The choice of the most
appropriate molecular marker for genetic and plant breeding studies must be
made on the basis of the ease of developing a useful technique coupled with the
efficiency of data evaluation, interpretation, and analysis. The chosen marker
must provide easy access and availability, rapid response and high
reproducibility, and allow information exchange between laboratories and
between populations and/or different species; it must also permit automation of
data generation and subsequent analysis. Other desirable characteristics
include a highly polymorphic nature, codominant inheritance (permitting the
identification of homozygous and heterozygous individuals), frequent occurrence
in the genome, and neutral selection (selection free from interference by
management practices and environmental conditions). In addition to the
characteristics of the marker, the goals of the project, the availability of
financial, structural, and personal resources, convenience, and the availability
of facilities for the development of the assay, as well as the genetic trait of
the species under study, should all be considered.
Of the markers described in
this chapter, AFLP allows the analysis of multiple loci in a single assay due
to its efficiency in wide and simultaneous sampling of the genome. The ability
of AFLP to differentiate individuals withina population makes it useful for
diversity studies, analysis of gene flow, and varietal discrimination
(fingerprint of varieties) (Arif et al., 2010). AFLP is also a useful
alternative for studies of species for which a limited number of SSR and SNP
markers are available because it can use universal primers regardless of the
species. However, assay and analysis of data from AFLP are complex and time
consuming compared with those of other markers. In addition, AFLP is a dominant
marker and requires relatively large quantities of high-quality DNA.
SSR markers are distinguished
by their highly polymorphic nature; consequently, they can be used to detect a
large number of alleles per locus. These markers are especially informative due
to their codominant and multiallelic nature and their high values of
heterozygosity and PIC (Polymorphism Information Content). Frequent and
distributed at random throughout the genome, SSRs combine informativity with a
wide coverage of the genome, robustness, and reproducibility, making them one
of the most desirable markers for detailed studies of genetic structure, mapping,
and fingerprinting of cultivars. The great disadvantage of the SSR technique
lies in the fact that it analyzes only a small sample of the genome in each
assay, even when multiplex testing is used. Because SSR markers are locus
specific, only a few loci are analyzed per experiment.
SNP markers offer the
advantages of distribution and frequency in the genome; they also permit
automated data collection and analysis. For these reasons, they are recommended
for work involving wide genomic selection and studies of kindred plants with
narrow genetic bases. Although SNP markers are biallelic in nature and offer
lower resolution than multi-allelic SSR markers, this deficiency is balanced by
the capacity to analyze a large number of loci pertest (Arif et al., 2010).
Another limitation of SNP markers lies in the cost of the equipment and the
assay. Although large-scale genotyping techniques (ultrahigh-throughput
genotyping) allow the broad coverage of the genome in a single assay with
relatively low cost per data point, the total cost of the experiment is still
quite high. Despite their recent development, DArT markers have been thoroughly
tested in several species (Wenzl et al., 2004; Akbari et al., 2006; Xie et al.,
2006; Mace et al., 2008; Tinker et al., 2009; Sansaloni et al., 2010;
Heller-Uszynska et al., 2011). In the majority of the species in which DArT has
been applied, the technique has been adapted and used in the characterization
of germplasm collections and genetic diversity, the construction of
high-resolution genetic maps, and the identification of QTL (Quantitative Trait
Loci). Because DArT markers are widely distributed in the genome and can be
used for genotyping on a large scale, the technique has great potential for use
in selective genomics. Furthermore, DArT markers have shown good performance in
analyses of polyploid species. This feature is very important because
polyploidy can affect the accuracy of marker technologies in various ways.
Techniques based on PCR, for example, can be affected by the presence of
alternative annealing primer sites on chromosomes, the dilution of correct
target sites or even competition with primers. Similarly, as in the case of
RFLP, technologies based on hybridization can be affected by the occurrence of
multiple hybridizations with the same probe. Markers whose development is based
on prior knowledge of the DNA sequence, such as SNPs and SSRs, are of limited
use in species for which there is little available information on the genome
sequence. This limitation especially affects polyploid species, in which sequencing
is technically more complicated. The results obtained with DArT in different
polyploid species such as wheat (Akbari et al., 2006), hexaploid oat (Tinker et
al., 2009), and sugar cane (Heller-Uszynska et al., 2011) have shown that
ploidy does not affect the usefulness or reproducibility of these markers in
detecting polymorphism. DArT markers, therefore, may be a good alternative for
genetic studies of polyploidy.
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