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Advances in Genetic Variability and Selection of Equines

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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: 30 September 2026 | Viewed by 6948

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Dr. János Posta

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Department of Animal Husbandry, Institute of Animal Science, Biotechnology and Nature Conservation, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, H-4032 Debrecen, Hungary
Interests: population genetics; gene conservation; selection response; genetic improvement

Special Issue Information

Dear Colleagues,

Advances in genetics have enabled new insights into genetic variability, gene conservation, and evaluations of selection responses in horses. Applications of new methods and software to maintain genetic variability of native and commercial breeds could provide new insights. The inclusion of new technology during the selection of livestock species could also support breeders in improving their breeding programs and give relevant information during the selection process. Important topics of study in this field include population genetics, molecular genetics, biodiversity, selection against genetic disorders, and understanding the inheritance of complex traits. The application of precision livestock farming in selection may also enhance genetic progress.

The aim of this Special Issue of Animals is to collate the latest advances and insights from the fields of population genetics and selection methods of horses. We strive for this Special Issue to contribute to a better understanding of the genetic variability of endangered populations and commercial breeds, as well as provide new approaches to maintaining genetic variability and selection progress in horses. Submissions of multiple article types, such as original research articles, reviews, and methods, are welcome.

Dr. János Posta
Guest Editor

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Keywords

population genetics
gene conservation
selection response
genetic improvement

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Published Papers (6 papers)

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Research

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20 pages, 4146 KB

Open AccessArticle

Genome-Wide Characterization of the TGF-β Gene Family in Donkey (Equus asinus) Reveals Lineage-Specific Gene Duplications and Deleterious Mutations

by Tanveer Nasir, Muhammad Tariq, Mohamed Tharwat, Muhammad Safdar, Yasmeen Junejo and Fahad A. Alshanbari

Animals 2026, 16(13), 2028; https://doi.org/10.3390/ani16132028 - 2 Jul 2026

Viewed by 852

Abstract

The transforming growth factor-beta (TGF-β) superfamily regulates diverse biological processes, including proliferation, differentiation, apoptosis, tissue remodeling, and reproductive signaling across metazoans. Here, we performed a genome-wide characterization of the TGF-β gene family in donkey (Equus asinus, ASM1607732v2) using comparative genomics and bioinformatics analyses, with horse (Equus caballus, EquCab3.0) as a reference to investigate evolutionary conservation and functional divergence. Genome assemblies and proteomes were retrieved from NCBI, and TGF-β genes were identified using BLASTp and HMMER searches (Pfam PF00019), followed by phylogenetic, conserved motif, synteny, Ka/Ks, mutation prediction, subcellular localization, and tissue-specific expression analyses. We identified 40 TGF-β genes in donkeys, exceeding the numbers reported in several mammals, suggesting possible lineage-specific expansion or differential gene retention within Equidae. Phylogenetic and motif analyses demonstrated strong evolutionary conservation across the two principal clades (TGF-β-like and BMP-like). Four segmental duplications were identified, with Ka/Ks ratios ranging from 0.28 to 0.43, indicating strong purifying selection on duplicated genes. Synteny analysis revealed extensive collinearity with the horse genome, supporting conserved equid genomic architecture. Comparative sequence analysis identified 160 amino acid variants, including 11 predicted deleterious mutations in key genes (GDF6, GDF9, GDF10, BMP15, and RGMA), suggesting potential functional divergence associated with reproductive and developmental pathways. Importantly, transcriptomic validation using publicly available donkey RNA-seq tissue expression data (NCBI BioProject: PRJNA1017964) revealed distinct tissue-specific expression patterns, with reproductive tissues (ovary and uterus) displaying enriched expression of TGF-β/BMP signaling components, particularly TGFBR1, TGFBR2, TGFB1, BMP2, BMP4, and BMP7, while canonical fecundity genes (GDF9 and BMP15) exhibited ovary-associated expression. This receptor-dominant signaling profile may have a coordinated TGF-β regulatory network underlying folliculogenesis, reproductive tissue remodeling, and fertility-related processes in donkeys. Subcellular localization predictions showed that most proteins (22/40) were extracellularly localized, consistent with conserved signaling functions. Together, this study provides the first integrated genomic and tissue-expression atlas of the donkey TGF-β superfamily, offering new insights into equid-specific evolutionary conservation, reproductive signaling, and functional divergence. Full article

