|Using genomic information increases accuracy in all traits.|
Illumina is a manufacturer of bead chips, chips which are used to identify SNPs from a genome. For example, the PorcineSNP60 chip has 65000 evenly spaced probes for recognizing SNPs. It can be used for four pig breeds: Duroc, Landrace, Pietran, and Large White. More information about the chip can be found from the product information sheet.
SimulationsThere are two ways for evaluating genetic variation in quantitative traits: simulations and experimental genetics. Simulations are cheap and easy to repeat, but the assumptions used in the simulation may not be realistic.Experimental genetics uses real data, but is more cost and labour intensive. Simulations are carried out with different computer programs. They estimate population evolution under different conditions. Each simulation is based on real data about
- allele and genotype frequencies
- linkages between markers and genes
- population and family structure
- effective population size
- reproduction parameters
- selection (if any)
- isolated / open population
- DNA alteration parameters
4Neμ is an important term in simulations. According to professor Alban Bouquet, in a mutation drift equilibrium the SNP (or allele) frequency depends on the variable 4Neμ. If 4Neμ < 1, the distribution is U-shaped. Large % of markers are fixed, and diversity is low. When 4Neμ = 1, the distribution is uniform, and when it's > 1, the distribution is curved out: only a few markers are fixed, and there's high diversity. In most mammals 4Neμ is about 0,001, so most loci are fixed at MDE and many markers need to be simulated.
Comparing the effectiveness of genomic and traditional selection
The study by Bouquet and Juga (2012) showed that with JS, using a multiple-ovulation embryo transfer (MOET) herd of 75 heifers genetic gain is significantly increased. MOET does not significantly increase inbreeding rates if over 33 AI sires used. Doubling the number of flushed heifers may change response to selection with over 50 AI sires, but only if the number of genotyped females is increased as well. Increasing the number of flushings per heifer from 2 to three increases both genetic and rate of inbreeding, and may not thus be advisable. All in all, MOET and JS combined impact production traits very strongly, but functional traits only little. Compared to traditional pedigree-based selection, the variance of response is slightly increased in JS schemes whereas genetic gain istremendously increased.