Comparative transcriptome analysis of mammary epithelial cells at different stages of lactation reveals wide differences in gene expression and pathways regulating milk synthesis between Jersey and Kashmiri cattle

Abstract

Jersey and Kashmiri cattle are important dairy breeds that contribute significantly to the total milk production of the Indian northern state of Jammu and Kashmir. The Kashmiri cattle germplasm has been extensively diluted through crossbreeding with Jersey cattle with the goal of enhancing its milk production ability. However, crossbred animals are prone to diseases resulting to unsustainable milk production. This study aimed to provide a comprehensive transcriptome profile of mammary gland epithelial cells at different stages of lactation and to find key differences in genes and pathways regulating milk traits between Jersey and Kashmiri cattle. Mammary epithelial cells (MEC) isolated from milk obtained from six lactating cows (three Jersey and three Kashmiri cattle) on day 15 (D15), D90 and D250 in milk, representing early, mid and late lactation, respectively were used. RNA isolated from MEC was subjected to next-generation RNA sequencing and bioinformatics processing. Casein and whey protein genes were found to be highly expressed throughout the lactation stages in both breeds. Largest differences in differentially expressed genes (DEG) were between D15 vs D90 (1,805 genes) in Kashmiri cattle and, D15 vs D250 (3,392 genes) in Jersey cattle. A total of 1,103, 1,356 and 1,397 genes were differentially expressed between Kashmiri and Jersey cattle on D15, D90 and D250, respectively. Antioxidant genes like RPLPO and RPS28 were highly expressed in Kashmiri cattle. Differentially expressed genes in both Kashmiri and Jersey were enriched for multicellular organismal process, receptor activity, catalytic activity, signal transducer activity, macromolecular complex and developmental process gene ontology terms. Whereas, biological regulation, endopeptidase activity and response to stimulus were enriched in Kashmiri cattle and, reproduction and immune system process were enriched in Jersey cattle. Most of the pathways responsible for regulation of milk production like JAK-STAT, p38 MAPK pathway, PI3 kinase pathway were enriched by DEG in Jersey cattle only. Although Kashmiri has poor milk production efficiency, the present study suggests possible physicochemical and antioxidant properties of Kashmiri cattle milk that needs to be further explored.

Comparative milk proteome analysis of Kashmiri and Jersey cattle identifies differential expression of key proteins involved in immune system regulation and milk quality

“…The GO analysis of significantly up-regulated proteins revealed only one significantly enriched GO term (extracellular region) after FDR correction in both breeds and limited functional overlap was found between the present proteomic data and our earlier transcriptome data [61] indicating the failure of RNA-based analyses to represent completely protein dynamics [62]. Pathway analysis helps in biological interpretation of proteomic and other high-throughput data in cells or organisms [63].…”

Weighted gene co-expression network analysis identifies modules and functionally enriched pathways in the lactation process

“…For instance, casein and whey protein genes are highly expressed throughout all lactation stages in cattle. It has been reported that during the lactation process, transcriptionally-regulated genes are mostly enriched in terms of receptor activity, catalytic activity, and signal transducer activity 6 . Moreover, the regulatory impacts of JAK-STAT , p38 MAPK , and the PI3 kinase pathway on lactation processes have been previously reported 6 .…”

Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight

“…MARVEL domain-containing 3/U6 spliceosomal RNA (Gene ID: S18_39186829) could be a novel marker related to milk trait because on relative expression analysis, its closest members (RNU6B, RNU5A and RNU1A) were used to assess the suitability of a combination of small nuclear RNAs as a reference RNA in milk somatic cells of lactating yaks [91,102,103]. MAPK-interacting and spindle-stabilizing protein-like (Gene ID: S24_1645) is involved in regulating milk synthesis [91,[104][105][106]. EF-hand domain-containing 2 (Gene ID: S25_42968291) is one of the most common calcium-binding structural motifs, and a well-defined helix-loop-helix structural domain, present in many calcium-binding proteins, has been identified in milk [107][108][109][110].…”