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Final Report Summary - SEQSEL (Global cooperation to develop next generation whole genome SEQuence SELection tools for novel traits)

The world’s human population is expected to grow to 9.1 billion by 2050. To satisfy the required 70% greater food demand from a constant or, likely, shrinking agricultural land base is a real and significant global challenge. This challenge must be achieved through greater efficiencies of production in both plants and animal production with no or minimal environmental consequences. Dairy products are, and will remain, a significant proportion of the staple human diet as a dietary source of essential amino acids, minerals and vitamins. Therefore feed efficiency, especially in dairy cattle, is of growing importance.

Most research to-date on feed intake and utilisation in cattle, however, has been undertaken in beef cattle. Factors hindering research on feed intake and efficiency in dairy cattle include: 1) lack of sufficient data within country and 2) knowledge of the most relevant trait to reflect feed efficiency in dairy cattle. The objective of the SEQSEL project was to build upon, solidify and formalise relationships between several world-leading research partners in the EU (Ireland, The UK, and the Netherlands) and Oceania (i.e., Australia and New Zealand) in order to conduct joint research and participate in knowledge exchange and to 1) develop the logistics for sharing data, 2) discuss the merits of alternative definitions of feed efficiency, and 3) identify regions of the bovine genome associated with feed intake and efficiency and its impact on genomic predictions.
Considerable discussions occurred on the most pertinent trait to reflect the feed intake complex in dairy cows and how accurate genetic/genomic evaluations could be generated for such a trait including low cost measures on farm. Results from both topics were presented at international conferences including the World Congress on Genetics Applied to Livestock Production. No consensus was reached on the most pertinent measure of feed efficiency for inclusion in breeding objectives and was concluded that it was probably country-specific. Based on these discussions Australia has included a “feed-saved” measure of feed intake in their national breeding goal. Other countries are likely to pursue other alternatives. Milk mid-infrared spectroscopy was deemed to be probably the most suitable approach to predict feed intake in dairy cows. The accuracy of predicting (i.e., correlation between predicted and actual values) energy intake, energy balance and residual energy intake from milk mid infrared spectroscopy in dairy cows was up to 0.88, 0.78 and 0.63, respectively based on cross-validation. Many countries are now embarking on research studies to evaluate the accuracy in their country and production system.
The largest database in the world on feed intake in dairy cows was collated consisting of 224,174 feed intake records from 10,068 lactations on 6,957 cows; the data originated from 10 populations in 9 countries. The heritability of feed intake across all countries was 0.34 indicating that 34% of the differences in feed intake among dairy cows was due to genetics. The genetic correlation between feed intake in cows and growing heifers was 0.67 suggesting that feed intake in growing heifers is somewhat under similar genetic control to feed intake in cows offering a mechanism to measure feed intake indirectly on cows at also at an earlier age. Sometimes the effect of genes on the expression of a trait can vary by the environment the animal is producing in – this phenomenon is called genotype-by-environment. The presence of genotype-by-environment interactions for feed intake across the 10 different populations was examined and did not exist with the exception of the genes underpinning feed intake in confinement cows being different to feed intake in grazing cows. This limits to potential benefit of sharing of feed intake data from cows fed indoors versus outdoors.
Genotype (i.e., DNA) data was also shared, as were the algorithms and pipelines for predicting the full DNA sequence (i.e., 3 billion pieces of DNA) of thousands of animals who only have tens of thousands of pieces of DNA. This process of prediction, termed imputation, was calculated to be 96.79% accurate. The implications of this are that the full DNA sequence of individuals can be generated with high accuracy at a cost of approximately €22 as opposed to having to generate directly for a cost of ~€1,500. All of the participating countries have imputed their genotypes to full DNA sequence. Following the sharing of DNA information between the SEQSEL participants, the usefulness of such an initiative to increase the accuracy of genomic evaluations for feed intake in the respective countries was quantified. The optimal scenario of sharing data evaluated, resulted in a mean prediction accuracy of 0.44 across all countries, ranging from 0.37 (Denmark) to 0.54 (the Netherlands). If no feed intake records were available in a country, the accuracy based on the data from the other populations ranged from 0.23 to 0.53.
The conclusions from the present study are that there was clearly a benefit in collaboration, because phenotypic information for feed intake from other countries can be used to augment the accuracy of genomic evaluations of individual countries. The consortium in the project has recently expanded to now include other countries with a view to routinely generating genetic/genomic evaluations for feed intake for use by the respective breeding industries. The social-economic implications of this research within and outside the farm gate are massive owing to 1) approximately 65 to 75% of total dietary energy intake of individual beef breeding cows is used solely for body maintenance and the beef cow breeding herd uses 65 to 85% of the energy required in a beef production system. Similarly, feed costs account for approximately 80% of total variable costs (excluding labour) associated with pastoral milk production in dairy cows; 2) security for the continuous availability of feedstuffs for animals especially at a reasonable price; 3) a 5% improvement in feed efficiency in growing beef cattle has a four-times greater economic impact than a 5% improvement in average daily gain, less is known of its impact in dairy cattle; 4) increasing feed efficiency will lead to a reduction in nutrient excretion and methane emissions for each unit of food produced thereby aiding environmental sustainability. Results from this study will be useful for farmers, breeders and breeding companies.

Further details from Donagh Berry - Donagh.berry@teagasc.ie

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