Advances in Molecular Genetics in Domestic Animals

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Farm Animal Production".

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 7873

Special Issue Editors

Department of Animal Science and Technology, Faculty of Agriculture University of Zagreb, 10000 Zagreb, Croatia
Interests: local breeds; animal genetic resources; phylogenetic studies; genetics and genomics; local foods; livestock technologies; equine breeding; cattle production
Special Issues, Collections and Topics in MDPI journals
Department of Animal Science and Technology, Faculty of Agriculture University of Zagreb, 10000 Zagreb, Croatia
Interests: molecular genetics; genetic diversity; animal genetic resources; equine breeding and using

Special Issue Information

Dear Colleagues,

The development of molecular genetics in recent decades has had a significant impact on the adaptation of animal production to a number of big challenges. There are needs for the sustainable production of animal food, increasing the quality of animal products, improving the welfare of domestic animals, automatization (robotization) of conventional production technologies, the need to reduce the negative impact of animal production on the environment is of great importance. The development of new methodological (analytical) methods of molecular genetics provides a powerful "tool" for numerous aspects of the adaptation and development of animal production. Advanced molecular genetics enables direct and complete understanding of phylogenetic processes within and between breeds, the improvement of selection efficiency, direct and indirect selection for preferred genotypes and traits, elimination (suppression) of certain genetic diseases, improvement of breeds fitness and resistance traits, and much more.

This Special Issue focuses on the advances in molecular genetics in domestic animals, the development and application of new analytical and methodological approaches in the field, various molecular genetic marker systems, computer-assisted analysis (software), and more.

Prof. Dr. Ante Ivanković
Dr. Jelena Ramljak
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agriculture is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 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

  • molecular genetics
  • genetic marker systems
  • genetic characterization
  • Sequencing
  • analytical software
  • genomic selection
  • phylogenetics
  • genetic improvement
  • animal production
  • farm animal genetic resources

Published Papers (5 papers)

