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Diversity arrays technology (DArT) markers in apple for genetic linkage maps.

Schouten HJ, van de Weg WE, Carling J, Khan SA, McKay SJ, van Kaauwen MP, Wittenberg AH, Koehorst-van Putten HJ, Noordijk Y, Gao Z, Rees DJ, Van Dyk MM, Jaccoud D, Considine MJ, Kilian A - Mol. Breed. (2011)

Bottom Line: Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions.The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage.ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.

View Article: PubMed Central - PubMed

ABSTRACT
Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Pedigree of the two mapping populations examined. Common parents are highlighted
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Fig1: Pedigree of the two mapping populations examined. Common parents are highlighted

Mentions: For mapping, two populations were used. The first, Prima × Fiesta, was used to examine the reliability of the DArT data by evaluating the ease by which the DArT markers were integrated in an existing, well-established linkage map. This population consists of 156 individuals (Maliepaard et al. 1998), of which a subset of 121 individuals were DArT genotyped. The second population, 2000–2012 (Soriano et al. 2009), was used to demonstrate the ease by which DArT markers allow for the alignment between mapping populations. In addition, this population was used to compare two DArT complexity reduction methods with respect to the number of markers and genome coverage. It comprises 894 individuals, 399 of which were used in the current study. The parentages of both populations are presented in Fig. 1.Fig. 1


Diversity arrays technology (DArT) markers in apple for genetic linkage maps.

Schouten HJ, van de Weg WE, Carling J, Khan SA, McKay SJ, van Kaauwen MP, Wittenberg AH, Koehorst-van Putten HJ, Noordijk Y, Gao Z, Rees DJ, Van Dyk MM, Jaccoud D, Considine MJ, Kilian A - Mol. Breed. (2011)

Pedigree of the two mapping populations examined. Common parents are highlighted
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3285764&req=5

Fig1: Pedigree of the two mapping populations examined. Common parents are highlighted
Mentions: For mapping, two populations were used. The first, Prima × Fiesta, was used to examine the reliability of the DArT data by evaluating the ease by which the DArT markers were integrated in an existing, well-established linkage map. This population consists of 156 individuals (Maliepaard et al. 1998), of which a subset of 121 individuals were DArT genotyped. The second population, 2000–2012 (Soriano et al. 2009), was used to demonstrate the ease by which DArT markers allow for the alignment between mapping populations. In addition, this population was used to compare two DArT complexity reduction methods with respect to the number of markers and genome coverage. It comprises 894 individuals, 399 of which were used in the current study. The parentages of both populations are presented in Fig. 1.Fig. 1

Bottom Line: Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions.The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage.ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.

View Article: PubMed Central - PubMed

ABSTRACT
Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus