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The 15th Anniversary of Genes: Feature Papers in the "Animal Genetics and Genomics" Section

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 6842

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Prof. Dr. Antonio Figueras

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Instituto de Investigaciones Marinas, IIM-CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain
Interests: aquaculture; fish; shellfish; genetics; genomics; transcriptomic; epigenomics
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Prof. Dr. Pedro Lorite Martínez

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Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain
Interests: insects; chromosome; heterochromatin; repetitive DNA; molecular cytogenetics; cytogenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, “The 15th Anniversary of Genes: Feature Papers in the Animal Genetics and Genomics Section”, aims to bring together high-quality review articles or research articles on all aspects of the most recent advances in interdisciplinary animal genetics fields and to share knowledge between scientists and professionals. It is dedicated to recent advances in the research area of genomics and genetic and comprises a selection of exclusive papers from the Editorial Board Members (EBMs) of the “Animal Genetics and Genomics” Section, as well as invited papers from relevant experts. We also welcome senior experts in the field to make contributions to this Special Issue. We aim to present our Special Issue as an attractive open access publishing platform for genomics and genetic research.

Prof. Dr. Antonio Figueras
Prof. Dr. Pedro Lorite Martínez
Guest Editors

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Keywords

applied genetics and genomics in species of economic importance
companion animal genetics and genomics
breeding and genetic selection
genetics and genomics of aquaculture species
genetics of immune response and disease resistance
genome-edited animals and animal epigenetics
animal population genetics, polymorphisms and genome annotation
genetics applied to the interaction of microbiome and genetic traits of interest
bioinformatics analysis in animal genetics
genomics and evolution
cytogenomics

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Published Papers (8 papers)

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Editorial

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3 pages, 138 KB

Open AccessEditorial

Genomics, Molecular Taxonomy, and Functional Genetics: Insights from a Diverse Collection of Studies

by Pedro Lorite and Antonio Figueras

Genes 2026, 17(5), 501; https://doi.org/10.3390/genes17050501 - 24 Apr 2026

Viewed by 200

Abstract

This Special Issue of Genes brings together a set of contributions that, despite their apparent thematic diversity, share a common methodological thread: the application of genomic and molecular tools to fundamental questions in animal biology, ranging from production traits in livestock to phylogenetic [...] Read more.

(This article belongs to the Special Issue The 15th Anniversary of Genes: Feature Papers in the "Animal Genetics and Genomics" Section)

Research

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32 pages, 11052 KB

Open AccessArticle

Genome Wide Association Studies with Different Weighting Approaches Reveals Genomic Windows Associated with Meat Quality Traits in Beef Cattle

by Hugo Borges Dos Reis, Amanda Marchi Maiorano, Elisângela Oliveira, Filippi Tonetto, Fernando Baldi, Breno de Oliveira Fragomeni and José Bento Sterman Ferraz

Genes 2026, 17(4), 385; https://doi.org/10.3390/genes17040385 - 28 Mar 2026

Cited by 1 | Viewed by 745

Abstract

Background/Objectives: Genome-wide association studies (GWAS) based on single-step genomic BLUP (ssGBLUP) commonly assume equal single nucleotide polymorphism (SNP) variances, which may not reflect the biological architecture of complex traits. Alternative weighting strategies can increase detection power but may affect stability. This study evaluated how different SNP weighting approaches influence genomic region detection and biological interpretation of ribeye area (REA) and subcutaneous fat thickness (SFT) in Guzerá cattle. Methods: Phenotypic records from 2729 animals and genotypes from 1405 individuals (43,039 SNPs after quality control) were analyzed. Heritabilities were estimated using Restricted Maximum Likelihood (REML), and GWAS were conducted under five approaches: unweighted method (UM), quadratic method (QM), and three Non-Linear A strategies with weighting constants (1.125, 1.2, and 1.5). Genomic windows of 20 adjacent SNPs explaining ≥0.5% of the additive genetic variance (AGV) were considered significant. Recurrent regions were prioritized, and functional enrichment analyses (KEGG, GO, and MeSH) were performed. Results: Heritability estimates were moderate for REA (0.26 ± 0.05) and SFT (0.22 ± 0.04). Weighted approaches increased detection sensitivity. For REA, UM identified 10 windows, whereas QM and A_1.5 detected 24 and 31 windows. For SFT, UM identified 8 windows, while QM and A_1.5 detected 30 and 23 windows. Recurrent chromosomes included 2, 4, 6, 12, 16, 19, and 22 for REA, and 2, 3, 5, 7, 11, 17, and 22 for SFT. Key genes included AKT3, NOS2, and MSTN. Enrichment highlighted pathways related to muscle growth and lipid metabolism. Conclusions: SNP-weighted GWAS increased detection sensitivity but involved trade-offs between signal amplification and stability. Integrating weighting strategies improves biological interpretation and supports robust candidate gene identification for genomic selection. Full article

