Genomic data enables genetic evaluation using data recorded on low-middle income country smallholder dairy farms
Authors: Powell Owen , Mrode Raphael , Gaynor R. Chris , Johnsson Martin , Gorjanc Gregor , Hickey John M. 
Published: November 2019

AbstractBackgroundGenetic evaluation is a central component of a breeding program. In advanced economies, most genetic evaluations depend on large quantities of data that are recorded on commercial farms. Large herd sizes and widespread use of artificial insemination create strong genetic connectedness that enables the genetic and environmental effects of an individual animal’s phenotype to be accurately separated. In contrast to this, herds are neither large nor have strong genetic connectedness in smallholder dairy production systems of many low to middle-income countries (LMIC). This limits genetic evaluation, and furthermore, the pedigree information needed for traditional genetic evaluation is typically unavailable. Genomic information keeps track of shared haplotypes rather than shared relatives. This information could capture and strengthen genetic connectedness between herds and through this may enable genetic evaluations for LMIC smallholder dairy farms. The objective of this study was to use simulation to quantify the power of genomic information to enable genetic evaluation under such conditions.ResultsThe results from this study show: (i) the genetic evaluation of phenotyped cows using genomic information had higher accuracy compared to pedigree information across all breeding designs; (ii) the genetic evaluation of phenotyped cows with genomic information and modelling herd as a random effect had higher or equal accuracy compared to modelling herd as a fixed effect; (iii) the genetic evaluation of phenotyped cows from breeding designs with strong genetic connectedness had higher accuracy compared to breeding designs with weaker genetic connectedness; (iv) genomic prediction of young bulls was possible using marker estimates from the genetic evaluations of their phenotyped dams. For example, the accuracy of genomic prediction of young bulls from an average herd size of 1 (μ=1.58) was 0.40 under a breeding design with 1,000 sires mated per generation and a training set of 8,000 phenotyped and genotyped cows.ConclusionsThis study demonstrates the potential of genomic information to be an enabling technology in LMIC smallholder dairy production systems by facilitating genetic evaluations with in-situ records collected from farms with herd sizes of four cows or less. Across a range of breeding designs, genomic data enabled accurate genetic evaluation of phenotyped cows and genomic prediction of young bulls using data sets that contained small herds with weak genetic connections. The use of smallholder dairy data in genetic evaluations would enable the establishment of breeding programs to improve in-situ germplasm and, if required, would enable the importation of the most suitable external germplasm. This could be individually tailored for each target environment. Together this would increase the productivity, profitability and sustainability of LMIC smallholder dairy production systems. However, data collection, including genomic data, is expensive and business models will need to be carefully constructed so that the costs are sustainably offset.