Etude de la portabilité de marqueurs microsatellites issus d'EST de ...

Bibliography – Organization of genetic resources
information is available, it can be used to design PCR-based STS primers. To date, STS
has been used to analyze the genetic diversity for several agricultural crops, such as in
Hordeum (Chen et al. 2005). To assess the genetic diversity among China’s cultivated
barley, sequence tagged site (STS) marker analysis was carried out to characterize 109
morphologically distinctive accessions originating from five Chinese eco-geographical
zones. Fourteen polymorphic STS markers representing at least one on each chromosome
were chosen for the analysis. They revealed a total of 47 alleles, with an average of 3.36
alleles per locus (range 2–8). The result suggested that the STS diversity in different zones
was quite different from the morphology diversity, and indicated that the STS variation
was partitioned into 17% among the zone and 83% within the zone (Chen et al. 2005).
3.4.4.7 Single Nucleotide Polymorphisms (SNPs)
Single Nucleotide Polymorphism or SNP is a DNA sequence variation, occurring when a
single nucleotide (adenine (A), thymine (T), cytosine (C) or guanine (G)) is altered in the
genome (i. e. substituted, deleted or added). It is estimated that there is probably one SNP
locus every 500 to 1,000 bp between two individuals randomly sampled in the same
species. This large abundance suggests that SNPs markers can be useful for numerous
genetic applications. For example, SNPs were approved as an effective mean of
characterizing the range of DNA variation at a genomic scale in Arabidopsis thaliana and
to build up a core collection (McKhann et al. 2004). Since SNPs appeared recently, only
few studies used this method for genetic diversity estimation in cereals and they were
focused on genes of interest. For example, in 2003, Yanagisawa et al. investigated a single
nucleotide polymorphism (SNP) in the Wx-D1 gene of wheat by using a derived cleaved
amplified polymorphic sequence (dCAPS) marker, and showed that the SNP in the Wx-D1
gene was responsible for the waxy character. Furthermore, this type of marker was also
demonstrated to be a very useful tool to study linkage disequilibrium in common wheat
(Ravel et al. 2005) as well as in barley (Potokina et al. 2006).
3.4.4.8 Expressed Sequence Tag (EST)
An Expressed Sequence Tag or EST is a short sub-sequence of a transcribed
protein-coding or non-protein-coding DNA sequence. ESTs can be derived in PCR-based
markers, which can detect length and sequence polymorphisms carried by the expressed
regions of plant genomes. This involves the designing of primers separated by an
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