Transcriptomic analysis of PBMCs reveals COX3, BCL2, ATP2B4, B4GALT1, LACTB, FASN and CSN family genes regulating milk performance in lactating Bos indicus cows of Southern India

The expression of genes related to lactogenesis in peripheral blood mononuclear cells (PBMCs) are less understood. To understand the biology of milk production in early lactating non pregnant cows in the blood, the transcriptome from PBMCs was analysed by RNA sequencing. We are able to generate a total of ~ 62.5 Gbp RNA-Seq data files (~ 24 million to ~ 35 million paired-end reads per sample) from high yielder (3) and low yielder (3) of Deoni and Hallikar breeds of Bos indicus (12 samples). The blood sample was collected from twelve early lactating non pregnant cows, the transcriptome from PBMCs was analysed by RNA sequencing. The QC passed reads were aligned against Bos taurus reference assemblies by using HiSAT2 alignment tool. An average of 79.25% and 74.28% reads were aligned in Deoni and Hallikar breeds, respectively. Amongst 85 genes were significantly differentially regulated between low yielder and high yielder of Deoni cows. On contrary, in Hallikar 492 genes were significantly differentially regulated between groups. Transcripts related to CSN gene family (CSN1S1, CSN1S2, CSN2 and CSN3) and FASN were significantly expressed in High yielders of Deoni cows. However, in low yielding Deoni cows and all Hallikar cows, these CSN gene family and FASN gene expression levels were poor or not at all expressed. However, the ATP2B4 (PMCA - Plasma membrane Ca2 + ATPase) gene is expressed only in Hallikar cows. Majority of the genes in lactating Deoni and Hallikar cows were linked to milk protein composition especially caseins, milk fat, lactose synthesis in milk and apoptosis activity in mammary glands. Our findings provide new insights into the understanding of molecular mechanism of differential milk yield among Bos indicus breeds. We believe that our study would be helpful in lactation biology and genetic selection.