Comparative transcriptome analysis of slow-twitch and fast-twitch muscles in Kazakh horses.

This study conducted a thorough analysis of the myofiber type composition in the extensor digitorum longus muscle (EDL) and soleus muscle (SOL) of Kazakh horses, across different genders (male and female). The results showed significant differences in myofiber type composition between EDL and SOL, with a higher proportion of Type I fibers in SOL muscles and a greater prevalence of Type II fibers in EDL muscles. Additionally, the myofiber diameter in Kazakh horses was relatively small, potentially related to the tenderness and edible quality of their muscles. Using high-throughput sequencing technology, we constructed 32 cDNA sequencing libraries and obtained high-quality read data. Gene expression analysis revealed 278 and 372 differentially expressed genes (DEGs) in EDL and SOL muscles, respectively, including genes related to muscle contraction, metabolism, and development. Intersection analysis of DEGs between genders showed that 60 DEGs were significantly different in both male and female horses. GO annotation and KEGG analysis further elucidated the roles of these DEGs in muscle structure, function, and cellular signaling. Protein-protein interaction (PPI) network analysis and identification of hub genes provided new insights into the molecular mechanisms underlying muscle growth and development. Finally, the reliability of the DEGs data was validated through quantitative real-time PCR (qRT-PCR). This study not only enhances our understanding of the biological characteristics of horse muscles but also provides potential molecular targets for improving horse muscle performance and health.

Investigating age-related differences in muscles of Kazakh horse through transcriptome analysis.

This study conducted transcriptome sequencing on the skeletal muscles of three different anatomical locations across various growth stages to investigate the impact of ages on crucial candidate genes and molecular mechanisms associated with muscle development in Kazakh horses. Sixteen Kazakh horses were selected, and they were divided into four age groups, each with four biological replicates. Tissue samples from the longest dorsal muscle, abdominal muscle, and diaphragm muscle were collected for analysis. The results revealed differential mRNA expression in the longest dorsal muscle between the eight-month group (Group O) and the 10-year group (Group F), with 434 up-regulated and 322 down-regulated genes. In the abdominal muscle, there were 125 up-regulated and 127 down-regulated genes, while in the diaphragm muscle, there were 73 up-regulated and 70 down-regulated genes. In this study, GO enrichment analysis focused on biological processes. KEGG pathway analysis highlighted the Oxidative Phosphorylation pathway for the longest dorsal muscle, annotating 37 differentially expressed genes (DEGs), including ATP5PF, NDUFB8, and ATP5MG, all of which were down-regulated. For the abdominal muscle, the ECM-receptor interaction pathway was enriched, annotating 7 DEGs such as COL4A2, COL4A1, and ITGA5. In the diaphragm muscle, the Hippo signaling pathway was enriched, annotating 6 DEGs, including SERPINE1, RASSF1, and FZD10. This study provides robust data support and a theoretical foundation for a comprehensive understanding of the influence of age on skeletal muscle development in horses.

Differential age-related transcriptomic analysis of ovarian granulosa cells in Kazakh horses.

Introduction: The Kazakh horse, renowned for its excellence as a breed, exhibits distinctive reproductive traits characterized by early maturity and seasonal estrus. While normal reproductive function is crucial for ensuring the breeding and expansion of the Kazakh horse population, a noteworthy decline in reproductive capabilities is observed after reaching 14 years of age. Methods: In this study, ovarian granulosa cells (GCs) were meticulously collected from Kazakh horses aged 1, 2, 7, and above 15 years old (excluding 15 years old) for whole transcriptome sequencing. Results: The analysis identified and selected differentially expressed mRNAs, lncRNAs, miRNAs, and circRNAs for each age group, followed by a thorough examination through GO enrichment analysis. The study uncovered significant variations in the expression profiles of mRNAs, lncRNAs, miRNAs, and circRNAs within GCs at different stages of maturity. Notably, eca-miR-486-3p and miR-486-y exhibited the highest degree of connectivity. Subsequent GO, KEGG, PPI, and ceRNA network analyses elucidated that the differentially expressed target genes actively participate in signaling pathways associated with cell proliferation, apoptosis, and hormonal regulation. These pathways include but are not limited to the MAPK signaling pathway, Hippo signaling pathway, Wnt signaling pathway, Calcium signaling pathway, Aldosterone synthesis and secretion, Cellular senescence, and NF-kappa B signaling pathway-essentially encompassing signal transduction pathways crucial to reproductive processes. Discussion: This research significantly contributes to unraveling the molecular mechanisms governing follicular development in Kazakh horses. It establishes and preliminarily validates a differential regulatory network involving lncRNA-miRNA-mRNA, intricately associated with processes such as cell proliferation, differentiation, and apoptosis and integral to the developmental intricacies of stromal follicles. The findings of this study provide a solid theoretical foundation for delving deeper into the realm of reproductive aging in Kazakh mares, presenting itself as a pivotal regulatory pathway in the context of horse ovarian development.

Transcriptome identification of differential mammary genes of Kazakh horses during early pregnancy.

Kazakh mares have attracted widespread attention with their outstanding lactation traits. Lactation is a complex dynamic process regulated by multiple factors. The extensive application of transcriptome sequencing technology enables researchers to further explore this biological issue. This study selected three pregnant and three non-pregnant Kazakh mares as the research subject. Their mammary glands were taken for transcriptome sequencing. The results show that there are 9 lncRNAs and 122 mRNAs differentially expressed between the two groups. GO enrichment analysis shows that there are 175 molecular functions, 59 cellular components, and 555 biological processes, including cellular hormone metabolic process, hormone catabolic process, and I-kappaB kinase/NF-kappaB signaling. KEGG enrichment analysis exhibits that these differential genes are mainly enriched in the NF-kappa B signaling pathway, steroid hormone biosynthesis, breast cancer, ECM-receptor interaction, and MAPK signaling pathway. WNT4, DPP4, and NFKBIA are key nodes regulating breast activation. Conclusions: Through the comparative analysis of the transcriptome data of mammary tissues of pregnant and non-pregnant mares, relevant differentially expressed genes are screened and analyzed. This study provides valuable fundamental data for investigating candidate genes related to the lactation regulation and mammogenesis of Kazakh horses.

