The application of genomics in commercial agriculture, such as genotyping for trait screening, has become indispensable to modern farming and breeding practices. Our microarray and next-generation sequencing (NGS) technologies are helping breeders and researchers evaluate and predict genetic merit in plants and animals, informing crucial decisions about selection and health.
Genetic information has largely replaced physical screening for many commercial agriculture applications, including selective breeding. Genetic markers linked to specific value traits can be used to screen large numbers of progeny to identify those with desired characteristics. Trait screening is ideal for multigenic traits that are difficult to manage using conventional breeding or propagation techniques, and even more difficult to identify phenotypically. Iterative screening of populations enables easier segregation of progeny possessing the desired traits for use as breeding stock. Illumina offers a comprehensive portfolio for both microarray- and sequencing-based solutions to help researchers screen herds and crops for desired traits.
The goal of backcrossing in commercial agriculture applications is to move a single trait of interest—such as drought tolerance, high productivity, or disease resistance—from a donor parent to progeny. Marker-assisted backcrossing using Illumina microarrays or NGS enables researchers to monitor the transmission of the trait gene via a genetically linked marker that can be easily screened. This process significantly accelerates backcrossing programs and reduces the time to release of commercially viable plant lines or breeding stock.
Animal identity verification and parentage are essential tools in maintaining the biosecurity of the world’s animal populations. Illumina genotyping platforms offer the speed, reliability, and throughput needed to track animals from birth, with the flexibility to perform iterative testing as necessary. The high throughput offered by genotyping is especially valuable for commercial agriculture applications that require large-scale production.
The recent emergence of novel infectious diseases in animal populations has required researchers to look beyond conventional diagnostic tests for ways to identify these new pathogens. The speed and affordability of NGS has fueled the field of metagenomics, enabling investigators to screen samples, detect infectious agents rapidly, and track disease outbreaks. Illumina NGS technology is quickly becoming a vital tool for microbial analysis and veterinary applications in commercial agriculture.
Genetic markers can be used to identify animals and understand the relationship of offspring to parents. Because a single marker may not yield definitive results, multiple markers are used to increase the probability of identifying the true parent. In linebreeding situations where multiple generations of males or females are present in the herd, the marker results are combined with the breeder’s knowledge of possible sires or dams to determine parentage.
Molecular characterization of genetically modified organisms (GMO) is necessary for event selection and, in many countries, regulatory approval. The simplicity and consistency of NGS makes this method a superior alternative to the existing process of Southern blotting and sequencing of PCR products. Deep sequencing of the whole genome allows determination of the number of insert sites, copy numbers at each site, sequence of the insert and the native site, and generational stability.