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Genetic Evaluation of Local Livestock Breeds

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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 (15 August 2023) | Viewed by 17206

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Dr. Maria Jose Sanchez Guerrero

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Guest Editor

Departamento de Agronomía, Universidad de Sevilla, Sevilla, Spain
Interests: animal production; genetic selection; horse

Prof. Dr. Ester Bartolomé

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Guest Editor

Departamento de Agronomía, Universidad de Sevilla, Sevilla, Spain
Interests: animal behaviour; genetic selection; horse

Special Issue Information

Dear Colleagues,

Many local livestock breeds are raised all over the world, being in many cases the best option due to its great adaptation to the territory, since there are many local breeds well adapted to the ecological limitations of their environment. These breeds have valuable genetic resources that can be decisive for their viability in the face of global changes. Unfortunately, the present and future of many of these breeds can be problematic, since they use to be less productive than selected and improved breeds and there is a tendency in the animal industry to prioritize high productions instead of adaptation to environment and resilience. Thus, it is important to disseminate the results of the research on local species and their genetic, phenotypic and social contribution on their environment.

It is important (i) to estimate the genetic diversity of these breeds, which determines the subsequent improvement of their characteristics and adaptation to the environment, and (ii) to describe their relationship with their own environment to highlight their specificity.

In this Special Issue, original research articles, short communications and reviews are welcome. Topics of interest include any genetic aspect of local livestock breeds, from the analysis of original genotypes adapted to environments, connections between populations to genetic selection to improve traits or genetic conservation efforts. We look forward to receiving your contributions.

Dr. Maria Jose Sanchez Guerrero
Prof. Dr. Ester Bartolomé
Guest Editors

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Dr. Maria Jose Jose Sanchez Guerrero
Prof. Dr. Ester Bartolomé
Guest Editors

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Keywords

local breeds
genetic conservation
genetic selection
domestic animals
native breeds

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Published Papers (7 papers)

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Research

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17 pages, 2552 KiB

Open AccessArticle

Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing

by Haile Berihulay Gebreselase, Hailemichael Nigussie, Changfa Wang and Chenglong Luo

Animals 2024, 14(2), 307; https://doi.org/10.3390/ani14020307 - 18 Jan 2024

Cited by 3 | Viewed by 2758

Abstract

Goats belong to a group of animals called small ruminants and are critical sources of livelihood for rural people. Genomic sequencing can provide information ranging from basic knowledge about goat diversity and evolutionary processes that shape genomes to functional information about genes/genomic regions. In this study, we exploited a whole-genome sequencing data set to analyze the genetic diversity, population structure and selection signatures of 44 individuals belonging to 5 Ethiopian goat populations: 12 Aberegalle (AB), 5 Afar (AF), 11 Begait (BG), 12 Central highlands (CH) and 5 Meafure (MR) goats. Our results revealed the highest genetic diversity in the BG goat population compared to the other goat populations. The pairwise genetic differentiation (F_ST) among the populations varied and ranged from 0.011 to 0.182, with the closest pairwise value (0.003) observed between the AB and CH goats and a distant correlation (F_ST = 0.182) between the BG and AB goats, indicating low to moderate genetic differentiation. Phylogenetic tree, ADMIXTURE and principal component analyses revealed a classification of the five Ethiopian goat breeds in accordance with their geographic distribution. We also found three top genomic regions that were detected under selection on chromosomes 2, 5 and 13. Moreover, this study identified different candidate genes related to milk characteristics (GLYCAM1 and SRC), carcass (ZNF385B, BMP-7, PDE1B, PPP1R1A, FTO and MYOT) and adaptive and immune response genes (MAPK13, MAPK14, SCN7A, IL12A, EST1 DEFB116 and DEFB119). In conclusion, this information could be helpful for understanding the genetic diversity and population structure and selection scanning of these important indigenous goats for future genetic improvement and/or as an intervention mechanism. Full article

(This article belongs to the Special Issue Genetic Evaluation of Local Livestock Breeds)

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14 pages, 821 KiB

Open AccessArticle

Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations

by Šarūnė Marašinskienė, Rūta Šveistienė, Violeta Razmaitė, Alma Račkauskaitė and Violeta Juškienė

