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9 pages, 569 KiB

Open AccessArticle

Digital Phenotyping Reveals Phenotype Diversity and Epistasis among White Spotting Alleles in the American Paint Horse

by Chelby Lynn Gossett, Danielle Guyer, Jessica Hein and Samantha A. Brooks

Genes 2023, 14(11), 2011; https://doi.org/10.3390/genes14112011 - 27 Oct 2023

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White spotting is an iconic feature of the American Paint Horse. The American Paint Horse Association (APHA) is dedicated to recording pedigree and performance of this stock-type breed, while preserving its distinctive coat color and conformation. Here, the depigmented proportion of the coat [...] Read more.

White spotting is an iconic feature of the American Paint Horse. The American Paint Horse Association (APHA) is dedicated to recording pedigree and performance of this stock-type breed, while preserving its distinctive coat color and conformation. Here, the depigmented proportion of the coat (% white coat) was measured using digital photograph analysis of 1195 registered American Paint Horses. Genotypes for nine white-spotting polymorphisms commonly found in Paint Horses, and two pigment-producing loci MCIR and ASIP genes, were also provided by the APHA. White-coat percent significantly increased in horses with more white-spotting alleles present, regardless of the number of loci bearing those alleles, likely due to a strong additive genetic effect at each white-spotting locus, as well as an additive epistatic effect among white spotting loci. Paint Horses with a chestnut base coat color (genotype e/e at MC1R) possessed a significantly higher white coat percentage, suggesting confirming an epistatic interaction between pigmentation signaling genes and loci for white spotting. The APHA registry categories of Regular versus Solid Paint-Bred also differed in their median white coat percentage (p < 0.0001), but not in the overall ranges of this phenotype, reenforcing the importance of the regional patterns of the depigmentation in the definition of the desired APHA phenotype. Multi-locus phenotype prediction models for white-coat percentage performed only moderately well, and improvements in the sample size and the number of loci genotyped will likely be needed before such an approach could be used practically by APHA breeders. In the future, models that enable phenotype prediction based on genotypes, and automated phenotype assessment could increase the production of valuable visual traits in the American Paint Horse population and improve the APHA member experience during the registration process. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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18 pages, 2136 KiB

Open AccessArticle

Identification of Differentially Expressed Genes after Endurance Runs in Karbadian Horses to Determine Candidates for Stress Indicators and Performance Capability

by Monika Reißmann, Abirami Rajavel, Zaur A. Kokov and Armin O. Schmitt

Genes 2023, 14(11), 1982; https://doi.org/10.3390/genes14111982 - 24 Oct 2023

Viewed by 1251

Abstract

RNA sequencing makes it possible to uncover genetic mechanisms that underlie certain performance traits. In order to gain a deeper insight into the genetic background and biological processes involved in endurance performance in horses, the changes in the gene expression profiles induced by [...] Read more.

RNA sequencing makes it possible to uncover genetic mechanisms that underlie certain performance traits. In order to gain a deeper insight into the genetic background and biological processes involved in endurance performance in horses, the changes in the gene expression profiles induced by endurance runs over long (70 km) and short (15 km) distances in the blood of Kabardian horses (Equus caballus) were analyzed. For the long-distance runs, we identified 1484 up- and 691 downregulated genes, while after short-distance runs, only 13 up- and 8 downregulated genes (FC > |1.5|; p < 0.05) were found. These differentially expressed genes (DEGs) are involved in processes and pathways that are primarily related to stress response (interleukin production, activation of inflammatory system) but also to metabolism (carbohydrate catabolic process, lipid biosynthesis, NADP metabolic process). The most important genes involved in these processes therefore represent good candidates for the monitoring and evaluation of the performance of horses in order to avoid excessive demands when endurance performance is required, like ACOD1, CCL5, CD40LG, FOS, IL1R2, IL20RA, and IL22RA2, on the one hand, and, on the other hand, for assessing the suitability of a horse for endurance races, like GATA2, GYG1, HIF1A, MOGAT1, PFKFB3, PLIN5, SIK1, and STBD1. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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12 pages, 932 KiB

Open AccessArticle

Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide

by Chujie Chen, Bo Zhu, Xiangwei Tang, Bin Chen, Mei Liu, Ning Gao, Sheng Li and Jingjing Gu

Genes 2023, 14(6), 1211; https://doi.org/10.3390/genes14061211 - 01 Jun 2023

Cited by 4 | Viewed by 1860

Abstract

In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data [...] Read more.

