Plant and animal genotyping can be used to create fine map traits and/or test a genotype-phenotype hypothesis. Quantitative trait loci (QTL) analyses can be performed on the results to characterize how differential gene expression might contribute to phenotypic variation.
A common form of natural diversity, copy number variation (CNV) is also heritable. It appears to play an important role in agrigenomics. CNV differences can correlate to health and production traits, and contribute to phenotypic diversity. The distribution of high density probes can be used to identify CNV breakpoints and ultimately accelerate genetic improvements. Studies are ongoing to determine if the impact of CNVs is the result of differences in copy number for key genetic segments, structural modification of the genome, or a combination of both.
Not every non-human organism has been extensively genetically investigated, resulting in an absence of commercial genotyping arrays for certain plant and animal species. Illumina offers custom genotyping arrays that can be designed with all the discovered markers for species of interest, enabling genotyping studies to identify variants associated with desired phenotypic traits. Through its ongoing work with major agrigenomics consortia, Illumina technology is being used to identify new, relevant markers in a wide range of species.
Association mapping across an entire genome provides insight into the genetic location and architecture of linking traits to species’ adaption (e.g. to a wide variety of environmental conditions). The results of these studies support plant and animal whole-genome selection applications (fingerprinting, net merit, marker-assisted breeding) that enhance the value of commercial crops and herds. Illumina offers focused content, custom capabilities, and convenient add-on content capabilities.