• Genomic prediction of dry matter intake in dairy cattle from an international data set consisting of research herds in Europe, North America, and Australasia

      de Haas, Y.; Pryce, J. E.; Calus, M. P. L.; Wall, E.; Berry, Donagh; Lovendahl, P.; Krattenmacher, N.; Miglior, F.; Weigel, K.; Spurlock, D.; et al. (Elsevier for American Dairy Science Association, 2015-07)
      With the aim of increasing the accuracy of genomic estimated breeding values for dry matter intake (DMI) in Holstein-Friesian dairy cattle, data from 10 research herds in Europe, North America, and Australasia were combined. The DMI records were available on 10,701 parity 1 to 5 records from 6,953 cows, as well as on 1,784 growing heifers. Predicted DMI at 70 d in milk was used as the phenotype for the lactating animals, and the average DMI measured during a 60- to 70-d test period at approximately 200 d of age was used as the phenotype for the growing heifers. After editing, there were 583,375 genetic markers obtained from either actual high-density single nucleotide polymorphism (SNP) genotypes or imputed from 54,001 marker SNP genotypes. Genetic correlations between the populations were estimated using genomic REML. The accuracy of genomic prediction was evaluated for the following scenarios: (1) within-country only, by fixing the correlations among populations to zero, (2) using near-unity correlations among populations and assuming the same trait in each population, and (3) a sharing data scenario using estimated genetic correlations among populations. For these 3 scenarios, the data set was divided into 10 sub-populations stratified by progeny group of sires; 9 of these sub-populations were used (in turn) for the genomic prediction and the tenth was used for calculation of the accuracy (correlation adjusted for heritability). A fourth scenario to quantify the benefit for countries that do not record DMI was investigated (i.e., having an entire country as the validation population and excluding this country in the development of the genomic predictions). The optimal scenario, which was sharing data, resulted in a mean prediction accuracy of 0.44, ranging from 0.37 (Denmark) to 0.54 (the Netherlands). Assuming near-unity among-country genetic correlations, the mean accuracy of prediction dropped to 0.40, and the mean within-country accuracy was 0.30. If no records were available in a country, the accuracy based on the other populations ranged from 0.23 to 0.53 for the milking cows, but were only 0.03 and 0.19 for Australian and New Zealand heifers, respectively; the overall mean prediction accuracy was 0.37. Therefore, there is a benefit in collaboration, because phenotypic information for DMI from other countries can be used to augment the accuracy of genomic evaluations of individual countries.
    • Meat provenance: Authentication of geographical origin and dietary background of meat

      Monahan, Frank J.; Schmidt, Olaf; Moloney, Aidan P; European Union; Department of Agriculture, Food and the Marine; FOOD-CT-2005–006942; 06/R&D/D/481; Teagasc Walsh Fellowship Programme (Elsevier, 2018-05-30)
      The authenticity of meat is now an important consideration in the multi-step food chain from production of animals on farm to consumer consumption of the final meat product. A range of techniques, involving analysis of elemental and molecular constituents of meat, fingerprint profiling and multivariate statistical analysis exists and these techniques are evolving in the quest to provide robust methods of establishing the dietary background of animals and the geographical origin of the meat derived from them. The potential application to meat authentication of techniques such as stable isotope ratio analysis applied to different animal tissues, measurement in meat of compounds directly derived from the diet of animals, such as fatty acids and fat soluble vitamins, and spectroscopy is explored. Challenges pertaining to the interpretation of data, as they relate to assignment of dietary background or geographical origin, are discussed.