utrerana chickens (28 per variety, partridge, black, white, and franciscan) were selected for hatching day sexing. Sex assignation was [...] Read more.
Sex determination is key to designing endangered poultry population conservation and breeding programs when sex distribution departs from Hardy–Weinberg equilibrium. A total of 112 Utrerana chickens (28 per variety, partridge, black, white, and franciscan) were selected for hatching day sexing. Sex assignation was performed through 10 methods. Three sex assignment criteria comprised criteria found in literature, opposite criteria to that in the literature, and composite criteria combining methods reporting the highest predictive success from the previous ones. This study aims to determine which method combinations may more successfully determine sex across the four varieties of Utrerana endangered hen breed to tailor noninvasive early specific models to determine sex in local chicken populations. Although the explanatory power of the three assignation criteria is equal (75%), assignation criteria 2 resulted to be the most efficient as it correctly assigns males more frequently. Only methods 3 (English method), 5 (general down feathers coloration), 7 (wing fan), and 10 (behavior/coping styles) reported significant differences regardless of the variety, hence, are appropriate for early sexing. Sex confirmation was performed at 1.5 months old. Identifying sex proportions enhances genetic management tasks in endangered populations, complementing more standardized techniques, which may result inefficient given the implicit diversity found in local populations. Full article
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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