In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had varying degrees of impact on various horse breeds. However, recent inbreeding events were uncommon, particularly among indigenous horse breeds. Consequently, the ROH-based genomic inbreeding coefficient could aid in monitoring the level of inbreeding. Using the Thoroughbred population as a case study, we discovered 24 ROH islands containing 72 candidate genes associated with artificial selection traits. We found that the candidate genes in Thoroughbreds were involved in neurotransmission (CHRNA6, PRKN, and GRM1), muscle development (ADAMTS15 and QKI), positive regulation of heart rate and heart contraction (HEY2 and TRDN), regulation of insulin secretion (CACNA1S, KCNMB2, and KCNMB3), and spermatogenesis (JAM3, PACRG, and SPATA6L). Our findings provide insight into horse breed characteristics and future breeding strategies. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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17 pages, 4066 KiB

Open AccessArticle

Donkey Oil-Based Ketogenic Diet Prevents Tumor Progression by Regulating Intratumor Inflammation, Metastasis and Angiogenesis in CT26 Tumor-Bearing Mice

by Huachen Zhang, Lan Xie, Ning Zhang, Xingzhen Qi, Ting Lu, Jingya Xing, Muhammad Faheem Akhtar, Lanjie Li and Guiqin Liu

Genes 2023, 14(5), 1024; https://doi.org/10.3390/genes14051024 - 30 Apr 2023

Cited by 1 | Viewed by 4557

Abstract

Colon cancer is one of the typical malignant tumors, and its prevalence has increased yearly. The ketogenic diet (KD) is a low-carbohydrate and high-fat dietary regimen that inhibits tumor growth. Donkey oil (DO) is a product with a high nutrient content and a [...] Read more.

Colon cancer is one of the typical malignant tumors, and its prevalence has increased yearly. The ketogenic diet (KD) is a low-carbohydrate and high-fat dietary regimen that inhibits tumor growth. Donkey oil (DO) is a product with a high nutrient content and a high bioavailability of unsaturated fatty acids. Current research investigated the impact of the DO-based KD (DOKD) on CT26 colon cancer in vivo. Our findings revealed that DOKD administration significantly lowered CT26⁺ tumor cell growth in mice, and the blood β-hydroxybutyrate levels in the DOKD group was significantly higher than those in the natural diet group. Western blot results showed that DOKD significantly down-regulated Src, hypoxia inducible factor-1α (HIF-1α), extracellular signal-related kinases 1 and 2 (Erk1/2), snail, neural cadherin (N-cadherin), vimentin, matrix metallopeptidase 9 (MMP9), signal transducer and activator of transcription 3 (STAT3), and vascular endothelial growth factor A (VEGFA), and it significantly up-regulated the expressions of Sirt3, S100a9, interleukin (IL)-17, nuclear factor-kappaB (NF-κB) p65, Toll-like receptor 4 (TLR4), MyD88, and tumor necrosis factor-α. Meanwhile, in vitro validation results showed that LW6 (a HIF-1α inhibitor) significantly down-regulated the expressions of HIF-1α, N-cadherin, vimentin, MMP9, and VEGFA, which supported those of the in vivo findings. Furthermore, we found that DOKD inhibited CT26⁺ tumor cell growth by regulating inflammation, metastasis, and angiogenesis by activating the IL-17/TLR4/NF-κB p65 pathway and inhibiting the activation of the Src/HIF-1α/Erk1/2/Snail/N-cadherin/Vimentin/MMP9 and Erk1/2/HIF-1α/STAT3/VEGFA pathways. Our findings suggest that DOKD may suppress colon cancer progression and help prevent colon cancer cachexia. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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18 pages, 1964 KiB