Plasma Non-targeted Metabolomics Analysis of Yili Horses Raced on Tracks With Different Surface Hardness.

In this study, the plasma non-targeted metabolomics of Yili horses were characterized before and after exercise on tracks that differed in surface hardness to better understand exercise-related biochemical changes. Blood samples were obtained from eight trained Yili horses before and immediately after exercise. Samples were used for metabolomic analysis by ultra-performance liquid chromatography-Q-EXACTIVE mass spectrometry. In total, 938 significantly different metabolites involving sugar, lipid, and amino acid metabolism were detected in the plasma, with significant increases in glucose, glucoheptanoic acid, lactic acid, malic acid, and methylmalonic acid and significant decreases in creatinine, D-tryptophan, carnitine, and citric acid after exercise. Among these metabolites, acetylcarnitine, tuliposide, vitamin C, and methylmalonic acid showed regular changes in concentration after exercise on tracks that differed in surface hardness, providing new insights into equine exercise physiology. The findings indicated the potential of vitamin C and methylmalonic acid as novel biomarkers of equine locomotor injury.

Correlation Analysis Between Stride Characteristics and Racing Ability of 2-year-old Yili Horses in Track Conditions.

In this study, we aimed to explore correlations among stride characteristics, time records, and bonus amounts to identify relevant indices for evaluating racing abilities of 2-year-old Yili horses. In total, 41 and 26 Yili horses were enrolled in the 1600 and 3600 m races, respectively. This experiment was performed by measuring their stride characteristics using a high-speed video and collecting time records during the competition and the bonus amounts. The results showed that the 2-year-old Yili horses' stride length (SL), stride frequency (SF), middle SL (mid SL), hind limb SL (hind SL), forelimb SL (fore SL), aerial duration SL (AD SL), stride angle, and advanced placement (AP) between the leading hind limb and trailing forelimb (AP LH-TF) were significantly and positively correlated with the bonus (P < .01). The bonus group had significantly higher values for these variables than the nonbonus group (P < .05); the stance duration and the overlap between LH and TF (overlap LH-TF) were negatively correlated with the bonus (P < .01), and the bonus group had a significantly lower overlap LH-TF value than the non-bonus group (P < .01). These findings indicated that 2-year-old Yili horses with greater SL, SF, mid SL, fore SL, AD SL, and stride angle values have better racing abilities. Likewise, smaller stance and overlap LH-TF values correspond to better horse racing abilities. The swing trailing hind limb, mid SL, AP LH-TF, and SF were filtrated by stepwise regression analysis as the primary indices for evaluating the racing ability of 2-year-old Yili horses.

Association of low race performance with mtDNA haplogroup L3b of Australian thoroughbred horses.

Mitochondrial DNA (mtDNA) encodes the genes for respiratory chain sub-units that determine the efficiency of oxidative phosphorylation in mitochondria. The aim of this study was to determine if there were any haplogroups and variants in mtDNA that could be associated with athletic performance of Thoroughbred horses. The whole mitochondrial genomes of 53 maternally unrelated Australian Thoroughbred horses were sequenced and an association study was performed with the competition histories of 1123 horses within their maternal lineages. A horse mtDNA phylogenetic tree was constructed based on a total of 195 sequences (including 142 from previous reports). The association analysis showed that the sample groups with poor racing performance history were enriched in haplogroup L3b (p = .0003) and its sub-haplogroup L3b1a (p = .0007), while those that had elite performance appeared to be not significantly associated with haplogroups G2 and L3a1a1a (p > .05). Haplogroup L3b and L3b1a bear two and five specific variants of which variant T1458C (site 345 in 16s rRNA) is the only potential functional variant. Furthermore, secondary reconstruction of 16s RNA showed considerable differences between two types of 16s RNA molecules (with and without T1458C), indicating a potential functional effect. The results suggested that haplogroup L3b, could have a negative association with elite performance. The T1458C mutation harboured in haplogroup L3b could have a functional effect that is related to poor athletic performance.

Potential role of maternal lineage in the thoroughbred breeding strategy.

Many studies have focused on identifying the genes or single nucleotide polymorphisms associated with the athletic ability of thoroughbreds, but few have considered differences in maternal and paternal heritability of athletic ability. Herein, we report on our association study of career race performances of 675 Australian thoroughbreds with their pedigrees. Racing performance data (prize money per start) were collected from the Bloodhound database. The performance of all horses was categorised as either poor or elite athletic achievement. Then, 675 foals were divided by their parents' performance (elite or poor) into four groups: (1) elite dams and elite sires; (2) elite dams and poor sires; (3) poor dams and elite sires; and (4) poor dams and poor sires. The performance of foals was then compared between the four groups. The results show that the heritability of race performance between dams and foals (r = 0.141, P < 0.001) is much higher than that between sires and foals (r = 0.035, P = 0.366), and that this difference is statistically significant (P < 0.05). We also examined the effect of the child-bearing age of dams and sires on the ratio of elite foals. We found a strong correlation between the number of elite foals and dams' child-bearing age (r = -0.105, P < 0.001), with the ratio of elite offspring reaching a high level between a child-bearing age of 8 and 11 years (χ2 = 14.31, d.f. = 1, P < 0.001). These findings suggest that the maternal line may play an important role in the selective breeding of athletic performance in thoroughbreds.