(This article belongs to the Special Issue The 15th Anniversary of Genes: Feature Papers in the "Animal Genetics and Genomics" Section)

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11 pages, 1145 KB

Open AccessArticle

Identification of Candidate Causal Polymorphisms in GGT1 and SLC5A1 Associated with Fat Area Ratio on BTA17 in Japanese Black Cattle

by Shinji Sasazaki, Hikari Ito, Ryoto Adachi, Eiji Iwamoto, Emi Yoshida, Fuki Kawaguchi, Kenji Oyama and Hideyuki Mannen

Genes 2026, 17(4), 363; https://doi.org/10.3390/genes17040363 - 24 Mar 2026

Cited by 1 | Viewed by 353

Abstract

Background/Objectives: Intramuscular fat deposition is a key determinant of beef quality in Japanese Black cattle, and the fat area ratio of the rib eye (FAR) is highly correlated with Beef Marbling Standard scores. Methods: To identify genetic variants underlying variation in the FAR, we conducted a genome-wide association study (GWAS) followed by whole-genome sequence–based fine mapping in a Hyogo Japanese Black population (n = 432). Animals were genotyped using the Illumina BovineSNP50v3 BeadChip, and association analysis was performed using residuals derived from a linear mixed model accounting for fixed and random effects. Results: A significant association signal was detected on BTA17 (λ = 1.09), with the top single nucleotide polymorphism (SNP) located at 17:72,329,662 (p = 3.60 × 10⁻⁶). To refine the candidate region, we analyzed whole-genome resequencing data from 42 Hyogo Japanese Black cattle and identified a distinct linkage disequilibrium (LD) block spanning 71–74 Mbp on BTA17. Among 4292 variants within genes showing LD (r² ≥ 0.1) with the top SNP, 96 variants with strong LD and predicted functional effects were selected for validation. Genotyping in the Hyogo population revealed that a missense variant in gamma-glutamyltransferase 1 (GGT1) (c.589G>A, p.Asp197Asn) showed the strongest association with FAR (p = 3.89 × 10⁻⁶). A 5′UTR variant in GGT1 (c. −256G>T) and a missense variant in solute carrier family 5 member 1 (SLC5A1) (c.32C>T, p.Thr11Met) also exhibited significant associations and strong LD with the top SNP (r² > 0.7). GGT1 is involved in glutathione metabolism, whereas SLC5A1 encodes a sodium–glucose cotransporter implicated in nutrient sensing and metabolic regulation. Conclusions: Although functional validation is required, these variants represent strong positional and biological candidates underlying the BTA17 quantitative trait loci (QTL). The identified polymorphisms may provide useful molecular markers for optimizing genetic improvement of marbling-related traits within the Hyogo Japanese Black population. Full article

(This article belongs to the Special Issue The 15th Anniversary of Genes: Feature Papers in the "Animal Genetics and Genomics" Section)

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14 pages, 6139 KB

Open AccessArticle

Molecular Taxonomy of Geckos Reveals a Second Tarentola Species (Reptilia: Squamata) on the Maltese Islands

by Noel Vella, Marina Zorrilla García and Adriana Vella

Genes 2026, 17(3), 271; https://doi.org/10.3390/genes17030271 - 26 Feb 2026

Cited by 1 | Viewed by 534

Abstract

Background/Objectives: The Maltese islands, situated in the Sicilian Channel, are known to host two gecko species, Hemidactylus turcicus and Tarentola mauritanica. However, gecko taxonomy is complicated by cryptic lineages within species complexes, requiring molecular approaches for accurate identification. Methods: In this study, we investigated species diversity using opportunistic sampling of 30 dead gecko specimens, including road-killed individuals, from across the Maltese islands. Due to the degraded condition of most samples, morphological identification was limited; therefore, mitochondrial markers (12S, 16S and COI) were employed to assign species identity. Results: Our analyses revealed the first records of the Tarentola fascicularis/deserti complex in Malta. This finding extends the known distribution of this complex and complements records from neighbouring islands in the Sicilian Channel, where T. mauritanica and T. fascicularis/deserti lineages occur in sympatry. Conclusions: Given the greater ecological affinity of the T. fascicularis/deserti complex for arid environments, these findings emphasise the importance of continued monitoring to clarify the dynamics of sympatry, potential ecological displacement, and the long-term effects of climate change and anthropogenic activity on the central Mediterranean herpetofauna. Full article

