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Veterinary Sciences
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Genetic Analysis in Domestic Animal Breeds and Performance
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Genetic Analysis in Domestic Animal Breeds and Performance

A special issue of Veterinary Sciences (ISSN 2306-7381). This special issue belongs to the section "Veterinary Biomedical Sciences".

Deadline for manuscript submissions: closed (17 September 2023) | Viewed by 20270

Special Issue Editors

Dr. Enrico D’Alessandro

E-Mail Website
Guest Editor
Department of Veterinary Sciences, University of Messina, Via Palatucci, 98168 Messina, ME, Italy
Interests: animal breeding; genetic improvement; genomic selection; conservation; biodiversity; gene regulation; breed traceability; coat color
Special Issues, Collections and Topics in MDPI journals
Dr. Vincenzo Lopreiato

E-Mail Website
Guest Editor
Department of Veterinary Sciences, Università degli Studi di Messina, Piazza Pugliatti, 1, 98122 Messina, ME, Italy
Interests: ruminant nutrition; animal physiology; dairy science; ketosis; digestive physiology; dairy management; precision livestock farming
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Luigi Liotta

E-Mail Website1 Website2
Guest Editor
Department of Veterinary Sciences, University of Messina, Via Palatucci, 98168 Messina, ME, Italy
Interests: companion animals; endangered local breeds
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Sufficient genetic variation in livestock populations is necessary both for adaptation to future changes in climate and consumer demand and for the continual genetic improvement of economically important traits. Unfortunately, the current trend is for reduced genetic variation, both within and across breeds.

To date, domestic animal genetic resources are facing different challenges related to the erosion of genetic diversity and the need to increase livestock production in developing countries. Moreover, biodiversity investigation could also be an important opportunity to face climate change: many breeds are more resistant to high temperature, and are able to provide food in difficult environmental conditions and with low nutrient input.

For this Special Issue, original research manuscripts and reviews covering all aspects of animal genetics, animal breeding, livestock performance, quantitative genetics, genetic variability, gene expression, gene polymorphisms, and livestock performance are welcome.

Dr. Enrico D’Alessandro
Dr. Vincenzo Lopreiato
Prof. Dr. Luigi Liotta
Guest Editors

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetic improvement
  • genomics selection
  • breeding
  • biodiversity
  • meat quality
  • milk quality
  • QTLs
  • immunometabolism
  • endangered local breeds
  • nutrition physiology
 

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Published Papers (7 papers)

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Research

18 pages, 2405 KiB  
Article
Influence of Sex and a High-Fiber Diet on the Gut Microbiome of Alentejano Pigs Raised to Heavy Weights
by André Albuquerque, Nicolás Garrido, Rui Charneca, Conceição Egas, Luísa Martin, Amélia Ramos, Filipa Costa, Carla Marmelo and José Manuel Martins
Vet. Sci. 2023, 10(11), 641; https://doi.org/10.3390/vetsci10110641 - 2 Nov 2023
Cited by 2 | Viewed by 3329
Abstract
This study investigates the influence of sex and a dietary transition on the gut microbiota of a local Portuguese pig breed. Three groups of male Alentejano pigs (n = 10 each) were raised between ~40 and 160 kg LW. Group C included [...] Read more.
This study investigates the influence of sex and a dietary transition on the gut microbiota of a local Portuguese pig breed. Three groups of male Alentejano pigs (n = 10 each) were raised between ~40 and 160 kg LW. Group C included pigs that were surgically castrated, while the I group included intact ones; both were fed with commercial diets. The third group, IExp, included intact pigs that were fed commercial diets until ~130 kg, then replaced by an experimental diet based on legumes and agro-industrial by-products between ~130 and 160 kg. Fecal samples were collected two weeks before slaughter. The total DNA was extracted and used for 16S metabarcoding on a MiSeq® System. The dietary transition from a commercial diet to the experimental diet substantially increased and shifted the diversity observed. Complex carbohydrate fermenting bacteria, such as Ruminococcus spp. and Sphaerochaeta spp., were significantly more abundant in IExp (q < 0.05). On the other hand, castrated pigs presented a significantly lower abundance of the potential probiotic, Roseburia spp. and Lachnospiraceae NK4A136 group (q < 0.01), bacteria commonly associated with better gut health and lower body fat composition. Understanding the role of gut microbiota is paramount to ensure a low skatole deposition and consumers’ acceptance of pork products from non-castrated male pigs. Full article
(This article belongs to the Special Issue Genetic Analysis in Domestic Animal Breeds and Performance)
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12 pages, 3505 KiB  
Article
Genetic Diversity of Kazakhstani Equus caballus (Linnaeus, 1758) Horse Breeds Inferred from Microsatellite Markers
by Zarina Orazymbetova, Daniya Ualiyeva, Kairat Dossybayev, Aibyn Torekhanov, Dauren Sydykov, Aizhan Mussayeva and Gabiden Baktybayev
Vet. Sci. 2023, 10(10), 598; https://doi.org/10.3390/vetsci10100598 - 30 Sep 2023
Cited by 1 | Viewed by 2616
Abstract
Understanding the genetic diversity and structure of domesticated horse (Equus caballus) populations is critical for long-term herd management and breeding programs. This study examines 435 horses from Kazakhstan, covering seven groups in three geographic areas using 11 STR markers. Identified are [...] Read more.
Understanding the genetic diversity and structure of domesticated horse (Equus caballus) populations is critical for long-term herd management and breeding programs. This study examines 435 horses from Kazakhstan, covering seven groups in three geographic areas using 11 STR markers. Identified are 136 alleles, with the mean number of alleles per locus ranging from 9 to 19. VHL20 is the most variable locus across groups, while loci HTG4, AHT4, AHT5, HTG7, and HMS3 are variable in most populations. The locus AHT5 in the Emba population shows the highest frequency of rare alleles, while the lowest frequency, 0.005, is observed in the Kulandy population. All loci were highly informative for the Kazakhstani populations of E. caballus, with PIC values higher than 0.5. Pairwise variations in Wright’s FST distances show that the examined varieties have little genetic differentiation (0.05%), indicating a high degree of admixture and a continuing lineage sorting process. Phylogenetic and population structure analyses reveal three major clusters of Kazakh horses, representing (I) the Uralsk population of the Kushum breed and the monophyly of two groups: (II) the Kozhamberdy population of the Mugalzhar breed, and (III) the Mugalzhar–Kushum breed populations. Kazakhstani horse populations, while being regionally isolated, were recently in contact with each other. Full article
(This article belongs to the Special Issue Genetic Analysis in Domestic Animal Breeds and Performance)
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13 pages, 3672 KiB  
Article
Cloning of the RNA m6A Methyltransferase 3 and Its Impact on the Proliferation and Differentiation of Quail Myoblasts
by Jing Liu, Wentao Zhang, Wei Luo, Shuibing Liu, Hongxia Jiang, Sanfeng Liu, Jiguo Xu and Biao Chen
Vet. Sci. 2023, 10(4), 300; https://doi.org/10.3390/vetsci10040300 - 18 Apr 2023
Cited by 4 | Viewed by 2249
Abstract
Methyltransferase 3 (METTL3), which has been demonstrated to play a crucial role in a variety of biological processes, is the key enzyme for catalyzing m6A modification in RNA. However, the complete protein sequence of METTL3 in quail has not been annotated, [...] Read more.
Methyltransferase 3 (METTL3), which has been demonstrated to play a crucial role in a variety of biological processes, is the key enzyme for catalyzing m6A modification in RNA. However, the complete protein sequence of METTL3 in quail has not been annotated, and its function in skeletal muscle of quails remains unknown. In the current study, the full-length coding sequence of the quail METTL3 was obtained through the 3′ rapid amplification of cDNA ends (3’ RACE) and its homology with that of other species was predicted based on a generated phylogenetic tree. A Cell Counting Kit-8 assay and flow cytometry in a quail myoblast cell line (QM7) demonstrated that METTL3 promotes myoblast proliferation. The overexpression of METTL3 in QM7 cells significantly increased the expression levels of the myoblast differentiation markers myogenin (MYOG), myogenic differentiation 1 (MYOD1), and myocyte enhancer factor 2C (MEF2C), further demonstrating that METTL3 promotes myoblast differentiation. Additionally, transcriptome sequencing following METTL3 overexpression revealed that METTL3 controls the expression of various genes involved in RNA splicing and the regulation of gene expression, as well as pathways such as the MAPK signaling pathway. Taken together, our findings demonstrated that METTL3 plays a vital function in quail myoblast proliferation and differentiation and that the METTL3-mediated RNA m6A modification represents an important epigenetic regulatory mechanism in poultry skeletal muscle development. Full article
(This article belongs to the Special Issue Genetic Analysis in Domestic Animal Breeds and Performance)
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11 pages, 2104 KiB  
Article
Polymorphism of the Prolactin (PRL) Gene and Its Effect on Milk Production Traits in Romanian Cattle Breeds
by Daniela Elena Ilie, Alexandru Eugeniu Mizeranschi, Ciprian Valentin Mihali, Radu Ionel Neamț, Ludovic Toma Cziszter, Mihai Carabaș and Andrei Cristian Grădinaru
Vet. Sci. 2023, 10(4), 275; https://doi.org/10.3390/vetsci10040275 - 4 Apr 2023
Cited by 5 | Viewed by 2724
Abstract
In the present study, we investigated one polymorphism of the PRL gene (rs211032652 SNP) and assessed its influence on milk production and chemical composition in two Romanian cattle breeds. A total of 119 cattle from two breeds reared in Western Romania (64 Romanian [...] Read more.
In the present study, we investigated one polymorphism of the PRL gene (rs211032652 SNP) and assessed its influence on milk production and chemical composition in two Romanian cattle breeds. A total of 119 cattle from two breeds reared in Western Romania (64 Romanian Spotted and 55 Romanian Brown) were included in the research herd. A PCR-RFLP genotyping assay was used for the identification of the rs211032652 SNP variants. Shapiro’s test and Levene’s test were used to verify ANOVA assumptions and ANOVA and Tukey’s test were employed to test the associations between PRL genotypes and five milk traits. Among the studied breeds, our results showed that PRL genotypes were significantly associated (p < 0.05) with fat and protein percentage in the milk of Romanian Brown cattle. The AA genotype was associated with a higher fat percentage in milk (4.76 ± 0.28) compared to the GG genotype (4.04 ± 0.22, p = 0.048), as well as a higher protein percentage (3.96 ± 0.32% vs. 3.43 ± 0.15%, p = 0.027) in Romanian Brown cattle. Moreover, the PRL locus favored a significantly higher fat (p = 0.021) and protein (p = 0.028) percentage in the milk of Romanian Brown cattle compared to the Romanian Spotted breed, with a difference of 0.263% and 0.170%, respectively. Full article
(This article belongs to the Special Issue Genetic Analysis in Domestic Animal Breeds and Performance)
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16 pages, 3681 KiB  
Article
Association of the IGF1 5′UTR Polymorphism in Meat-Type Sheep Breeds Considering Growth, Body Size, Slaughter, and Meat Quality Traits in Turkey
by Vasfiye Kader Esen and Selim Esen
Vet. Sci. 2023, 10(4), 270; https://doi.org/10.3390/vetsci10040270 - 2 Apr 2023
Cited by 7 | Viewed by 3189
Abstract
This investigation was conducted to determine how the growth and carcass traits of meat-type sheep breeds raised in Turkey are associated with IGF1 5′UTR polymorphisms. Overall, 202 lambs from five breeds were evaluated. We identified eight nucleotide changes (seven substitutions and one deletion) [...] Read more.
This investigation was conducted to determine how the growth and carcass traits of meat-type sheep breeds raised in Turkey are associated with IGF1 5′UTR polymorphisms. Overall, 202 lambs from five breeds were evaluated. We identified eight nucleotide changes (seven substitutions and one deletion) in three variants of IGF1 5′UTR by SSCP analysis and nucleotide sequencing. It was found that the P1 variants had a unique deletion (g.171328230 delT), while the P2 variants were identified by SNPs rs401028781, rs422604851, and g.171328404C > Y. The P3 variants possessed one heterozygous substitution (g.171328260G > R) and three homozygous substitutions (g.171328246T > A, g.171328257T > G, g.171328265T > C) not observed in P1 or P2. Based on the growth and production traits, a statistically significant difference was found only in chest width at weaning (p < 0.01) and leg circumferences at yearling (p < 0.05). The P1 variants showed a leaner profile with a higher Musculus longissimus dorsi, but the differences were not significant (p > 0.05). The P2 variants had a higher percentage of rack (p < 0.01) and loin (p > 0.05). Moreover, there was no discernible difference between variants, even though the P3 variants had a higher percentage of neck and leg and the P1 variants had a higher percentage of the shoulder. It is concluded that nucleotide changes in IGF1 5′UTR could be exploited utilizing a marker-assisted selection technique to increase growth and production attributes, as well as carcass quality traits. Full article
