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The article "Whole genome sequencing and de novo genome assembly of the Kazakh native horse Zhabe" published in Frontiers in Genetics discusses the genetic characteristics of the Kazakh horse breed, specifically the Zhabe type. The study presents high-quality genome assemblies for six Kazakh horses of the Zhabe type, highlighting the importance of genetic research and conservation of genetic diversity in economically important animal varieties. The research utilized Oxford Nanopore Technology for sequencing and assembly, providing valuable insights into the genetic makeup of the Kazakh horse breed. The findings suggest that the Kazakh horse breed has a mixed origin in the maternal lineage, indicating high levels of genetic variability and serving as an important reservoir of genetic biodiversity. [Extracted from the article]

The aim of this experiment was to study the difference of intestinal microflora of Kazakh horses in grass group and hay group after transfer. Twenty Kazakh mares aged five to six years old under uniform feeding and management conditions in the Tacheng area of Xinjiang were selected and divided into two groups: Fresh Grass Group (QC group) and Dry Grass Group (GC group). They were fed 2 kg of concentrate feed per horse per day. QC group consumed fresh grass daily, while the GC group consumed dry grass daily. At 30 days of the experiment, fecal samples of all horses were collected, and the characteristic sequences of microbial species such as 16S amplified by PCR were detected by high-throughput sequencing technology. There were 28 865 OTU in fecal flora of Kazakh horses in the two groups, and the OTU amount in fecal flora of Kazakh horses in QC group was higher than that in GC group. The results showed that Firmicute, Bacteroidota, Proteobacteria, Verrucomicrobiota, and Spirochaetota were the dominant bacteria in the manure of Kazakh horses in the two groups. The dominant bacteria genera were Solibacillus, Acinetobacter, Rikenellaceae_RC9_gut_group, Treponema, and Ruminococcaceae NK4A214_group. Compared with the GC group, the relative abundances of Actinobacteriota and Rummeliibacillus in feces of Kazakh horses in QC group were significantly increased (P<0.05). LEfSe analysis showed that 65 kinds of bacteria were significantly different in fecal flora of Kazakh horses in the two groups, among which 36 kinds of bacteria were significantly up-regulated in QC group and 29 kinds of bacteria were significantly up-regulated in GC group. The study indicates that the composition structure and community of fecal flora of Kazakh horses were affected by different forage, but the diversity and richness of intestinal flora did not change significantly. More important microbial groups played an important role in fecal flora of Kazakh horses in QC group than in GC group. [ABSTRACT FROM AUTHOR]

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• Kazakh horse skeletal muscle development. • Difference of skeletal muscle in three parts of Kazakh horses at different ages. • Developmental characteristics of skeletal muscle of Kazakh horses at different ages. • Identification of mRNAs in skeletal muscle of Kazakh horses at different ages. • Enrichment analysis of mRNAs pathway differentially expressed in skeletal muscle. 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. [ABSTRACT FROM AUTHOR]

There is an increasing demand for horse milk, but the current domestic performance of the horse milk has not yet conducted a systematic in-depth study. We carried out a pilot study on 13 single nucleotide polymorphisms (SNPs) located within five genes in Kazakh horse using Kompetitive Allele Specific PCR (KASPTM). An association study with average daily milk production of 60 Kazakh mares was performed for 6/13 polymorphic SNPs. The results showed that only two SNPs rs114262445 (NUMB), rs1136347938 (CA8) out of the 6 polymorphic markers were significantly associated with milk production in Kazakh horses. These results indicate the potential of using SNPs for the NUMB and CA8 genes as candidate genes for selection and farm production outputs. This study is relevant for future horse genomic studies.

Background miRNA has an important role in cell differentiation, biological development, and physiology. Milk production is an important quantitative trait in livestock and miRNA plays a role in the amount of milk produced. Methods The role of regulatory miRNAs involved in equine milk production is not fully understood. We constructed two miRNA libraries for Kazakh horse milk production from higher-producing (H group) and lower-producing (L group) individuals, and used RNA-Seq technology to identify the differentially expressed miRNAs between the two milk phenotypes of Kazakh horses. Results A total of 341 known and 333 novel miRNAs were detected from the H and L groups, respectively. Eighty-three differentially expressed miRNAs were identified between the H and L group s, of which 32 were known miRNAs (27 were up-regulated, five were down-regulated) and 51 were novel miRNAs (nine were up-regulated, 42 were down-regulated). A total of 2,415 genes were identified. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that these genes were annotated to mammary gland development, mammary gland morphogenesis, tissue development and PI3K-Akt signaling pathways, insulin signaling pathway and TGF-beta signaling pathway, among others. Five miRNAs (miR-199a-3p, miR143, miR145, miR221, miR486-5p) were identified as affecting horse milk production and these five miRNAs were validated using qRT-PCR. Conclusions We described a methodology for the transcriptome-wide profiling of miRNAs in milk, which may help the design of new intervention strategies to improve the milk yield of Kazakh horses.