Animals 2023, 13(22), 3506; https://doi.org/10.3390/ani13223506 - 13 Nov 2023

Cited by 1 | Viewed by 1377

Abstract

The purpose of the study was to investigate the genetic variability of open Lithuanian Red and Red-and-White (LRWP) and Lithuanian Black-and-White (LBWP) dairy cattle populations and indicate the differences from the old genotypes of Lithuanian Black-and-White (LBW) and Lithuanian Red cattle (LR), which are currently under a conservation program. In order to gain a better understanding of the populations under conservation and to minimize the potential influence of other breeds, a distinct subgroup was formed that comprised animals whose father and mother belonged to the same breed (LR_pure and LBW_pure). The genetic variability was estimated using the number of founders, pedigree completeness, number of males and females in reproduction and age distribution, generation interval (GI), inbreeding coefficient (F) and effective population size (Ne). The highest average pedigree completeness values in the second generations of the old genotype LR and LBW were 100%. Higher ages of females in the populations under conservation were related to a higher GI and their longer life expectancy. In 2021, the reproductive age of bulls used for insemination within these populations ranged from 5.1 to 27.8 years. The proportions of males producing offspring in their older age indicate that the semen was used from the national gene bank of commercial artificial insemination companies. The GI (>5) in LR and LBW females was higher than that in LRWP and LBWP. The analysis of the data over the 15-year period showed that the GI of males in LRWP and LBWP decreased equally by 38%, while in LR_pure population, it increased by 80%. A high (9.24%) average inbreeding coefficient (F) was found in inbred animals of LR_pure population, while in LBW_pure, it was 5.35% in 2021. The coefficient of inbreeding varied within the different cattle populations. In the open LR population, it ranged from 1.48% to 2.7%, while in the LRWP population, it fell between 2.12% and 3.72%. The lowest effective population size (Ne) concerning the rate of inbreeding was observed in LBW_pure (23) and LR_pure (59), with the highest Ne identified in the LBWP population (462). When considering Ne based on the number of parents, LR_pure displayed the lowest Ne (42), while the highest Ne was found in LBWP (4449). An analysis of local cattle populations reveals that LR faces the most critical situation. This particular population has been steadily declining for a number of years, necessitating additional measures and efforts to safeguard the LR’s ancestral genetic makeup. The results of the LBWP analysis also highlight a concerning trend. Even in very large populations with open breeding programs, the effective population size per generation can experience a significant decrease. Full article

(This article belongs to the Special Issue Genetic Evaluation of Local Livestock Breeds)

12 pages, 615 KiB

Open AccessArticle

The Relevance of the Expected Value of the Proportion of Arabian Genes in Genetic Evaluations for Eventing Competitions

by María José Sánchez-Guerrero, María Ripollés-Lobo, Ester Bartolomé, Davinia Isabel Perdomo-González and Mercedes Valera

Animals 2023, 13(12), 1973; https://doi.org/10.3390/ani13121973 - 13 Jun 2023

Viewed by 4802

Abstract

The Arabian horse is a generally reliable sport horse, and continues to be a remarkable endurance horse, so the relevance of the expected value of the proportion of Arabian genes (EV%AG) in horses participating in eventing could be a relevant factor. A total of 1089 horses participating in eventing (8866 records) were used. A GLM revealed that the EV%AG was significant in dressage, show jumping and cross-country. A BLUP genetic evaluation was computed with five genetic models (without the EV%AG (0) using as a covariate (A), as a fixed effect (B), with variance heterogeneity, and in genetic groups without (C) and with (D)). Dressage heritability ranged from 0.103 to 0.210, show jumping ranged from 0.117 to 0.203 and cross-country ranged from 0.070 to 0.099. The lowest DIC value was used as a criterion of fitness. The best fits (those which included variance heterogeneity) showed fewer than two points of difference in DIC values. The highest average estimated breeding value in dressage, show jumping and cross-country was found for horses with an expected value of the proportion of Arabian genes of 0%, ≥1% to <25%, and 100%, respectively. Therefore, the best way to model the EV%AG effect seems to be by considering the variance heterogeneity. Full article

(This article belongs to the Special Issue Genetic Evaluation of Local Livestock Breeds)