(This article belongs to the Special Issue Genetic Analysis in Domestic Animal Breeds and Performance)
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17 pages, 2743 KiB  
Article
Multi-Tissue Transcriptome Study of Innate Immune Gene Expression Profiling Reveals Negative Energy Balance Altered the Defense and Promoted System Inflammation of Dairy Cows
by Lingli Dai, Zaixia Liu, Lili Guo, Yuan Chai, Yanda Yang, Yu Wang, Yanfen Ma, Caixia Shi and Wenguang Zhang
Vet. Sci. 2023, 10(2), 107; https://doi.org/10.3390/vetsci10020107 - 1 Feb 2023
Cited by 5 | Viewed by 2470
Abstract
Negative energy balance (NEB) during the perinatal period leads to metabolic and immunological disorders in dairy cows, resulting in systemic responses and inflammation. The innate immune system is crucial for the host’s protection and inflammatory response. However, systematic research is still lacking on [...] Read more.
Negative energy balance (NEB) during the perinatal period leads to metabolic and immunological disorders in dairy cows, resulting in systemic responses and inflammation. The innate immune system is crucial for the host’s protection and inflammatory response. However, systematic research is still lacking on how NEB affects the innate immune system to alter the ’host defense capability and inflammatory response. In this investigation, raw transcriptome data of adipose, blood, endometrial, hypothalamus, and liver tissues were downloaded from a public database, cleaned, aligned, quantified, and batch-corrected. The innate immune gene list was retrieved from innateDB, followed by the expression matrix of innate immune genes in various tissues for differential expression analysis, principle component analysis (PCA), and gene set enrichment analysis (GSEA). Under the effect of NEB, adipose tissue had the most differentially expressed genes, which were predominantly up-regulated, whereas blood GSEA had the most enriched biological processes, which were predominantly down-regulated. The gene sets shared by different tissues, which are predominantly involved in biological processes associated with defense responses and inflammation, were dramatically down-regulated in endometrial tissues and highly up-regulated in other tissues. Under the impact of NEB, LBP, PTX3, S100A12, and LCN2 play essential roles in metabolism and immunological control. In conclusion, NEB can downregulate the defensive response of innate immune genes in endometrial, upregulate the immune and inflammatory response of other tissues, activate the host defense response, and increase the systemic inflammatory response. The analysis of the effects of NEB on innate immune genes from the multiple tissues analysis provides new insights into the crosstalk between metabolism and immunity and also provides potential molecular targets for disease diagnosis and disease resistance breeding in dairy cows. Full article
(This article belongs to the Special Issue Genetic Analysis in Domestic Animal Breeds and Performance)
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15 pages, 3134 KiB  
Article
Transcriptome RNA Sequencing Reveals That Circular RNAs Are Abundantly Expressed in Embryonic Breast Muscle of Duck
by Jing Liu, Shuibing Liu, Wentao Zhang, Xiaolong Hu, Huirong Mao, Sanfeng Liu and Biao Chen
Vet. Sci. 2023, 10(2), 75; https://doi.org/10.3390/vetsci10020075 - 19 Jan 2023
Cited by 7 | Viewed by 2150
Abstract
Circular RNAs are widespread in various species and have important roles in myogenesis. However, the circular RNAs involved in breast muscle development in ducks have not yet been studied. Here, to identify circular RNAs during duck skeletal muscle development, three pectorales from Shan [...] Read more.
Circular RNAs are widespread in various species and have important roles in myogenesis. However, the circular RNAs involved in breast muscle development in ducks have not yet been studied. Here, to identify circular RNAs during duck skeletal muscle development, three pectorales from Shan Ma ducks at E13 and E19, which represent undifferentiated and differentiated myoblasts, respectively, were collected and subjected to RNA sequencing. A total of 16,622 circular RNAs were identified, of which approximately 80% were exonic circular RNAs and 260 were markedly differentially expressed between E19 and E13. The parental genes of the differentially expressed circular RNAs were significantly enriched in muscle-related biological processes. Moreover, we found that the overexpression of circGAS2-2 promoted cell cycle progression and increased the proliferation viability of duck primary myoblasts; conversely, knockdown of circGAS2-2 retarded the cell cycle and reduced the proliferation viability of myoblasts. Taken together, our results demonstrate that circular RNAs are widespread and variously expressed during the development of duck skeletal muscle and that circGAS2-2 is involved in the regulation of myogenesis. Full article
(This article belongs to the Special Issue Genetic Analysis in Domestic Animal Breeds and Performance)
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