Open AccessArticle

Selection and Validation of Reference Genes for Gene Expression Studies in an Equine Adipose-Derived Mesenchymal Stem Cell Differentiation Model by Proteome Analysis and Reverse-Transcriptase Quantitative Real-Time PCR

by Angela L. Riveroll, Sabrina Skyba-Lewin, K. Devon Lynn, Glady’s Mubyeyi, Ahmad Abd-El-Aziz, Frederick S. T. Kibenge, Molly J. T. Kibenge, Alejandro M. Cohen, Blanca Esparza-Gonsalez, Laurie McDuffee and William J. Montelpare

Genes 2023, 14(3), 673; https://doi.org/10.3390/genes14030673 - 08 Mar 2023

Cited by 2 | Viewed by 1464

Abstract

Adipose-derived stem cells (ADSCs) are used in tissue regeneration therapies. The objective of this study is to identify stable reference genes (RGs) for use in gene expression studies in a characterized equine adipose-derived mesenchymal stem cell (EADMSC) differentiation model. ADSCs were differentiated into [...] Read more.

Adipose-derived stem cells (ADSCs) are used in tissue regeneration therapies. The objective of this study is to identify stable reference genes (RGs) for use in gene expression studies in a characterized equine adipose-derived mesenchymal stem cell (EADMSC) differentiation model. ADSCs were differentiated into adipocytes (ADs) or osteoblasts (OBs), and the proteomes from these cells were analyzed by liquid chromatography tandem mass spectrometry. Proteins that were stably expressed in all three cells types were identified, and the mRNA expression stabilities for their corresponding genes were validated by RT-qPCR. PPP6R1, CCDC97, and then either ACTB or EPHA2 demonstrated the most stable mRNA levels. Normalizing target gene C_q data with at least three of these RGs simultaneously, as per MIQE guidelines (PPP6R1 and CCDC97 with either ACTB or EPHA2), resulted in congruent conclusions. FABP5 expression was increased in ADs (5.99 and 8.00 fold, p = 0.00002 and p = 0.0003) and in OBs (5.18 and 5.91 fold, p = 0.0011 and p = 0.0023) relative to ADSCs. RUNX2 expression was slightly higher in ADs relative to ADSCs (1.97 and 2.65 fold, p = 0.04 and p = 0.01), but not in OBs (0.9 and 1.03 fold, p = 0.58 and p = 0.91). Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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13 pages, 1906 KiB

Open AccessArticle

Whole-Genome Sequence Analysis Reveals the Origin of the Chakouyi Horse

by Ying Li, Yu Liu, Min Wang, Xiaoran Lin, Yuanyuan Li, Tao Yang, Mo Feng, Yao Ling and Chunjiang Zhao

Genes 2022, 13(12), 2411; https://doi.org/10.3390/genes13122411 - 19 Dec 2022

Cited by 3 | Viewed by 1533

Abstract

The Chakouyi horse is an ancient Chinese indigenous horse breed distributed in Gansu Province in northwestern China, and is also one of the key breeds protected by the government. However, the origin of the Chakouyi horse remains unclear. As it is distributed in [...] Read more.

