Livestock has an important role in an agriculture based country like Pakistan with a large number of dairy animals. However the average daily milk yield of dairy animals is very low. There is need to improve milk yield by the selection of superior dairy animals using latest genomic selection procedures. Selection of superior animals on the basis of genetic markers has a tremendous potential for breed improvement across the globe. Substantial advances have been made over the past decades through the application of molecular genetics used in industry programs for several decades and is growing, the extent of use has not lived up to initial expectations. Most applications to date have been integrated in existing programs on temporary basis.
Among various molecular markers the Single Nucleotide Polymorphism (SNP) is one of the major genetic marker used worldwide. Through SNP genotyping selection of phenotypic superior animals can be done. There are many techniques used for SNP genotyping but the most advanced technique is Veracode GoldenGate Assay by Illumina. Illumina's VeraCode technology with the BeadXpress (BX) Reader is ideal for high-throughput small to mid-scale genotyping studies and SNP validation. BX leverages the power of digital holographic codes and the robust GoldenGate Genotyping Assay to provide a detection method for multiplex assays requiring high precision, accuracy, and speed. A custom assay of 48, 96, 144,192 and up to 384-SNPs OPA (Oligos Pool All) is designed using Illumina's Assay Design Tool and manufactured by Illumina.
As a first step for designing of Veracode GoldenGate Assay the development of Oligo Pool All (OPA) is necessary. The OPA was designed by using the genes for milk production, growth, fertility, health and other performance traits. The SNP's in these genes was searched from different gene banks and after proper arrangement the files were sent to Illumina for scoring. After scoring the OPA was finalized for the Veracode GoldenGate Assay for the selection of superior dairy animals in the country using the highly robust BeadXpress technology. The development of OPA for the selection of superior dairy animals was done for the very first of its kind based on modern technology, Veracode GoldenGate Assay in Pakistan. This will greatly help the livestock and dairy development departments, livestock owners, breeders, forensic agencies and researchers to use this unique panel of molecular markers for the selection of superior animals on the basis of marker assisted selection.