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V. It is not covered by exclusive patent rights, but on the contrary open-source (i.e. it is designed for open use and shared improvement). (Semagn et al. 2006)

1.3.10.2 This technique has also its own limitations:

I. DArT is a microarray-based technique that involves several steps, including preparation of genomic representation for the target species, cloning, and data management and analysis. The latter requires dedicated software’s such as DArTsoft and DArTdb. The establishment of DArT system, therefore, is highly likely to demand an extensive investment both in laboratory facility and skilled manpower.

II. DArT assays for the presence of a specific DNA fragment in a representation. Hence, DArT markers are primarily dominant (present or absent) or differences in intensity, which limits its value in some applications.

For quantitative trait analysis, DArT has many potential applications. Till now, DArT marker patterns have been principally applied to the assessment of genetic variability in a group of organisms, such the development of wild barley (Hordeum chilense) by Suárez et al. (2012). Wenzl et al. (2004, 2006) gives an example of such a map, showing how the standard techniques of map construction using linkage disequilibrium can be applied using DArT markers. DArT is especially appropriated to QTL mapping (Wittenburg et al. 2005), and can be used to construct medium-density linkage maps relatively quickly. As these studies clarified, the most accurate diversity analysis requires proportional amounts of clones from all individuals tested to be present on the array. If alleles from a genotype are under-represented on an array, then DArT will indicate potentially greater differences from the population average.

DArT markers can be used to track phenotypic traits in breeding like other molecular markers, and the high throughput and low cost nature of the technology makes DArT more affordable for marker assisted selection. Multiple loci can be involved in the selection process, but using an array means all loci is dealt with simultaneously. Such markers can then be tracked though an introgression or crossing program, and used to supplement phenotyping to reduce potential miss-identification of a trait due to environmental effects (Lande & Thompson 1990), as per any other marker-aided selection tool. Even though DArT can be applied in the absence of sequence information, individual DArT markers are sequence-ready and can be used in the development of probe-based markers for further research (Kilian, 2004). One shortcoming of DArT is the number of positions on a DArT array that are consistently non-polymorphic, i.e. non-marker clones. This has been recognised since the inception of this technology (Jaccoud [et al. 2001), and recent studies detail how polymorphic markers can be identified in an initial discovery array process, then re-arrayed for genotypic applications as polymorphism-enriched arrays (Wenzl et al. 2004, Xia et al. 2005).]

5- It is not covered by exclusive patent rights, but on the contrary open-source (i.e., it

is designed for open use and shared improvement).

This technique, however, has also its own limitations:

1- DArT is a microarray-based technique that involves several steps, including preparation of genomic representation for the target species, cloning, management and analysis. The latter requires dedicated software’s such as DArTsoft and DArTdb. The establishment of DArT system, therefore, is highly likely to demand an extensive investment both in laboratory facility and skilled manpower.

2- DArT assays for the presence (or amount) of a specific DNA fragment in a presentation. Hence, DArT markers are primarily dominant (present or absent) or differences in intensity, which limits its value in some applications.

3- [...]

[p.15:]

For quantitative trait analysis, DArT has many potential applications. So far, DArT marker patterns have been principally applied to the assessment of genetic variability in a group of organisms, such the assessment of cassava diversity by Xia et al. (2005), and barley diversity by

[p.16:] Wenzl et al. (2004). As these studies illustrate, the most accurate diversity analysis require proportional amounts of clones from all individuals tested to be present on the array. If alleles from a genotype are under-represented on an array, then DArT will indicate potentially greater differences from the population average. DArT is especially suited to QTL mapping (Wittenburg et al. 2005), and can be used to construct mediumdensity linkage maps relatively quickly. Wenzl et al. (2004) gives an example of such a map, showing how the standard techniques of map construction using linkage disequilibrium can be applied using DArT markers. DArT markers can be used to track phenotypic traits in breeding like other molecular markers, and the high throughput and low cost nature of the technology makes DArT more affordable for marker assisted selection. Multiple loci can be involved in the selection process, but using an array means all loci is dealt with simultaneously. Such markers can then be tracked though an introgression or crossing program, and used to supplement phenotyping to reduce potential miss-identification of a trait due to environmental effects (Lande & Thompson 1990), as per any other marker-aided selection tool. Even though DArT can be applied in the absence of sequence information, individual DArT markers are sequence-ready and can be used in the development of probe-based markers for further research (Kilian 2004). One shortcoming of DArT is the number of positions on a DArT array that are consistently non-polymorphic, i.e. non-marker clones. This has been recognised since the inception of this technology (Jaccoud et al. 2001), and recent studies detail how polymorphic markers can be identified in an initial discovery array process, then re-arrayed for genotypic applications as polymorphism-enriched arrays (Wenzl et al. 2004, Xia et al. 2005).

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