Tissue expression and variation analysis of three bovine adipokine genes revealed their effect on growth traits in native Chinese cattle

Combined transcriptome and proteome analyses reveal differences in the longissimus dorsi muscle between Kazakh cattle and Xinjiang brown cattle

Objective

With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects.

Methods

Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3).

Results

In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results.

Conclusion

Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.

Longissimus Dorsi Muscle Transcriptomic Analysis of Simmental and Chinese Native Cattle Differing in Meat Quality

With the rapid development of economy, the demand for beef, with regard to quantity and quality, by consumers has been increasing in China. Chinese native cattle are characterized by their abundant genetic resources, unique origins, large breeding stocks, and robust environmental adaptability. Thus, to explore the genetic mechanisms on regulating meat quality in Chinese native cattle is of great importance to satisfy increased requirements for beef production. In this study, we investigated three breeds of cattle, namely Yunling, Wenshan, and Simmental, at the age of 12 months. Animals were classified into three groups (n = 5/breed). Growth traits including body weight and body size and plasma hormone levels were measured. Body weight of Wenshan cattle was significantly lower than that of Yunling and Simmental cattle (P < 0.05). Again, body size indexes, such as withers height, body slanting length, chest circumference, and hip and rump length, were significantly lower in Wenshan cattle than those in Yunling and Simmental cattle (P < 0.05). However, there were no significant differences in those indexes between Yunling and Simmental cattle (P > 0.05). Cattle were slaughtered at the age of 18 months and then meat color, pH, pressing losses, muscle tenderness, and cooking losses were measured at 0, 1, 2, 3, 5, and 7 days. Data revealed differences in meat quality among the three breeds analyzed. Based on transcriptomic sequencing and bioinformatic analysis, we observed 3,198 differentially expressed genes related to meat quality, of which 1,750 genes were upregulated. Moreover, we found two important signaling pathways closely linked to meat quality, namely adipocytokine signaling pathway [e.g., Leptin receptor (LEPR)] and protein processing in the endoplasmic reticulum [e.g., signal transducer and activator of transcription 3 (STAT3), heat shock protein (HSPA12A), and calpain 1 (CAPN1)]. The results of transcripts were further verified by qRT-PCR. Using correlation analysis between gene expression levels and shear force, we also identified two functional genes (e.g., HSPA12A and CAPN1) associated with meat quality. Overall, this study provides new sights into novel targets and underlying mechanisms to modulate meat quality in Chinese native cattle.

Exploring of InDel in bovine PSAP gene and their association with growth traits in different development stages

PSAP (prosaposin) is widely expressed in different organs, and plays an important role in fat deposit. Insertion/Deletion (InDel) is a relatively simple and effective DNA marker. However, the association of molecular marker at different stages of animal development has not received enough attention, especially fat deposition related traits. Therefore, eight cattle breeds were used to explore novel InDels variants within bovine PSAP gene, and to evaluate their effects on growth traits in different development stages. Herein, two novel InDels (P5:NC037355.1g.27974439-27974440 ins AGTGTGGTTAATGTCAAC and P8:NC037355.1g.27980734-27980752 del GTCAAAAAATCAGGGGAAAC) within the bovine PSAP gene were found, and their association with growth traits in different development stages were analyzed. Interestingly, the dominant genotype was different in different development stages both in NY cattle and JX cattle for daily gain and body weight. PSAP Gene expression patterns were analyzed in this study, high expression in the middle stage of adipocytes differentiation suggests that it plays a certain role in fat development. It reveals that InDels could affect phenotype in different development stages, which depend on the expression pattern of the host gene and their function in different tissues. These findings could provide a new way for molecular marker studies in bovine breeding and genetics.