Investigation of the genetic basis of novel phenotypes linked to welfare, sustainability and efficiency in dairy cattle

The Project

Gen2Phen summary

Ruminants provide an indispensable source of nutrients for consumption by man in many parts of the world, while also providing hides and fibres for clothing, faeces as fuel and fertilizer, and a means of conserving wealth in poor countries. The number of ruminants in the world is of 3.45 billions, 1.53 cattle and buffalos and 1.92 sheep and goats. The world demand for milk is 680 millions of tons. According to FAO (Food and Agricultural Organization of the United Nations) and other reliable estimates, the trend for the demand of foods of animal origin is expanding also for ruminant milk, due to an increasing consumption of dairy products in South Asia and South America. Also Asia, where the allele for lactase persistence has a low frequency, sees an increase in milk consumption. In Western countries dairy products are important sources of calcium and proteins and their market demand is expected to remain constant in the next years. In Italy, the dairy cattle sectors has a primary economic role in the national agriculture. The National Institute of Statistics in December 2008 estimates the presence in Italy of 1,83 millions dairy cows in about 62 thousand farm, an overall milk production of 10.9 thousand tons corresponding to a value of 4.4 billions Euro.

Dairy farming is occurring in a world scenario of human population growth; need to stop the erosion of natural resources (e.g. forests); increased competition among humans, animals and energy in the use of cereals; increased environmental impact of human activities, affecting also climate dynamics. These trends strongly call for an increase in efficiency of dairy cattle production, to decrease the environmental impact of this activity, still satisfying the market demand for milk and dairy products. In addition, recently public and expert attention has risen substantially on animal welfare and product quality for human health.

So, higher efficiency, decreased environmental impact, increased welfare and higher animal product quality are the main challenges of future dairy cattle farming and the main problems addressed by the present proposal, that exploits existing information and new technologies to produce new knowledge and tools for a more efficient dairy cattle management and breeding.

GEN2PHEN is investigating the genetic basis and the biology of i) feed efficiency; ii) stress tolerance; iii) methane emission and iv) milk fat composition in dairy cattle. To accomplish these tasks it considers a set of biomarkers known from the literature to be associated to the target traits and dissects them to asses the genomic, metagenomic, transcriptomic and epigenomic components. The final aims of the project are on the one side a better understanding of the biology of the traits investigated, on the other side to test and optimise biomarkers and genomic tools potentially useful in selection programs and herd management.

The project is divided in tasks carried out by four Research Units.

The work plan comprises six logically and sequentially interlinked work packages. WP1 is dedicated to project management, to ensure the timely achievement of milestones and deliverables; implement contingency plans in the case of unexpected problems; prepare model agreements with the farms involved in the project; manage intellectual property rights and publications. WP2 is dedicated to the set up of all procedures and tools functional to the progress of the project: a common set of Standard Operating Procedures (SOPs) to apply across research sites for sample and trait recording; laboratory protocols for Biomarker assays; the data repository. In WP3 samples are collected and subjected to Biomarker analyses and genotyping. In WP4 subsets of animals falling in opposite tails of the Biomarker distributions are further characterised by trancriptomic, epigenomic and rumen metagenomic analyses, to deeper examine the biology of traits investigated. Data will be modelled in WP5 by a combination of advanced statistical approaches, bioinformatics and systems biology. The whole project will be disseminated in transversal WP6.