نوع مقاله : مقاله پژوهشی
نویسندگان
1 دانشجوی دکتری، گروه علوم دامی، دانشکده کشاورزی، دانشگاه کردستان
2 استادیار گروه علوم دامی، دانشکده کشاورزی، دانشگاه کردستان، سنندج، ایران
3 گروه علوم دامی، مؤسسه تحقیقات علوم دامی کشور، کرج، ایران
4 دانشیار گروه علوم دامی، دانشکده کشاورزی، دانشگاه کردستان، سنندج، ایران
چکیده
کلیدواژهها
موضوعات
عنوان مقاله [English]
نویسندگان [English]
Background and Objectives: The Sistani cattle, as one of Iran’s valuable indigenous breeds, is known for its high resistance to diseases, tolerance to heat and nutritional stress, and excellent adaptation to the harsh climatic conditions of the eastern regions of the country. However, its low milk and meat production has limited its commercial utilization. Crossbreeding with high-yielding exotic breeds such as Simmental can create a balance between production efficiency and the preservation of native adaptive traits. Transcriptomic studies using RNA-Seq technology provide a powerful tool to investigate gene expression changes induced by crossbreeding and to identify molecular markers associated with economic and adaptive traits. The aim of this study was to analyze differential gene expression between purebred Sistani cattle and their crosses with the Simmental breed, and to identify the affected biological pathways.
Materials and Methods: Blood samples were collected from the coccygeal vein of purebred Sistani cattle and Sistani × Simmental crossbreds (two biological replicates per treatment) at the Zabol Livestock Breeding Center under identical nutritional, environmental, and management conditions. Total RNA was extracted using the Qiagen RNeasy kit, and its quality (including RIN) was assessed using a Bioanalyzer, while purity was evaluated with a NanoDrop spectrophotometer (A260/A280 ratio between 1.9 and 2.1). Samples were sent to BGI (China) for library preparation and sequencing. Initial quality control was performed using FastQC v0.12.1, and reads were trimmed with Trimmomatic (minimum length of 50 bp). High-quality reads were aligned to the bovine reference genome. Transcript assembly and quantification were performed using Cufflinks (FPKM), and differential expression analysis was conducted with Cuffdiff in the R environment. Genes with q-value < 0.05 were identified as differentially expressed genes (DEGs). Gene Ontology (GO) and pathway enrichment analyses were performed using the PANTHER database and Fisher’s exact test with FDR correction.
Results: After quality control and alignment, a total of 143 genes showed significant differential expression between the two groups. Data quality was satisfactory, with approximately 74% of forward reads and 73% of reverse reads in the purebred Sistani group, and about 81% and 82% in the crossbred group, uniquely aligned to the reference genome. Among the 20 genes with the greatest expression differences, genes such as UNC80, FBXO16, PKHD1, SCN10A, and RGS16 showed significantly reduced expression in purebred Sistani cattle, whereas genes such as BOLA-DQB, PRSS2, PPP1R1B, and BOLA-DQA5 were upregulated. GO and pathway analyses indicated that these genes are mainly involved in processes such as ion transport, regulation of cell growth, response to stimuli, and immune function. Five enriched pathways with FDR < 0.05 were identified, the most important of which included G Alpha (i) signaling, GPCR downstream signaling, signaling by GPCR, G Alpha (q) signaling, and chemokine receptor binding to chemokines. These pathways are associated with extracellular signal transduction and responses related to reproduction, milk production, growth, and immune function under stress conditions.
Conclusion: The results indicate that crossbreeding Sistani cattle with the Simmental breed induces profound changes in gene expression profiles and biological pathways, and can be an effective strategy to improve livestock productivity while maintaining adaptation to challenging environments. These findings provide a valuable foundation for marker-assisted breeding programs and targeted selection in indigenous Iranian cattle breeds.
کلیدواژهها [English]
)