author(s)
Shakil A Bhat, Syed Mudasir Ahmad, TA Raja, Riaz A Shah, NA Ganai, MM Darzi, Syed Shanaz and Mir Shabir

abstract
The milk epithelial cells (MECs) are one of the most representative of mammary gland tissues and can be used to study the expression kinetics of mammary gland specific genes. The objective of the present investigation was to study the expression pattern of major milk protein genes at three different stages of lactation using high through put RNA-Sequencing technology. A total number of six (n=6) Jersey milch animals were selected for the study. Morning milk samples were obtained at day 15 (D15), D90 and D250 for quality analysis and isolation of MECs. The RNA isolated from MECs showed highest quality with average RIN values of more than 8, which indicates the reliability of using MECs for transcriptome study. The milk quality analysis revealed highest protein percentage during late lactation period (D250) followed by early lactation (D15) and mid lactation (D90). RNA-Seq analysis revealed that 70% of the transcripts were constituted by protein genes only. All the major milk protein associated genes were significantly (p<0.05) expressed during late-lactation period. The highest differential expression was shown by CSN3 and CSN2 with fold change of 4.10 and 3.14, respectively. Future studies will be needed to understand molecular mechanisms in MECs including regulation of expression and translation throughout lactation.