Molecular Genotyping

Traditionally the identification of cultivars has been based on the visual assessment of a number of specific traits such as leaf shape and size, growth habit and flower colour. The advent of molecular techniques provides an opportunity to generate specific genome marker systems for the identification and study of cultivars. Whilst current work has mainly been centred around the use of random genomic markers such as microsatellites (SSR) the development of single nucleotide polymorphisms (SNP’s) which can be associated with specific genes, provides an opportunity to predict specific characteristics of a cultivar on the basis of a laboratory assay.

Barley Genotyping

Single nucleotide polymorphisms (SNPs) are the smallest unit of genetic variation and are abundant in animal and plant genomes. They are an excellent choice for studies on plant genetics and breeding. Many SNPs have been discovered in the barley genome and it is hoped that shortly SNPs will be identified that are directly linked to key traits measured during the DUS testing of varieties. At SASA we are using the relatively new method of temperature switch PCR (TSP) to differentiate barley varieties on the basis of their SNPs. If successful this method can be used by other laboratories that do not have access to hi-tech equipment such as DNA sequencers or real-time PCR machines as the TSP products can be separated by simple agarose gel electrophoresis. Preliminary results are encouraging and all of the varieties tested can be differentiated using 25 markers.

Dendogram constructed from the TSP SNP profiles for 12 barley varieties Dendogram constructed from the TSP SNP profiles for 12 barley varieties

 

Bere Barley Genotyping

Bere barley (Hordeum vulgare) is a traditional Scottish barley landrace that is still grown using a traditional system by growers mainly in the islands. It is probably the oldest cereal ‘variety’ grown commercially in Europe and possibly the world. Bere barley has adapted to enable it to grow in the poorer acidic soils found on in Northern Scotland and there is renewed interest in its use in breeding programs.

Bere barley samples from the Scottish islands were collected and analysed using 29 microsatellite markers.

Scottish islands where Bere barley samples were collected

Scottish islands where Bere barley samples were collected

Tree showing molecular relationships amongst Bere barley samples from the islands

Tree showing molecular relationships amongst Bere barley samples from the islands

 

Significant genetic variance was observed between the 3 island groups, possibly explainable by their geographical isolation.

No accounts of seed exchange between island groups, only within island groups which would support the suggestion of isolated populations.

The oral and genetic data suggests that the bere barley from each island group has been separated for some time.

Western Isles demonstrated the highest level of genetic diversity of the 3 island groups (also the most diverse ecological environment).

Potato Genotyping

The European Union Common Catalogue (EUCC) for potato contains over 1,000 varieties. Each year member states add varieties to the list after they have undergone Distinctness, Uniformity and Stability (DUS) testing according to international guidelines. Identification of cultivars by morphological characteristics is a highly skilled and time-consuming task. For these reasons a rapid and robust method for variety identification to aid the management and maintenance of existing variety collections and for the screening of new candidate varieties would therefore be a highly useful tool for DUS testing stations. SASA has developed a rapid and robust identification system using 12 microsatellite markers.

 

Microsatellite profiles for 3 varieties with marker SSR1

Microsatellite profiles for 3 varieties with marker SSR1.

 

Over 1,300 varieties have been analysed using the system and virtually all varieties can clearly be differentiated by their unique molecular profiles. The only exceptions are somaclonal variants e.g. King Edward and Red King Edward.

Differentiation of some popular potato varieties grown in Scotland (scale % similarity)

Differentiation of some popular potato varieties grown in Scotland (scale % similarity).

 

The fingerprinting method is fast with only 1 to 2 days required and any part of the plant can be used for identification. It is also possible to type some food products (e.g. potato crisps). SASA now offers DNA fingerprinting of potato varieties as a service. For information contact Helen Ventisei (dnafingerprinting@sasa.gsi.gov.uk) or Alex Reid (Alex.Reid@sasa.gsi.gov.uk).