Agriculture Reference
In-Depth Information
Simple Sequence Repeats (SSR)
SSR are high quality and consistent DNA markers, but they are the most expensive
to develop. SSR markers require extensive band sequencing data for each marker
developed, and often the markers are species and even cultivar specific. However
they are molecular markers of choice in crop plants.
Amplified Fragment Length Polymorphism (AFLP)
AFLP requires enzymatic degradation of DNA and careful fragment separation,
where only a sub-fraction of the population genetic data is sampled by PCR. It can
provide too much information at any time. It is more technically demanding and
information can be difficult to interpret. It produces very good high quality data,
which is suitable for high output sources and automation.
Single Nucleotide Polymorphism (SNP)
SNP relies on the fact that the vast majority of differences in eukaryotic organisms
are surprising point mutations in their DNA. So there are a vast number of poly-
morphisms that are SNPs. The biggest advantage is automation and techniques that
do not require electrophoresis to separate fragments. However it does require DNA
sequencing which can be costly. SNPs are becoming more and more important as
molecular markers for genome information and advancement in crop plants.
Expressed Sequence Tags (EST)
ESTs require cDNA synthesis from RNA, and therefore are the only markers list-
ed which are based on RNA. Preferences for this method should be for crop spe-
cies where there is already extensive sequencing, and part or full EST data present
(Sect. 3).
NCBI—Plant Markers
A genetic marker web database that contains molecular markers such as SNP, SSR
and conserved ortholog set cosmid (COS) markers and primers from various plant
resources (Heesacker et al. 2008 ).
GrainGenes
Theweb site for Triticeae genomics, and provides considerable detail of DNA mark-
ers and chromosome linkage map data on wheat, barley, rye and oat (Carollo et al.
2005 ).
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