Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing

• Main Authors: Ramesh Menon, Anand B. Patel, Chaitanya Joshi
• Format: Article
• Language: English
• Published: PeerJ Inc. 2016-07-01
• Series: PeerJ
• Subjects: Buffalo; Single nucleotide polymorphism; Milk-yield; Quantitative trait loci; Mammary transcriptome; Exome sequencing
• Online Access: https://peerj.com/articles/2147.pdf

River buffalo (Bubalus bubalis) milk plays an important role in economy and nutritious diet in several developing countries. However, reliable milk-yield genomic markers and their functional insights remain unexposed. Here, we have used a target capture sequencing approach in three economically important buffalo breeds namely: Banni, Jafrabadi and Mehsani, belonging to either high or low milk-yield group. Blood samples were collected from the milk-yield/breed balanced group of 12 buffaloes, and whole exome sequencing was performed using Roche 454 GS-FLX Titanium sequencer. Using an innovative approach namely, MultiCom; we have identified high-quality SNPs specific for high and low-milk yield buffaloes. Almost 70% of the reported genes in QTL regions of milk-yield and milk-fat in cattle were present among the buffalo milk-yield gene candidates. Functional analysis highlighted transcriptional regulation category in the low milk-yield group, and several new pathways in the two groups. Further, the discovered SNP candidates may account for more than half of mammary transcriptome changes in high versus low-milk yielding cattle. Thus, starting from the design of a reliable strategy, we identified reliable genomic markers specific for high and low-milk yield buffalo breeds and addressed possible downstream effects.