The Chakouyi horse is an ancient Chinese indigenous horse breed distributed in Gansu Province in northwestern China, and is also one of the key breeds protected by the government. However, the origin of the Chakouyi horse remains unclear. As it is distributed in a key region of the Silk Road, it was speculated that the origin of the Chakouyi horse might involve the foreign horse breeds found along this ancient commercial artery. In this study, whole-genome resequencing data of 12 horse breeds, including both indigenous and foreign horses, were applied to reveal the genetic relationships between the Chakouyi horse and other breeds, as well as the ancestry of this ancient breed. An analysis of the population structure and admixture showed that there is no close genetic affinity between the Chakouyi horse and the foreign horses while Chinese indigenous horse populations were grouped together in accordance with their geographic locations, and the Chakouyi horse showed a closer relationship with Kazak horses, Mongolian horses, and Tibetan horses. The results from the ancestral composition prediction indicated that the Kazak horse and the Mongolian horse might be two ancestors of the Chakouyi horse. Furthermore, the genome-wide selection signature analysis revealed that the DMRT3 gene was positively selected in the Chakouyi horse and related to the gait trait of the breed. Our results provide insights into the native origin of the Chakouyi horse and indicate that Kazak and Mongolian horses played important roles in the formation of the Chakouyi horse. Genetic communication between the Chakouyi horse and other horse populations could be attributed, at least partially, to population migrations and trade activities along the ancient commercial routes. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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16 pages, 2333 KiB

Open AccessArticle

Transcriptional Specificity Analysis of Testis and Epididymis Tissues in Donkey

by Mubin Yu, Xiaoyuan Zhang, Jiamao Yan, Jianhua Guo, Fali Zhang, Kexin Zhu, Shuqin Liu, Yujiang Sun, Wei Shen and Junjie Wang

Genes 2022, 13(12), 2339; https://doi.org/10.3390/genes13122339 - 11 Dec 2022

Cited by 2 | Viewed by 1562

Abstract

Donkeys, with high economic value for meat, skin and milk production, are important livestock. However, the current insights into reproduction of donkeys are far from enough. To obtain a deeper understanding, the differential expression analysis and weighted gene co-expression network analysis (WGCNA) of [...] Read more.

Donkeys, with high economic value for meat, skin and milk production, are important livestock. However, the current insights into reproduction of donkeys are far from enough. To obtain a deeper understanding, the differential expression analysis and weighted gene co-expression network analysis (WGCNA) of transcriptomic data of testicular and epididymis tissues in donkeys were performed. In the result, there were 4313 differentially expressed genes (DEGs) in the two tissues, including 2047 enriched in testicular tissue and 2266 in epididymis tissue. WGCNA identified 1081 hub genes associated with testis development and 6110 genes with epididymal development. Next, the tissue-specific genes were identified with the above two methods, and the gene ontology (GO) analysis revealed that the epididymal-specific genes were associated with gonad development. On the other hand, the testis-specific genes were involved in the formation of sperm flagella, meiosis period, ciliary assembly, ciliary movement, etc. In addition, we found that eca-Mir-711 and eca-Mir-143 likely participated in regulating the development of epididymal tissue. Meanwhile, eca-Mir-429, eca-Mir-761, eca-Mir-200a, eca-Mir-191 and eca-Mir-200b potentially played an important role in regulating the development of testicular tissue. In short, these results will contribute to functional studies of the male reproductive trait in donkeys. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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15 pages, 1455 KiB

Open AccessArticle

Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule

by Xiujuan Ren, Yuanyi Liu, Yiping Zhao, Bei Li, Dongyi Bai, Gerelchimeg Bou, Xinzhuang Zhang, Ming Du, Xisheng Wang, Tugeqin Bou, Yingchao Shen and Manglai Dugarjaviin

Genes 2022, 13(12), 2188; https://doi.org/10.3390/genes13122188 - 23 Nov 2022

Viewed by 1732

Abstract

Interspecific hybridization often shows negative effects on hybrids. However, only a few multicellular species, limited to a handful of plants and animals, have shown partial genetic mechanisms by which hybridization leads to low fitness in hybrids. Here, to explore the outcome of combining [...] Read more.

