Biology Reference
In-Depth Information
information and explores the bioinformatics tools to rapidly develop markers
associated with the traits of interest. In TRAP, the fixed primers are designed
against known sequences of annotated putative genes and used in
combination with other primers of arbitrary sequence to trap polymorphism
in the targeted genomic region. Since the fixed primers are targeting the
candidate gene sequences, TRAP offers a potentially higher probability of
amplifying markers linked to the phenotype under investigation than RAPD
and AFLP, which generate random polymorphic markers across the genome.
TRAP has been successfully used in developing markers for five important
agronomic traits of sunflower: a dominant gene conferring resistance to
several races of downy mildew (Hu et al. 2004b), a recessive gene controlling
apical branching (Rojas-Barros et al. 2008), a recessive gene governing
complete male sterility (Chen et al. 2006), a recessive gene governing light
green leaf color caused by reduced chlorophyll content, one of the two genes
controlling lemon ray flower color (Yue et al. 2008b) and QTL for resistance
to Sclerotinia head rot (Yue et al. 2008a). TRAP was also used to generate
markers in defining the sunflower linkage group ends with fixed primers
designed against the Arabidopsis -type telomere sequence repeat (Hu 2006).
3.3.7 SNP
SNP (single nucleotide polymorphism) refers to a DNA sequence variation
at a single nucleotide position in the genome among homozygous
individuals (or between paired chromosomes of a heterozygous individual)
and is the most common type of genetic variation. Theoretically, a SNP
could have four alleles because there are four possible nucleotides at every
nucleotide position. In practice, nearly all reported SNPs have only two
alleles and occur in genes as well as in intergenic regions. Compared to the
typical multi-allelic RFLP, SSR and SSLP (simple sequence length
polymorphisms), SNPs are less informative. However, this disadvantage
can be offset by a greater marker density and by the stability of SNPs. In
plant genomes, the usual frequency of SNPs is one in every 100-300 bp
(Gupta et al. 2001). In sunflower, a relatively high frequency of SNPs has
been reported. Liu and Burke (2006) investigated nine genomic loci of a total
length of 8,207 bp in 32 individuals sampled from wild populations,
primitive and improved germplasm accessions. They found 444
polymorphic sites among the samples with an average of 1 SNP for every
16.8 bp of sequence. The wild sunflowers harbored 392 polymorphic sites
(1 SNP/19.1 bp), whereas the cultivated sunflower harbored 194
polymorphic sites (1 SNP/38.8 bp). Kolkman et al. (2007) surveyed the
nucleotide diversity of 82 previously mapped RFLP marker loci in two wild
and 10 elite inbred lines. They identified 1,078 SNPs in 49.4 kbp of DNA/
genotype with an average of 1 SNP/45.7 bp. Non-coding sequences harbored
 
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