Transcriptome study underling difference of milk yield during peak lactation of Kazakh horse

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.

Transcriptome analysis of the Bactrian camel (Camelus bactrianus) reveals candidate genes affecting milk production traits

BACKGROUND

Milk production traits are complex traits with vital economic importance in the camel industry. However, the genetic mechanisms regulating milk production traits in camels remain poorly understood. Therefore, we aimed to identify candidate genes and metabolic pathways that affect milk production traits in Bactrian camels.

METHODS

We classified camels (fourth parity) as low- or high-yield, examined pregnant camels using B-mode ultrasonography, observed the microscopic changes in the mammary gland using hematoxylin and eosin (HE) staining, and used RNA sequencing to identify differentially expressed genes (DEGs) and pathways.

RESULTS

The average standard milk yield over the 300 days during parity was recorded as 470.18 ± 9.75 and 978.34 ± 3.80 kg in low- and high-performance camels, respectively. Nine female Junggar Bactrian camels were subjected to transcriptome sequencing, and 609 and 393 DEGs were identified in the low-yield vs. high-yield (WDL vs. WGH) and pregnancy versus colostrum period (RSQ vs. CRQ) comparison groups, respectively. The DEGs were compared with genes associated with milk production traits in the Animal Quantitative Trait Loci database and in Alashan Bactrian camels, and 65 and 46 overlapping candidate genes were obtained, respectively. Functional enrichment and protein-protein interaction network analyses of the DEGs and candidate genes were conducted. After comparing our results with those of other livestock studies, we identified 16 signaling pathways and 27 core candidate genes associated with maternal parturition, estrogen regulation, initiation of lactation, and milk production traits. The pathways suggest that emerged milk production involves the regulation of multiple complex metabolic and cellular developmental processes in camels. Finally, the RNA sequencing results were validated using quantitative real-time PCR; the 15 selected genes exhibited consistent expression changes.

CONCLUSIONS

This study identified DEGs and metabolic pathways affecting maternal parturition and milk production traits. The results provides a theoretical foundation for further research on the molecular mechanism of genes related to milk production traits in camels. Furthermore, these findings will help improve breeding strategies to achieve the desired milk yield in camels.

Effect of Supplementary Feeding on Milk Volume, Milk Composition, Blood Biochemical Index, and Fecal Microflora Diversity in Grazing Yili Mares

Grazing is a common approach to rearing. We investigated the effects of supplementation during grazing on milk yield and composition, blood biochemistry, and fecal microflora in Yili horses. The control mares grazed normally, while those in groups I and II received 1 kg/d of concentrate and 1 kg/d of concentrate + 0.4 kg/d of coated FA, respectively. Milk volumes were significantly higher in groups I and II than in the control group, and among the previous two, milk volumes were significantly higher in group II than in group I. Milk fat, lactose, and protein levels were significantly higher in group II than in the others. BUN was highly significantly lower in group I than in the control group. Specific FAs, total SFA, and total UFA were significantly higher in group II than in the other groups. After feeding, plasma GLU, free FA, TG, LDL, and VLDL were significantly higher in group II than in the other groups. The control group, group I, and group II had 4984, 5487, and 5158 OTUs, respectively, and 3483 OTUs were common to all groups. The abundance of Bacteroidetes and Firmicutes was >75%. The abundance of Verrucomicrobia was significantly higher in groups I and II than in the control group and, among the previous two, significantly higher in group II than in group I. The abundance of Treponema_saccharophilum significantly differed between the control and other groups, and WCHB 1_41, Kiritimatiellae, and Verrucomicrobia abundances significantly differed between groups II and the other groups.

Integrating genome-wide methylation and transcriptome-wide analyses to reveal the genetic mechanism of milk traits in Kazakh horses

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.