Interspecific hybridization often shows negative effects on hybrids. However, only a few multicellular species, limited to a handful of plants and animals, have shown partial genetic mechanisms by which hybridization leads to low fitness in hybrids. Here, to explore the outcome of combining the two genomes of a horse and donkey, we analyzed the whole-genome sequences from an Equus parent-offspring trio using Illumina platforms. We generated 41.39× and 46.21× coverage sequences for the horse and mule, respectively. For the donkey, a 40.38× coverage sequence was generated and stored in our laboratory. Approximately 24.86 million alleles were discovered that varied from the reference genome. Single nucleotide polymorphisms were used as polymorphic markers for assigning alleles to their parental genomic inheritance. We identified 25,703 Mendelian inheritance error single nucleotide polymorphisms in the mule genome that were not inherited from the parents through Mendelian inheritance. A total of 555 de novo single nucleotide polymorphisms were also identified. The rate of de novo single nucleotide polymorphisms was 2.21 × 10⁻⁷ in the mule from the Equus parent-offspring trio. This rate is obviously higher than the natural mutation rate for Equus, which is also consistent with the previous hypothesis that interracial crosses may have a high mutation rate. The genes associated with these single nucleotide polymorphisms are mainly involved in immune processes, DNA repair, and cancer processes. The results of the analysis of three genomes from an Equus parent-offspring trio improved our knowledge of the consequences of the integration of parental genomes in mules. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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10 pages, 2061 KiB

Open AccessArticle

Identification of Candidate Genes for Twinning Births in Dezhou Donkeys by Detecting Signatures of Selection in Genomic Data

by Taifeng Xie, Shuer Zhang, Wei Shen, Guoliang Zhang, Rong Guo, Wei Zhang, Yanhang Cao, Qingjie Pan, Fengxin Liu, Yujiang Sun and Shuqin Liu

Genes 2022, 13(10), 1902; https://doi.org/10.3390/genes13101902 - 19 Oct 2022

Cited by 1 | Viewed by 1290

Abstract

Twinning trait in donkeys is an important manifestation of high fecundity, but few reports are available elucidating its genetic mechanism. To explore the genetic mechanism underlying the twin colt trait in Dezhou donkeys, DNA from 21 female Dezhou donkeys that had birthed single [...] Read more.

Twinning trait in donkeys is an important manifestation of high fecundity, but few reports are available elucidating its genetic mechanism. To explore the genetic mechanism underlying the twin colt trait in Dezhou donkeys, DNA from 21 female Dezhou donkeys that had birthed single or twin colts were collected for whole-genome resequencing. F_ST, θπ and Tajima’s D were used to detect the selective sweeps between single and twin colt fecundity in the Dezhou donkey groups. Another set of 20 female Dezhou donkeys with single or multiple follicles during estrus were selected to compare concentrations of reproductive hormone including follicle-stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E₂) and progesterone (P₄). Four candidate genes including ENO2, PTPN11, SOD2 and CD44 were identified in the present study. The CD44 gene had the highest F_ST value, and ENO2, PTPN11 and SOD2 were screened by two joint analyses (F_ST and θπ, θπ and Tajima’s D). There was no significant difference in the LH, FSH and P₄ levels between the two groups (p > 0.05); however, the serum E₂ content in the multi-follicle group was significantly higher than that in the single-follicle group (p < 0.05). The identified candidate genes may provide new insights into the genetic mechanism of donkey prolificacy and may be useful targets for further research on high reproductive efficiency. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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11 pages, 1800 KiB

Open AccessArticle

MSTN Regulatory Network in Mongolian Horse Muscle Satellite Cells Revealed with miRNA Interference Technologies

by Undarmaa Budsuren, Tseweendolmaa Ulaangerel, Yingchao Shen, Guiqin Liu, Toli Davshilt, Minna Yi, Demuul Bold, Xinzhuang Zhang, Dongyi Bai, Dulguun Dorjgotov, Gantulga Davaakhuu, Tuyatsetseg Jambal, Bei Li, Ming Du, Manglai Dugarjav and Gerelchimeg Bou

Genes 2022, 13(10), 1836; https://doi.org/10.3390/genes13101836 - 11 Oct 2022

Cited by 2 | Viewed by 1822

Abstract

Myostatin (MSTN), a member of the transforming growth factor-β superfamily, inhibits the activation of muscle satellite cells. However, the role and regulatory network of MSTN in equine muscle cells are not well understood yet. We discovered that MSTN knockdown significantly reduces [...] Read more.