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12 pages, 1777 KiB

Open AccessArticle

The Genetic Diversity of Mink (Neovison vison) Populations in China

by Tietao Zhang, Hu Li, Peter Foged Larsen, Hengxing Ba, Hongyu Shi, Haihua Zhang and Zongyue Liu

Animals 2023, 13(9), 1497; https://doi.org/10.3390/ani13091497 - 27 Apr 2023

Cited by 2 | Viewed by 2066

Abstract

The American mink (Neovison vison) is a semiaquatic species of Mustelid native to North America that is now widespread in China. However, the knowledge of genetic diversity of mink in China is still limited. In this study, we investigated the genetic diversity and identified significant single nucleotide polymorphisms (SNPs) in mink populations of five different color types in three different mink farms in China. Using double-digest restriction site-associated DNA sequencing, we identified a total of 1.3 million SNPs. After filtering the SNPs, phylogenetic tree, Fst, principal component, and population structure analyses were performed. The results demonstrated that red mink and black mink grouped, with separate clustering of all other color types. The population divergence index (Fst) study confirmed that different mink populations were distinct (K = 4). Two populations with different coat colors were subjected to the selection signature analysis, and 2300 genes were found to have a clear selection signature. The genes with a selection signature were subjected to Gene Ontology (GO) categorization and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, the results revealed that the genes with a selection signature were enriched in the melanogenesis pathway. These study’s findings have set the stage for improved breeding and conservation of genetic resources in real-world practical mink farming. Full article

(This article belongs to the Special Issue Genetic Evaluation of Local Livestock Breeds)

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13 pages, 591 KiB

Open AccessCommunication

Evaluation of Single Nucleotide Polymorphisms (SNPs) Associated with Genetic Resistance to Bovine Paratuberculosis in Marchigiana Beef Cattle, an Italian Native Breed

by Piera Mazzone, Antonella Di Paolo, Linda Petrucci, Martina Torricelli, Sara Corneli, Carla Sebastiani, Marcella Ciullo, Martina Sebastianelli, Silva Costarelli, Eleonora Scoccia, Fiorella Sbarra, Federica Gabbianelli, Giovanni Chillemi, Alessio Valentini, Giovanni Pezzotti and Massimo Biagetti

Animals 2023, 13(4), 587; https://doi.org/10.3390/ani13040587 - 7 Feb 2023

Cited by 3 | Viewed by 1886

Abstract

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis (PTB), a widespread chronic enteritis of ruminants. The progression of the infection depends on the containment action of innate and cell-mediated immunity (CMI), and it is related to environmental and genetic factors. In particular, PTB susceptibility seems to be associated with specific genes coding for immune regulators involved in the cell-mediated response during the infection. The aim of this preliminary study was to verify, in Italian beef cattle, an association between MAP infectious status and the presence of single nucleotide polymorphisms (SNPs) in candidate genes. To the best of our knowledge, this is the first investigation conducted on a native beef cattle breed, known as Marchigiana, reared in Central Italy. The present research, based on a longitudinal study, aimed to identify and correlate phenotypic and genetic profiles characteristic of the subjects potentially able to contrast or contain PTB. In a MAP-infected herd, ELISA, IFN-γ tests, qPCR, and cultures were performed at a follow-up, occurring within a period ranging from three to six years, to evaluate the individual state of infection. Animals testing positive for at least one test were considered infected. DNA samples of 112 bovines, with known MAP statuses, were analyzed to verify an association with SNPs in the genes encoding gamma-interferon (BoIFNG), interleukin receptor 10 (IL10RA), interleukin receptor 12 (IL12RB2), and toll-like receptors (TLR1, TLR2, TLR4). Regarding statistical analysis, the differences among target genes and pairs of alleles in the analyzed groups of animals, were evaluated at a significance level of p < 0.05. For IL10RA and for IL12RB2 genes, relevant differences in genotypic frequencies among the considered cattle groups were observed. For all candidate genes studied in this investigation, SNP genotypes already associated with PTB resistance were found more frequently in our population, suggesting potential resistance traits in the Marchigiana breed. Full article

(This article belongs to the Special Issue Genetic Evaluation of Local Livestock Breeds)