(This article belongs to the Special Issue Advances in Genetic Variability and Selection of Equines)

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18 pages, 4961 KB

Open AccessArticle

Machine Learning-Based Genome-Wide Association Study Reveals Genetic Loci Associated with Body Measurement Traits in Yili Horses

by Zhehong Shen, Liping Yang, Yuheng Xue, Xiaokang Chang, Jingxuan Shen, Weijun Sun, Yaqi Zeng, Jun Meng and Xinkui Yao

Animals 2026, 16(9), 1373; https://doi.org/10.3390/ani16091373 - 29 Apr 2026

Viewed by 475

Abstract

Body measurement traits are key indicators for evaluating growth performance, production potential, and breeding value in Yili horses. However, studies investigating the association between body measurement traits and mutation loci in Yili horses remain limited. In this study, 255 adult Yili mares were used as the study population, including 152 speed-type and 103 meat-type individuals. Whole-genome resequencing was performed, and four phenotypic traits and body weight were measured. A mixed linear model (MLM)-based genome-wide association study (GWAS) was conducted using GEMMA (v 0.98.5), incorporating age, farm effects, and top three principal components as covariates. In parallel, a machine learning-based GWAS (ML-GWAS) framework integrating Lasso regression for feature selection and Random Forest (RF) with five-fold cross-validation was applied to improve the detection of complex genetic signals. Using both conventional GWAS methods and machine learning-based GWAS approaches, a total of 238 mutation loci significantly associated with body measurement traits were identified, and 277 candidate genes were annotated. These genes may play a role in several biological processes, including skeletal development, muscle formation, cell growth, energy metabolism, and protein synthesis. The findings suggest that genetic variations have already manifested among the studied groups. The results indicate that genetic differences have already emerged among different Yili horse populations at the genomic level. Furthermore, this study demonstrates that integrating machine learning with conventional GWAS effectively improves the detection efficiency of loci associated with complex traits, while also providing new molecular evidence for understanding the genetic mechanisms underlying differences in body measurement traits among Yili horse groups. Full article

(This article belongs to the Special Issue Advances in Genetic Variability and Selection of Equines)

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10 pages, 226 KB

Open AccessFeature PaperArticle

Pedigree Investigation of Polish Sport Horses in Show Jumping: Insights for Global Breeding

by Tomasz Próchniak

Animals 2026, 16(8), 1152; https://doi.org/10.3390/ani16081152 - 10 Apr 2026

Viewed by 1048

Abstract

The aim of this study was to characterise the pedigree and genetic structure of Polish Sport Horses competing in Grand Prix show jumping events and to assess the implications for international sport horse breeding. Pedigrees of 513 horses were analysed, encompassing a total of 18,836 individuals over a maximum of 16 generations. The completeness and depth of the pedigrees allowed for a reliable estimation of inbreeding coefficients and genetic diversity. The mean inbreeding coefficient was low (0.645%), yet 82% of the horses exhibited some degree of inbreeding. The greatest loss of genetic variability was observed in non-founder generations, most likely due to the intensive use of a limited number of high-value stallions with domestic mares—a bottleneck effect. The most significant founders contributing to the population were the Thoroughbred stallions Ladykiller and Rantzau, as well as the Anglo-Arab stallion Ramzes, highlighting the international influence on the contemporary population. These findings emphasise the need for systematic monitoring of genetic diversity and the strategic use of pedigree data to minimise inbreeding and preserve the genetic potential of Polish Sport Horses for international breeding programmes. Full article

(This article belongs to the Special Issue Advances in Genetic Variability and Selection of Equines)

21 pages, 1669 KB

Open AccessArticle

Population Structure and Genetic Diversity Among Lipizzan Mare Families in Hungary Based on Microsatellite Genotyping

by Máté Kovács, Bettina Hegedűs, Sándor Mihók, Renáta Knop, Csaba Szabó and János Posta

