An Integrative Approach to Milk Genomics

An Integrative Genomics Program to Explore Lactating Systems to Improve Herd Genetics and Develop Dairy Produce

The Australian dairy co-operative research centre (CRC) has established a gene discovery program to exploit recent advances in genomics for developments in the dairy industry. The program has established projects that address issues from across the supply chain, with an emphasis on dairy herd genetics, physiological genomics and milk genomics, underpinned by expertise in comparative bioinformatics.

Genome-wide genotyping was performed using a16,000 SNP panel and over 1,500 bulls selected from primary AI stock from the Australian herd improvement scheme. Data was analysed for haplotype structure and LD, and for association with 45 dairy traits. Further, using data from herd performance records, an accurate molecular breeding value (MBV) has been developed for Holstein Friesian cattle as a forerunner to a whole genome selection program for future dairy herd genetic improvement.

Utilization of genome-wide genetic analysis with the dairy CRCs physiological genomics projects has resulted in the integration of functional and comparative mammary gland development and lactation datasets. Using this approach a systems-level annotation of lactation is emerging that identifies gene networks and key pathways. This will be illustrated by analysis of the Jak-Stat pathway, which is known to have components responsive to mammary development and lactation. Overall the data has been mined for a range of potential applications including development of health and performance diagnostics, as well providing a knowledgebase for annotation of milk microcomponents. 

The dairy bioactives project utilizes information from both the physiological and genetic datasets, as described in the preceding sections. Using an integrated proteomic, in silico and gene expression approach, the milk genome has been screened for bioactive proteins. The discoveries have been collated into a library of prospective dairy bioactive components, which provides the platform for a dairy functional food and nutraceutical product pipeline. This has resulted in continued bio-evaluation of over 200 proteins at intermediate stages of investigation ranging from early stage characterisation, to dairy company milk processing stream analysis. One lead candidate has been advanced into a pilot plant stage to assess benefits and applications in human well-being.