Whole-Genome Genotyping

Useful traits in agricultural plants and animals are genetically determined. For most crops, genetic improvement in the last 50 or more years has delivered large gains in productivity and significant improvement in quality of the products. Most of the breeding performed so far has relied on phenotypic evaluation of individuals and families.

Progress in biological knowledge and in genetic technology now allows an increased emphasis on molecular genetics in approaches to crop improvement. The genetic fingerprint (genotype) of an individual can now be determined, and the relationship between the genotype and the phenotypic value of the individual can be established. Therefore, efficient genotyping technologies are going to play an increasing role in future breeding.

Better knowledge of genomic diversity and better tools to recombine that diversity productively will accelerate breeding of improved individuals with superior characteristics. Efficient and cost-effective genotyping tools play a key role in this strategy.

Diversity Arrays Technology (DArT^®) is a novel genotyping method that provides for low cost, high throughput, sequence-independent genotyping and is therefore very appropriate for delivering comprehensive genome profiles to plant breeders.

With many genetic marker systems, high cost and low throughput limit the practical use of whole genome profiles to the most lucrative applications, therefore excluding many agricultural applications. Taking advantage of technological progress allowing for hybridisation-based parallel analysis, DArT^® was developed by Dr Andrzej Kilian’s team to offer an alternative, affordable system of genetic markers.

Triticarte was formed to deliver DArT^® and some complementary technologies to wheat and barley breeders.

Applications of whole-genome genotyping

A comprehensive (or “genome-wide") genetic fingerprint of an individual is very useful in the following areas:

• Unambiguous identification of the individual, and its degree of relatedness to other individuals (e.g. for pedigree information and for intellectual property protection)
• Identification of genomic regions linked to phenotypic traits of interest (association studies, QTL studies)
• Fine mapping of specific genes, as a first step towards gene isolation
• Acceleration of breeding programs by screening progeny on the basis of their genotype
• Evaluation of genetic diversity in the available germplasm
• Creation of novel varieties by facilitating efficient combination, e.g. between adapted cultivars and wild relatives, or between closely related germplasm.