(This article belongs to the Special Issue The 15th Anniversary of Genes: Feature Papers in the "Animal Genetics and Genomics" Section)

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17 pages, 9051 KB

Open AccessArticle

Cytogenomics of the Flea Beetle Podagrica fuscicornis (Coleoptera, Chrysomelidae): Karyotype and Satellitome Analysis of an Alticinae Species with a High Chromosome Number

by José M. Rico-Porras, Diogo C. Cabral-de-Mello, Pedro Lorite and Pablo Mora

Genes 2026, 17(2), 216; https://doi.org/10.3390/genes17020216 - 10 Feb 2026

Cited by 1 | Viewed by 759

Abstract

Background/Objectives: Flea beetles (Coleoptera, Chrysomelidae: Alticinae) show extensive karyotypic diversity, yet cytogenetic and genomic data remain scarce for many taxa. Species of the genus Podagrica are characterized by unusually high chromosome numbers compared with the modal condition in Alticinae, suggesting a history of chromosomal fissions. This study aimed to characterize the karyotype and repetitive DNA composition of Podagrica fuscicornis, with special emphasis on the satellitome and its contribution to chromosome organization. Methods: Male specimens of P. fuscicornis collected in southern Spain were analyzed using conventional cytogenetic techniques, including Giemsa staining, DAPI staining, and C-banding. Fluorescence in situ hybridization was employed to map nucleolar organizer regions (NORs), telomeric repeats, and major satellite DNA (satDNA) families. The satellitome was characterized using Illumina short-read sequencing and analyzed with the RepeatExplorer2/TAREAN pipeline to identify satDNA families and estimate their genomic abundance and divergence. Results: The male karyotype of P. fuscicornis was 2n = 40 (38 + XY), with an Xy_p sex chromosome system. Constitutive heterochromatin was mainly pericentromeric, and the Y chromosome was largely heterochromatic. NORs were located on a single autosomal pair, and the ancestral insect telomeric motif (TTAGG)_n was detected at chromosome ends. The satellitome comprised at least 70 different satDNA families, representing 9.51% of the genome, some of them related to transposable elements. Ten of these 70 satDNAs are shared in other Alticinae species. The most abundant families were primarily localized in pericentromeric regions and showed differential distribution between autosomes and sex chromosomes. Conclusions: These results indicate that extensive chromosomal fissions and high satDNA dynamics could drive the high chromosome number and heterogeneous genome organization in P. fuscicornis, highlighting the role of repetitive DNA in karyotype evolution within Chrysomelidae. Full article

(This article belongs to the Special Issue The 15th Anniversary of Genes: Feature Papers in the "Animal Genetics and Genomics" Section)

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11 pages, 3613 KB

Open AccessArticle

Sequencing and Analysis of mtDNA Genomes from the Teeth of Early Medieval Horses in Poland

by Edyta Pasicka, Mateusz Baca, Danijela Popović, Daniel Makowiecki and Maciej Janeczek

Genes 2026, 17(1), 95; https://doi.org/10.3390/genes17010095 - 18 Jan 2026

Cited by 1 | Viewed by 691

Abstract

Background: This study presents the sequencing and analysis of mitochondrial DNA (mtDNA) genomes from nine early medieval horse remains excavated across archaeological sites in Silesia region in present day Poland. Methods: Using aDNA extraction protocols optimized for short fragments, combined with target enrichment and high-throughput sequencing, we reconstructed partial mtDNA sequences for seven of the specimens. Results: The authenticity of the aDNA was confirmed through damage pattern analysis. Phylogenetic reconstruction revealed that the specimens belonged to six distinct mtDNA lineages (B, D, E, G, L, and M), indicating a high level of mitochondrial diversity within medieval Silesian horse population. Conclusions: These findings highlight the extensive mtDNA variability among domestic horses, reflecting the diversity of their ancestral populations rather than modern breed differentiation. This research enhances our understanding of horse population structure in medieval Europe, emphasizing the genetic complexity present during this period. Full article