Myostatin (MSTN), a member of the transforming growth factor-β superfamily, inhibits the activation of muscle satellite cells. However, the role and regulatory network of MSTN in equine muscle cells are not well understood yet. We discovered that MSTN knockdown significantly reduces the proliferation rate of equine muscle satellite cells. In addition, after the RNA sequencing of equine satellite cells transfected with MSTN-interference plasmid and control plasmid, an analysis of the differentially expressed genes was carried out. It was revealed that MSTN regulatory networks mainly involve genes related to muscle function and cell-cycle regulation, and signaling pathways, such as Notch, MAPK, and WNT. Subsequent real-time PCR in equine satellite cells and immunohistochemistry on newborn and adult muscle also verified the MSTN regulatory network found in RNA sequencing analysis. The results of this study provide new insight into the regulatory mechanism of equine MSTN. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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16 pages, 2258 KiB

Open AccessArticle

An Integrated Analysis of Lactation-Related miRNA and mRNA Expression Profiles in Donkey Mammary Glands

by Yaqi Fei, Yedan Gai, Qingchao Liao, Linxi Zhang, Zheng Li, Bojiang Li, Man Bai, Na Li and Liang Deng

Genes 2022, 13(9), 1637; https://doi.org/10.3390/genes13091637 - 12 Sep 2022

Cited by 2 | Viewed by 1554

Abstract

Donkey milk is consumed by humans for its nutritional and therapeutic properties. MicroRNAs (miRNAs) and messenger RNAs (mRNAs) have been implicated in the regulation of milk component synthesis and mammary gland development. However, the regulatory profile of the miRNAs and mRNAs involved in [...] Read more.

Donkey milk is consumed by humans for its nutritional and therapeutic properties. MicroRNAs (miRNAs) and messenger RNAs (mRNAs) have been implicated in the regulation of milk component synthesis and mammary gland development. However, the regulatory profile of the miRNAs and mRNAs involved in lactation in donkeys is unclear. We performed mRNA-seq and miRNA-seq and constructed coexpression regulatory networks for the mammary glands during the lactating and nonlactating period of jennies. We identified 3144 differentially expressed (DE) mRNAs (987 upregulated mRNAs and 2157 downregulated mRNAs) and 293 DE miRNAs (231 upregulated miRNAs and 62 downregulated miRNAs) in the lactating group compared to the nonlactating group. The DE miRNA target mRNA were significantly associated with pathways related to RNA polymerase, glycosphingolipid biosynthesis, mRNA surveillance, ribosome biogenesis in eukaryotes, glycerophospholipid metabolism, Ras signaling, and the fly hippo signaling pathway. The mRNA–miRNA coregulation analysis showed that novel-m0032-3p, miR-195, miR-26-5p, miR-23-3p, miR-674-3p, and miR-874-3p are key miRNAs that target mRNAs involved in immunity and milk lipid, protein, and vitamin metabolism in the jenny mammary gland. Our results improve the current knowledge of the molecular mechanisms regulating bioactive milk component metabolism in the mammary glands and could be used to improve milk production in donkeys. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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Review

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16 pages, 1738 KiB

Open AccessReview

Unlocking Horse Y Chromosome Diversity

by Irene Cardinali, Andrea Giontella, Anna Tommasi, Maurizio Silvestrelli and Hovirag Lancioni

Genes 2022, 13(12), 2272; https://doi.org/10.3390/genes13122272 - 02 Dec 2022

Cited by 3 | Viewed by 2200

Abstract

The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y [...] Read more.

The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds. Full article

(This article belongs to the Special Issue Equine Genetics and Genomics)

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