Animals 2026, 16(7), 1062; https://doi.org/10.3390/ani16071062 - 31 Mar 2026

Viewed by 557

Abstract

The conservation of genetic diversity in historically structured horse breeds requires fi-ne-scale population genetic evaluation beyond conventional pedigree-based approaches. The present study assessed genetic diversity, population structure, and mare family differentiation in a Lipizzan horse population using 16 ISAG/FAO-recommended microsatellite markers. A total of 172 mares representing 29 mare families were genotyped. All loci were polymorphic, with a mean number of alleles per locus of 6.69 and a mean effective number of alleles of 3.56. The average polymorphism information content (PIC = 0.66) indicated high marker informativeness. Mean observed heterozygosity was slightly lower than expected heterozygosity, although the overall negative inbreeding coefficient suggested general heterozygote excess and low population-level inbreeding, whilst the genetic differentiation among mare families was moderate. The principal components and the STRUCTURE analysis indicated admixture among mare families. Seven private alleles were detected across six loci, highlighting the presence of rare lineage-specific variants. These findings emphasize the importance of mare family-based analyses for identifying hidden genetic structures that may not be captured by population-level averages. The integration of microsatellite-based diversity evaluation provides a robust framework for de-signing sustainable breeding and conservation strategies aimed at preserving both overall variability and rare lineage-specific genetic components. Full article

(This article belongs to the Special Issue Advances in Genetic Variability and Selection of Equines)

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15 pages, 6161 KB

Open AccessArticle

Differential Expression and Analysis of TBX3 Gene in Skin Tissues of Dun Mongolian Horses with and Without Bider Markings

by Tana An and Manglai Dugarjaviin

Animals 2026, 16(2), 297; https://doi.org/10.3390/ani16020297 - 18 Jan 2026

Cited by 3 | Viewed by 978

Abstract

(1) Background: The dun coat color, a wild-type phenotype in horses characterized by pigment dilution and primitive markings, is regulated by TBX3. This study explored the expression and localization of TBX3 in the Bider marking (a primitive mark unique to the shoulder of horses); (2) Methods: We compared skin tissues from Bider-marked and non-Bider dun Mongolian horses. Samples were collected from the Bider area (dark-colored/light-colored shoulder), dorsal midline, and croup. Histological staining, qRT-PCR, and Western blotting were used to analyze pigment distribution and TBX3 expression at mRNA and protein levels; (3) Results: Histology revealed asymmetric pigment deposition in hair shafts from light-colored areas of both Bider and non-Bider horses, whereas dark areas showed symmetric distribution. qRT-PCR and Western blotting showed TBX3 expression was significantly higher in the shoulder of non-Bider horses compared to Bider horses. Conversely, Bider horses exhibited higher TBX3 levels in all other sampled areas. Immunohistochemistry localized TBX3 protein to the epidermis and hair follicle bulbs in both groups; (4) Conclusions: In dun Mongolian horses, TBX3 expression differences between dark and light skin areas correlate with Bider markings. TBX3 is implicated in this specific pigment marking, though its upstream regulation requires further study. These findings provide key insights into the mechanism behind Bider marking formation. Full article

(This article belongs to the Special Issue Advances in Genetic Variability and Selection of Equines)

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Review

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21 pages, 1647 KB

Open AccessReview

The Donkey Genome: From Evolutionary Insights to Sustainable Breeding Strategies

by Qifei Zhu, Muhammad Zahoor Khan, Yadi Jing, Mingyang Geng, Xuemin Zhang, Yunfan Zheng, Xianggang Cao, Yongdong Peng and Changfa Wang

Animals 2026, 16(1), 93; https://doi.org/10.3390/ani16010093 - 29 Dec 2025

Cited by 3 | Viewed by 2415

Abstract

Donkeys (Equus asinus) are economically and ecologically important livestock species whose genetic potential remains underexplored. This review synthesizes recent advances in donkey genomics, tracing their evolutionary history while evaluating current applications in selective breeding, conservation genetics, and agricultural management. By integrating evidence from population genomics, functional genomics, and comparative evolutionary studies, we summarize major genomic discoveries and identify persistent knowledge gaps, with a focus on translating genomic information into practical breeding outcomes. High-quality reference genomes, population resequencing, and ancient DNA analyses have clarified the African origin, global dispersal history, and environmental adaptation of donkeys. Genome-wide approaches, including GWAS, QTL mapping, and multi-omics analyses, have further identified genes and regulatory pathways associated with thermotolerance, metabolism, reproduction, and milk production. Nevertheless, progress is still limited by small sample sizes, variable sequencing depth, and inconsistencies in phenotyping and bioinformatic pipelines, which constrain cross-population comparisons and practical applications. Addressing these challenges through standardized phenotyping, improved data integration, and collaborative research frameworks will lay the groundwork for effective conservation strategies and sustainable genomic breeding of global donkey populations. Full article

(This article belongs to the Special Issue Advances in Genetic Variability and Selection of Equines)

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