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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.

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. [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]

• 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]