Abstract
The expression of genes and their regulation during lactation in buffaloes remains less understood. To understand the interplay of various genes and pathways, the milk transcriptome from three lactation stages of Murrah buffalo was analyzed by RNA sequencing. The filtered reads were mapped to the Bubalus bubalis as well as Bos taurus reference assemblies. The average mapping rate to water buffalo and Btau 4.6 reference sequence, was 75.5% and 75.7% respectively. Highly expressed genes (RPKM > 3000), throughout lactation included CSN2, CSN1S1, CSN3, LALBA, SPP1 and TPT1. A total of 12833 transcripts were common across all the stages, while 271, 205 and 418 were unique to early, mid and late lactation respectively. Majority of the genes throughout lactation were linked to biological functions like protein metabolism, transport and immune response. A discernible shift from metabolism in early stage to metabolism and immune response in mid stage, and an increase in immune response functions in late lactation was observed. The results provide information of candidate genes and pathways involved in the different stages of lactation in buffalo. The study also identified 14 differentially expressed and highly connected genes across the three lactation stages, which can be used as candidates for future research.
Highlights
Comparison of the Differentially expressed (DE) genes in early and mid stages of lactation revealed 76 upregulated and 140 downregulated genes
The majority of the genes throughout lactation were involved in biological functions like protein metabolism, transport and immune response
There appeared to be a discernible shift from metabolism in early stage to metabolism and immune response in mid stage, and an increase in immune response in the late lactation
Summary
Comparison of the DE genes in early and mid stages of lactation revealed 76 upregulated and 140 downregulated genes. These DE genes could be classified into 130 functional categories with 87 GO terms for biological process, 22 terms for cellular components and 21 terms for molecular functions. Some of the significant (p < 0.05) GO terms for the upregulated genes were immune response, positive regulation of GTPase activity, lipopolysaccharide-mediated signaling pathway, transcription factor complex, chemokine activity and transcriptional activator activity. The downregulated genes were linked to regulation of cell proliferation, focal adhesion and calcium ion binding
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