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Research

14 pages, 1334 KiB  
Article
Effect of FASN, SCD, and GH Genes on Carcass Fatness and Fatty Acid Composition of Intramuscular Lipids in F1 Holstein × Beef Breeds
Agriculture 2023, 13(3), 571; https://doi.org/10.3390/agriculture13030571 - 26 Feb 2023
Cited by 2 | Viewed by 1275
Abstract
To improve beef quality, a selection of specific breeds for crossbreeding, genotyping, and selection of specific candidate genes in breeding animals can be some of the solutions. The objective of this study was to determine the effects of FASN, SCD, and GH [...] Read more.
To improve beef quality, a selection of specific breeds for crossbreeding, genotyping, and selection of specific candidate genes in breeding animals can be some of the solutions. The objective of this study was to determine the effects of FASN, SCD, and GH genes on carcass fatness and fatty acid (FA) composition of intramuscular lipids of crossbred Holstein × beef breeds (Simmental, Belgian Blue, Limousin, and Piemontese). The allelic and genotypic distribution of polymorphisms in the FASN, SCD, and GH genes was studied in 80 crossbreed animals. Genomic DNA was isolated from musculus longissimus dorsi, whose chemical composition was determined by near infrared transmittance spectrophotometry, while the fatty acid composition was determined by gas chromatography. DNA polymorphism was analyzed by restriction fragment length polymorphism analysis. The FASN (g. 17924A>G) polymorphism was significantly associated with C19:1 n-9 and C24:1 n-9, whereas GH (g.2141C>G) was significantly associated with C16:0 and C20:1 n-9. The SCD (g.8586C>T) polymorphism was significantly associated with C16:0, C18:0, C20:0, C14:1 n-5, C16:1, C18:1, C18:2 n-6, C18:3 n-3, C20:2 n-6, and C20:4 n-6, and analyzed the sum and ratios of fatty acids. Sex had significant effect on carcass fatness and fatty acid composition. This study provided useful results for the above candidate genes and their association with some FA, supporting their influence as genes associated with fats and fatty acid composition in beef meat. Full article
(This article belongs to the Special Issue Advances in Molecular Genetics in Domestic Animals)
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10 pages, 1002 KiB  
Article
Matrilineal Composition of the Reconstructed Stock of the Szekler Horse Breed
Agriculture 2023, 13(2), 456; https://doi.org/10.3390/agriculture13020456 - 15 Feb 2023
Cited by 2 | Viewed by 1326
Abstract
The Szekler horse was a small-sized mountain horse of the Carpathian Mountains whose official stud book ceased to exist after WWII. Despite that, individual horses preserving all the characteristics of the Szekler horse remained scattered in remote areas. This study aims to evaluate [...] Read more.
The Szekler horse was a small-sized mountain horse of the Carpathian Mountains whose official stud book ceased to exist after WWII. Despite that, individual horses preserving all the characteristics of the Szekler horse remained scattered in remote areas. This study aims to evaluate the mitochondrial D-loop sequence (608 bp) of the founder population (n = 59) in 2021 of a breed reconstruction project started in 2012. D-loop showed 68 polymorphic sites. The number of haplotypes was 34, with haplotype diversity (Hd) 0.966 and nucleotide diversity (π) 0.02232. The value of Fu’s Fs statistic (−6.566) was significant (p < 0.001), which rejects a stable population status. Thirteen haplogroups (HG) were found with a nearly equal number of representatives (HG(n)—A (5), D (1), E (2), G (4), I (4), J–K (1), M (4), N (2), O’P (4), and R (1)). In contrast, the Q, L, and B HGs occurred in more horses (15, 9, and 7, respectively). Based on a large number of polymorphic sites and haplotypes, the founder stock is considered diverse. Since the HG Q is characteristic of Asian horses, the examined stock haplotype distribution reflects the eastern origin of the Hungarian horses brought from the East in 896 AD. It is complemented by the gene pool of horses from Europe (e.g., L) and the Middle East (e.g., B). Full article
(This article belongs to the Special Issue Advances in Molecular Genetics in Domestic Animals)
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9 pages, 1023 KiB  
Article
A Single Nucleotide Polymorphism in the WIF1 Promoter Region Regulates the Wool Length in Rabbits
Agriculture 2022, 12(11), 1858; https://doi.org/10.3390/agriculture12111858 - 05 Nov 2022
Viewed by 1303
Abstract
Wool length is an important trait in the rabbit wool industry. Wnt inhibitory factor 1 (WIF1), a key gene, regulates hair follicle growth and development. This study explores the WIF1 gene relationship with wool production traits in three different rabbit breeds, [...] Read more.
Wool length is an important trait in the rabbit wool industry. Wnt inhibitory factor 1 (WIF1), a key gene, regulates hair follicle growth and development. This study explores the WIF1 gene relationship with wool production traits in three different rabbit breeds, Rex rabbit, New Zealand rabbit, and Angora rabbit. The rabbit WIF1 gene sequence was obtained from GenBank, and PCR and Sanger sequencing were applied to screen SNP (single nucleotide polymorphism) from the gene exons and promoter regions. Sequencing results found no SNP in the PCR products of 10 exons from the rabbit WIF1 gene, indicating that the WIF1 gene was not polymorphic. Thus, the gene was conserved in all three rabbit breeds. Only one SNP was found in the WIF1 promoter region, associated with wool-producing traits in rabbits. Luciferase activity assays showed that the AA genotype had higher transcriptional activities than the AG or GG genotype (p < 0.01). In addition, WIF1 was significantly upregulated in the Rex rabbit compared to the New Zealand rabbit and Angora rabbit (p < 0.01). In summary, a key SNP in the WIF1 promoter region was found to be associated with rabbit fiber length trait. Full article
(This article belongs to the Special Issue Advances in Molecular Genetics in Domestic Animals)