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Review

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32 pages, 433 KiB

Open AccessReview

Origin, Selection and Current Status of the Utrerana Chicken Breed: A Review

by Antonio Plata-Casado, Carmelo García-Romero and Pedro González-Redondo

Animals 2023, 13(18), 2982; https://doi.org/10.3390/ani13182982 - 21 Sep 2023

Cited by 1 | Viewed by 1253

Abstract

The conservation of threatened local livestock genetic resources involves characterising them to implement conservation strategies. The Utrerana is a Mediterranean-type chicken breed, included in the Official Catalogue of Livestock Breeds of Spain and in the Domestic Animal Diversity Information System (DAD-IS) of the Food and Agriculture Organization (FAO), native to south Spain created in 1926 by a farmer from Utrera (Seville province). It was selected for laying performance and with four plumage varieties (White, Black, Black-barred and Partridge), reaching average yields of 180 eggs per hen per year. It was widely used in commercial farming in the second quarter of the 20th century, being subsequently displaced in the second half of the 20th century by the spreading of the improved foreign breeds and lines. The Utrerana breed was reared from then on for its aesthetic values and in backyard systems, being endangered with a vulnerable local risk status (1822 birds in 2022 with an increasing trend) and having worsened its laying performance as selection for productivity ceased. The breed has received little attention from the research community. Therefore, this work aims to review the literature on the origin, selection, genetic and productive characterisation and status of the populations of the breed, as well as the conservation strategies. The Utrerana chicken is a polymorphic breed showing high genetic diversity, sexual dimorphism and morpho-functional differences among varieties. Currently, Utrerana hens start laying at 6 months of age, and a hen lays 94–121 high quality eggs (59–64 g) per year, showing seasonality. It is a slow-growing breed with mature weights of 2.4–2.6 kg for roosters and 1.9–2.0 g for hens. The Utrerana chicken breed is rustic and adapted to alternative farming systems. This review has identified research gaps to be filled, such as characterising the carcass and meat quality of the Utrerana chicken, and evidences the need to make efforts to promote the breed and expand its populations. Full article

(This article belongs to the Special Issue Genetic Evaluation of Local Livestock Breeds)

23 pages, 352 KiB

Open AccessReview

Exploring Genetic Markers: Mitochondrial DNA and Genomic Screening for Biodiversity and Production Traits in Donkeys

by Bingjian Huang, Muhammad Zahoor Khan, Wenqiong Chai, Qudrat Ullah and Changfa Wang

Animals 2023, 13(17), 2725; https://doi.org/10.3390/ani13172725 - 27 Aug 2023

Cited by 9 | Viewed by 2172

Abstract

Donkeys (Equus asinus) play a pivotal role as essential livestock in arid and semi-arid regions, serving various purposes such as transportation, agriculture, and milk production. Despite their significance, donkey breeding has often been overlooked in comparison to other livestock species, resulting in limited genetic improvement programs. Preserving donkey genetic resources within each country necessitates the establishment of breed conservation programs, focusing on managing genetic diversity among populations. In recent years, significant strides have been made in sequencing and analyzing complete mitochondrial DNA (mtDNA) molecules in donkeys. Notably, numerous studies have honed in on the mitochondrial D-loop region, renowned for its remarkable variability and higher substitution rate within the mtDNA genome, rendering it an effective genetic marker for assessing genetic diversity in donkeys. Furthermore, genetic markers at the RNA/DNA level have emerged as indispensable tools for enhancing production and reproduction traits in donkeys. Traditional animal breeding approaches based solely on phenotypic traits, such as milk yields, weight, and height, are influenced by both genetic and environmental factors. To overcome these challenges, genetic markers, such as polymorphisms, InDel, or entire gene sequences associated with desirable traits in animals, have achieved widespread usage in animal breeding practices. These markers have proven increasingly valuable for facilitating the selection of productive and reproductive traits in donkeys. This comprehensive review examines the cutting-edge research on mitochondrial DNA as a tool for assessing donkey biodiversity. Additionally, it highlights the role of genetic markers at the DNA/RNA level, enabling the informed selection of optimal production and reproductive traits in donkeys, thereby driving advancements in donkey genetic conservation and breeding programs. Full article

(This article belongs to the Special Issue Genetic Evaluation of Local Livestock Breeds)

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