• Identification of mammary gland molecular mechanism in mares during early pregnancy. • Rich regulation of differential mRNA and LncRNA target gene signaling pathways. • MAPK pathway and NF-kappa B signaling pathway mediate the initiation of lactation. • VNT4, DPP4, and NFKBIA are the key nodes of ceRNA. 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. [ABSTRACT FROM AUTHOR]

Abstract The utility of high-density single nucleotide polymorphism (SNP) data help to accurately identify genomic regions that have undergone positive selection. In this study, the Affymetrix Equine 670 K high-density SNP array was used to genotype Kazakh and Yili horse population. After quality control, 370,227 autosomal SNPs were used to detect selection signatures by using global fixation index (F ST) and cross-population extended haplotype homozygosity (XP-EHH). The database of Ensemble, Genecards, and NCBI were used to make gene annotation and functional analysis. The results showed that there were 134 candidate SNPs overlapped between F ST and XP-EHH in Kazakh horse. We also discovered some potential selective sweep regions associated with milk trait, including NUMB, LGALS2 , ADCY8 , SLC25A30 , and CA8 genes. New findings from this research have potential value for milk traits selecting in horse. Highlights • SNPs of one hundred and thirty-four were selected by two methods (F ST and XP-EHH). • Overlapping regions of thirty-nine were found by two selection signal methods. • Five candidate genes (NUMB , LGALS2 , ADCY8 , SLC25A30 , CA8) related to lactation traits were identified. [ABSTRACT FROM AUTHOR]

In order to understand the characteristics of genetic resources of Kazakh horses in Xinjiang, their body size, phenotypes and coat colors were investigated and analyzed using the methods of resources survey and body size measurement. The results showed that the coat color of Kazakh horses in Xinjiang is very rich, covering more than 90% of the world's horse coat colors. The influencing factors of Kazakh horse body size data might include the environment and geographical distribution of Kazakh horses. The gap between Xinjiang Kazakh horse and Kazakhstan Kazakh horse was relatively large, which was related to the degree of breeding. There were some differences in the appearance of Kazakh horses between Altay and Di regions with different ecological environment. The Kazakh horses in Altay were relatively strong in size, well developed in coat and long hair, long and dense in fuzz in winter, and rich in coat color. But the Kazakh horses in Iii were compact in size, less in coat than those in Altay, and have a single coat color. [ABSTRACT FROM AUTHOR]

• We identified 27,172 differential methylated regions (DMRs) and 8268 DMR-related genes (DMGs). • By combining the WGBS-seq and the previous RNA-seq data, a total of 94 overlap genes were obtained. • We found that 9 DMGs were likely to be involved in milk production of Kazakh horse. Horse Milk has important quantitative characteristics and high economic value. However, the DNA methylation regulators involved in horse milk traits have not been clarified. To explore the important role of genome-wide DNA methylation in regulating equine milk yield, this study systematically investigated the genome-wide DNA methylation profiles of Kazakh horse blood by comparing a high-production group (HP, average daily milk yield of 7.5 kg) and low-production group (LP, average daily milk yield of 3.2 kg) using deep whole-genome bisulfite sequencing. First, both groups showed similar proportions of methylation at CpG sites. Subsequently, we identified 26,677 differential methylated regions (DMRs) of CG, 15 DMRs of CHG, 480 DMRs of CHH and 8268 DMR-related genes (DMGs). GO and KEGG analyses revealed that some DMGs were involved in regulating milk and milk component formation. By combining the WGBS-seq and the previous RNA-seq data, a total of 94 overlapping genes were obtained. Finally, we found that 9 DMGs are likely involved in milk production by Kazakh horses. [ABSTRACT FROM AUTHOR]

• Total RNA was extracted from the milk fat during the peak of lactation period. • A total of 310 differentially expressed genes (P < 0.05, Fold change ≥2) were screened. • We performed quantitative PCR to validated 5 selected DEGs and the results were in agreement with RNA-seq analysis. This study was designed to provide a basis for further understanding of the mechanism of lactation based on mRNA expression differences in milk fat between different milk yields in Kazakh horses. Total RNA was extracted from the milk fat during the peak of lactation period. A total of 310 differentially expressed genes (DEGs) were identified by comparative transcriptome analysis of the high-yield and low-yield group. These DEGs regulate lactation by participated in AMPK signaling pathway, FoxO signaling pathway, ErbB signaling pathway, VEGF signaling pathway. In addition, we performed quantitative PCR to validated 5 selected DEGs and the results were in agreement with RNA-seq analysis. A new profile has been established for revealing the mechanism of equid's mammalian lactation. [ABSTRACT FROM AUTHOR]