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19 pages, 10929 KiB  
Article
Comparative Transcriptome Analysis Reveals the Key Genes Involved in Lipid Deposition in Pekin Ducks (Anas platyrhynchos domesticus)
Agriculture 2022, 12(11), 1775; https://doi.org/10.3390/agriculture12111775 - 26 Oct 2022
Viewed by 1345
Abstract
There are differences in lipid deposition in fatty-type (FT) and lean-type (LT) ducks. Fatty ducks have a higher rate of sebum and abdominal fat, lower meat yield and hepatic lipid contents than LT ducks. However, the underlying changes in gene expression profiles regarding [...] Read more.
There are differences in lipid deposition in fatty-type (FT) and lean-type (LT) ducks. Fatty ducks have a higher rate of sebum and abdominal fat, lower meat yield and hepatic lipid contents than LT ducks. However, the underlying changes in gene expression profiles regarding the lipid deposition between FT and LT ducks have not yet been clarified. To identify the differentially expressed genes in the liver, sebum, and abdominal fat between both ducks, we identified the gene expression profiles in the liver, sebum, and abdominal fat derived from FT and LT ducks by comparing the multistage transcriptomes. Our results showed that there were 622, 1536, and 224 differentially expressed genes (DEGs) in the liver, sebum, and abdominal fat between the FT and LT ducks, respectively. KEGG enrichment showed that the DEGs related to lipid metabolism were enriched in the biosynthesis of unsaturated fatty acid, glycerolipid and fatty acid metabolism in the liver; and were enriched in the fatty acid metabolism, fatty acid biosynthesis, glycerolipid metabolism, linoleic acid metabolism, and the PPAR signaling pathway in the sebum. There was no pathway related to a lipid metabolism enriched in abdominal fat. A gene functional analysis showed that the DEGs involved in adipogenesis were found to be upregulated. In contrast, those involved in lipolysis were downregulated in the liver and serum of FT ducks. The DEGs showed that ATP-binding cassette sub-family G member 8 (ABCG8), fatty acid synthase (FASN), and phospholipid transfer protein (PLTP) were highly expressed in the liver of FT ducks, and acyl-CoA synthetase long-chain family member3 (ACSL3), ACSL5, ACSL6, 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (AGPAT1), AGPAT9, ELOVL fatty acid elongase 6 (ELVOL6), fatty acid desaturase 1 (FADS1), FADS2, monoacylglycerol O-acyltransferase 1 (MOGAT1), serine/threonine kinase 17a (STK17A), and serine/threonine kinase 39 (STK39) were highly expressed in the sebum of FT ducks. A weighted correlation network analysis (WGCNA) of the DEGs showed ABCG8, FADS2, ACSL5, and ELOVL6 positively correlated with hepatic fatty acid synthesis, and AGPAT1, STK17A, STK32A, FADS1, and ACSL3 positively correlated with lipid deposition in the sebum. In summary, ABCG8 might be the key gene for the reduced hepatic lipid deposition in FT Pekin ducks, and FADS2, ACSL5, ELOVL6, AGPAT1, STK17A, STK32A, FADS1, and ACSL3 were the key genes for lipid deposition in the sebum of FT Pekin ducks. Our results provide new insights into the transcriptome regulation in lipid deposition of Pekin ducks and will be helpful for duck breeding. Full article
(This article belongs to the Special Issue Advances in Molecular Genetics in Domestic Animals)
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17 pages, 2378 KiB  
Article
Single Nucleotide Polymorphisms in the Fatty Acid Binding Protein 4, Fatty Acid Synthase and Stearoyl-CoA Desaturase Genes Influence Carcass Characteristics of Tropical Crossbred Beef Steers
Agriculture 2022, 12(8), 1171; https://doi.org/10.3390/agriculture12081171 - 06 Aug 2022
Cited by 2 | Viewed by 2013
Abstract
This study explored the identification of single nucleotide polymorphisms (SNP) in fatty acid binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD), and fatty acid synthase (FASN) genes that may influence the carcass traits of tropical crossbred beef cattle. [...] Read more.
This study explored the identification of single nucleotide polymorphisms (SNP) in fatty acid binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD), and fatty acid synthase (FASN) genes that may influence the carcass traits of tropical crossbred beef cattle. The hypothesis tested was that SNP in the FABP4, SCD, and FASN genes are associated with chiller-assessed carcass traits of tropically adapted northern Australian crossbred beef cattle. Fifty Bos indicus and Bos taurus crossbred steers were backgrounded on either buffel grass only, or buffel grass and desmanthus mixed pastures for 147 days and finished in a commercial feedlot for 110 days. Steers were slaughtered within 48 h of leaving the feedlot within a lairage period not exceeding 12 h and carcasses graded 12 h after slaughter. Next-generation sequencing of the FASN, FABP4, and SCD genes identified multiple SNP loci that were correlated and significantly associated with carcass traits. The FABP4 g.44677205A>G locus was significantly associated with hump height and correlated with loin eye muscle area (EMA; p < 0.05). Polymorphism in the SCD gene g.21275851C>A locus was associated with subcutaneous fat depth and marbling score (p < 0.05). The CC genotype had a higher subcutaneous fat depth and marbling score (p < 0.05) than the AA genotype. Significant correlations were observed between carcass marbling score and subcutaneous fat depth within the FASN SNP locus (p < 0.05). Therefore, the hypothesis that SNP in the FABP4, SCD, and FASN genes are associated with chiller-assessed carcass traits of tropically adapted northern Australian crossbred beef cattle was accepted. These findings suggest that SNP in the FABP4, SCD, and FASN genes may be used in carcass grading and meat quality improvement through marker-assisted selection of northern Australian crossbred beef cattle. Full article
(This article belongs to the Special Issue Advances in Molecular Genetics in Domestic Animals)
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