Buffalo milk transcriptome: A comparative analysis of early, mid and late lactation

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.

Maternal genes and pathways affecting birth weight and weaning weight traits in sheep: A GWAS and pathway enrichment analysis

“…The FTH1 gene encodes for the heavy subunit of ferritin. The presence of ferritin in cow's and buffalo's milk has been reported [40,47].…”

“…Many GO terms related to protein metabolism and transport and fatty asides metabolism were identified. Recently, in a transcriptome analysis study on buffalo milk, protein metabolism (GO:0019538) pathway identified as a significant term [47]. Changes in the amount of fatty acid synthesis during late-pregnancy and lactation have been long and newly reported for a variety of species including the rat, rabbit, pig, and cow [48,49].…”

“…Terms related to calcium and other ions metabolism and transport were also significant. Several different comparative transcriptome analyses have reported the role of calcium metabolism-related pathways in the lactation process [47,50]. Phosphorylation (GO:0016310) term was identified as a significant pathway associated with PWW and LMWW traits.…”

“…GTPase activator activity (GO:0005096) GO term was identified as a significant pathway related to the composite traits at weaning. GTPases are known to be involved in numerous secretory processes and play an important role in translation and translocation of proteins, secretion of the milk fat globule, and probably other milk components [47]. Many GO terms associated with cell proliferation and differentiation were also detected as significant.…”

Characterization and Comparative Analysis of Transcriptional Profiles of Porcine Colostrum and Mature Milk Across Multiple Parities

“…To our knowledge, there have been no studies that have reported direct sequencing of porcine whole milk samples. In fact, only six livestock RNA-sequencing (RNA-Seq) studies have reported sequencing of milk, including three in cattle [9,21,22], one in goat [23], one in sheep [24], and one in buffalo [25]. The emphasis of these studies was gene expression related to the lactation process, and as such, milk somatic cells were sequenced as a proxy for the mammary gland tissue [26].…”