Mitochondrial DNA D-loop SNPs unveil molecular signatures of milk production variation in Murrah buffalo.

BACKGROUND: The Murrah buffalo, pivotal in Asian agriculture, faces challenges in maximizing milk production despite significant breeding efforts. Recognizing its economic importance, this study investigates mtDNA D-loop variations in Murrah buffalo as potential indicators of milk production variability, addressing challenges in maximizing yield despite significant breeding efforts. METHODS AND RESULTS: Analyzing mtDNA D-loop sequences from 50 buffaloes, we categorized them into Low (Group 1), Medium (Group 2), and High ECM (Group 3) groups based on milk yields, fat and protein percentage of a 30-day period data. Somatic cell mtDNA D-loop analysis revealed distinct genetic variations, with significant differences among ECM groups. Group 2 showed higher SNP prevalence, group 3 had more insertions/deletions, and Group 1 exhibited the highest transition frequency. Notably, a consistent "C" deletion at the 714th position occurred in Groups 1 and 3, prevalent in 68% of Group 2. A G-A variation at the 93rd position was specific to the medium ECM group. Negative Tajima D values indicated unique variations in each group, with Group 1 having the highest number, and a specific SNP linked to Group 2 was identified. These SNPs in the D-loop region could impact mtDNA replication, influencing mitochondrial content among animals. Our results provide valuable insights into the role of mtDNA D-loop polymorphisms in milk production traits in Murrah buffalo. CONCLUSIONS: Our research highlights the potential for valuable markers of cellular energy efficiency in Murrah buffalo. Exploring diverse cytoplasmic backgrounds opens avenues for mtDNA-based selection strategies, enhancing milk production and optimizing genetic traits for the dairy industry.

Differential Expression of Nuclear-Encoded Mitochondrial Protein Genes of ATP Synthase Across Different Tissues of Female Buffalo.

The physiological well-being of buffaloes, encompassing phenotypic traits, reproductive health, and productivity, depends on their energy status. Mitochondria, the architects of energy production, orchestrate a nuanced interplay between nuclear and mitochondrial domains. Oxidative phosphorylation complexes and associated proteins wield significant influence over metabolic functions, energy synthesis, and organelle dynamics, often linked to tissue-specific pathologies. The unexplored role of ATP synthase in buffalo tissues prompted a hypothesis: in-depth exploration of nuclear-derived mitochondrial genes, notably ATP synthase, reveals distinctive tissue-specific diversity. RNA extraction and sequencing of buffalo tissues (kidney, heart, brain, and ovary) enabled precise quantification of nuclear-derived mitochondrial protein gene expression. The analysis unveiled 24 ATP synthase transcript variants, each with unique tissue-specific patterns. Kidney, brain, and heart exhibited elevated gene expression compared to ovaries, with 10, 8, and 19 up-regulated genes, respectively. The kidney showed 3 and 12 down-regulated genes compared to the brain and heart. The heart-brain comparison highlighted ten highly expressed genes in ATP synthase functions. Gene ontology and pathway analyses revealed enriched functions linked to ATP synthesis and oxidative phosphorylation, offering a comprehensive understanding of energy production in buffalo tissues. This analysis enhances understanding of tissue-specific gene expression, emphasizing the influence of energy demands. Revealing intricate links between mitochondrial gene expression and tissue specialization in buffaloes, it provides nuanced insights into tissue-specific expression of nuclear-encoded mitochondrial protein genes, notably ATP synthase, advancing the comprehension of buffalo tissue biology.

Nuclear Genome-Encoded Mitochondrial OXPHOS Complex I Genes in Female Buffalo Show Tissue-Specific Differences.

Buffalo physiology intricately balances energy, profoundly influencing health, productivity, and reproduction. This study explores nuclear-mitochondrial crosstalk, revealing OXPHOS Complex I gene expression variations in buffalo tissues through high-throughput RNA sequencing. Unveiling tissue-specific disparities, the research elucidates the genomic landscape of crucial energy production genes, with broader implications for veterinary and agricultural progress. Post-slaughter, tissues from post-pubertal female buffaloes underwent meticulous processing and RNA extraction using the TRIzol method. RNA-Seq library preparation and IlluminaHiSeq 2500 sequencing were performed on QC-passed samples. Data underwent stringent filtration, mapping to the Bubalus bubalis genome using HISAT2. DESeq2 facilitated differential expression gene (DEG) analysis focusing on 57 Mitocarta 3-derived genes associated with OXPHOS complex I. Nuclear-encoded mitochondrial protein transcripts of OXPHOS complex 1 exhibited tissue-specific variations, with 51 genes expressing significantly across tissues. DEG analysis emphasized tissue-specific expression patterns, highlighting a balanced OXPHOS complex I subunit expression in the kidney vs. brain. Gene Ontology (GO) enrichment showcased mitochondria-centric terms, revealing distinct proton motive force-driven mitochondrial ATP synthesis regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses emphasized Thermogenesis and OXPHOS pathways, enriching our understanding of tissue-specific energy metabolism. Noteworthy up-regulation of NDUFB10 in the heart and kidney aligned with heightened metabolic activity. Brain-specific up-regulation of NDUFAF6 indicated a focus on mitochondrial function, while variations in NDUFA11 and ACAD9 underscored pivotal roles in the heart and kidney. GO and KEGG analyses highlighted tissue-specific mitochondrial ATP synthesis and NADH dehydrogenase processes, providing molecular insights into organ-specific metabolic demands and regulatory mechanisms. Our study unveils conserved and tissue-specific nuances in nuclear-encoded mitochondrial OXPHOS complex I genes, laying a foundation for understanding diverse energy demands and potential health implications.