(This article belongs to the Special Issue The 15th Anniversary of Genes: Feature Papers in the "Animal Genetics and Genomics" Section)

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16 pages, 2537 KB

Open AccessArticle

Transcriptome of Sterile Testes in dnd-Depleted Atlantic Salmon (Salmo salar L.) Highlights Genes Involved in Gonadal and Brain Development

by Aleksei Krasnov, Sergey Afanasyev, Jens-Erik Dessen, Marianne H. S. Hansen, Marianne Vaadal, Helge Tveiten and Øivind Andersen

Genes 2025, 16(9), 1095; https://doi.org/10.3390/genes16091095 - 16 Sep 2025

Viewed by 993

Abstract

Background/Objectives: Inactivation of the dnd gene involved in the development of primordial germ cells (PGCs) leads to the loss of gametes and halts reproductive development. Studies on sterile fish allow for the identification of genes and processes associated with GC differentiation. Methods: Atlantic salmon with GC-ablated testes were produced by temporal silencing of dnd. Gene expression was analyzed in sterile and fertile testes using 44k microarray and qPCR. Results: In sterile testes, transcripts of several GC markers were detected at low levels, suggesting the presence of cells with a GC-related expression profile that failed to initiate spermatogenesis. Expression of 260 genes was undetectable in the gonads of sterile males and females, and 61.5% of these were also inactivated during first maturation of fertile testes. This group was enriched with genes highly expressed in the brain, including those involved in endocrine and paracrine regulation, synaptic transmission, and numerous genes critical for brain development; among them, 45 genes encoding homeobox proteins. Another group of 229 genes showed increased expression in developing testes and included genes involved in neurosecretion and brain development regulation. GC-ablated testes showed increased expression of reproductive regulators such as amh and sdy and numerous immune genes, suggesting a reprogramming of GC-depleted testes. Temporal silencing of dnd indicated common developmental processes in the brains and gonads of Atlantic salmon testis that become inactive in testes at first maturation. These processes may play roles in PGC homing, the creation of a specific environment required for spermatogenesis, or facilitating communication between the gonads. Full article

(This article belongs to the Special Issue The 15th Anniversary of Genes: Feature Papers in the "Animal Genetics and Genomics" Section)

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Review

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20 pages, 364 KB

Open AccessReview

CSN1S1 and CSN1S2: Two Remarkable Examples of Genetically Modulated Alternative Splicing via Identification of Allele-Specific Splicing Events

by Gianfranco Cosenza, Andrea Fulgione, Emanuele D’Anza, Sara Albarella, Francesca Ciotola and Alfredo Pauciullo

Genes 2025, 16(9), 1011; https://doi.org/10.3390/genes16091011 - 27 Aug 2025

Cited by 1 | Viewed by 1643

Abstract

Splicing regulatory sequences are cornerstones for exon recognition. Mutations that modify them can severely compromise mRNA maturation and protein production. A wide range of mutations, including SNPs and InDels, can influence splicing regulatory signals either directly (e.g., altering canonical donor and acceptor dinucleotides) or indirectly (e.g., creating cryptic splice sites). CSN1S1 and CSN1S2 genes encode for the two main milk proteins, αs1 and αs2 caseins, respectively. They represent a remarkable and unique example of the possibilities for alternative splicing of individual genes, both due to the high number of alternative splices identified to date and for recognized allele-specific splicing events. To date, at least 13 alleles of CSN1S1 originating from mutations that affect canonical splice sites have been described in Bos taurus (CSN1S1 A, A1, and H), Ovis aries (E, H, and I), Capra hircus (D and G), Bubalus bubalis (E, F) and Camelidae (A, C, and D). Similarly, allele-specific splicing events have been described at the CSN1S2 locus in B. taurus. (CSN1S2 D), C. hircus (CSN1S2 D), B. bubalis (CSN1S2 B, B1, and B2), Equus asinus (CSN1S2 I B), and Camelidae. This review highlights that mutations affecting canonical splice sites, particularly donor sites, are significant sources of genetic variation impacting the casein production of the main dairy livestock species. Currently, a key limitation on this topic is the lack of detailed functional and proteomic studies. Future research should leverage advanced omics technologies like long-read transcriptomics and allele-resolved RNA sequencing to characterize these splicing mechanisms, guiding precision breeding strategies. Full article

(This article belongs to the Special Issue The 15th Anniversary of Genes: Feature Papers in the "Animal Genetics and Genomics" Section)

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