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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

Alignment of the 17 linkage groups of the mapping populations Prima × Fiesta (PF) and 2000–2012 (012). DArT markers are displayed in bold, those segregating in both parents are in italics and those generated with the alternative complexity reduction method are underlined. The + and − symbols next to a marker name indicate that the DArT marker was polymorphic in the mother and father, respectively. The # symbols indicate the DArT markers that have been sequenced
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Fig2: Alignment of the 17 linkage groups of the mapping populations Prima × Fiesta (PF) and 2000–2012 (012). DArT markers are displayed in bold, those segregating in both parents are in italics and those generated with the alternative complexity reduction method are underlined. The + and − symbols next to a marker name indicate that the DArT marker was polymorphic in the mother and father, respectively. The # symbols indicate the DArT markers that have been sequenced

Mentions: Of the aforementioned 776 Prima × Fiesta DArT markers, 247 (32%) were mapped to a unique position (Fig. 2). The other 68% were eliminated during the mapping process for several reasons (Table 1). Only 4.6% of the markers were discarded due to possible scoring problems. Of these, 3.5% were due to incomplete data on the mapping parents, leaving only 1.1% of the markers being possibly discarded for inadequate scoring, remaining ungrouped or showing irregular segregation patterns. The two latter phenomena could also be due to reasons other than scoring difficulties, such as a lack of marker coverage of the genomic regions or the presence of duplicated loci. Online Resource 1b documents the fact that adding DArT markers did not affect the previous high overall map quality, as measured by the average χ2 value.Fig. 2


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)

Alignment of the 17 linkage groups of the mapping populations Prima × Fiesta (PF) and 2000–2012 (012). DArT markers are displayed in bold, those segregating in both parents are in italics and those generated with the alternative complexity reduction method are underlined. The + and − symbols next to a marker name indicate that the DArT marker was polymorphic in the mother and father, respectively. The # symbols indicate the DArT markers that have been sequenced
© Copyright Policy
Related In: Results  -  Collection

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

Fig2: Alignment of the 17 linkage groups of the mapping populations Prima × Fiesta (PF) and 2000–2012 (012). DArT markers are displayed in bold, those segregating in both parents are in italics and those generated with the alternative complexity reduction method are underlined. The + and − symbols next to a marker name indicate that the DArT marker was polymorphic in the mother and father, respectively. The # symbols indicate the DArT markers that have been sequenced
Mentions: Of the aforementioned 776 Prima × Fiesta DArT markers, 247 (32%) were mapped to a unique position (Fig. 2). The other 68% were eliminated during the mapping process for several reasons (Table 1). Only 4.6% of the markers were discarded due to possible scoring problems. Of these, 3.5% were due to incomplete data on the mapping parents, leaving only 1.1% of the markers being possibly discarded for inadequate scoring, remaining ungrouped or showing irregular segregation patterns. The two latter phenomena could also be due to reasons other than scoring difficulties, such as a lack of marker coverage of the genomic regions or the presence of duplicated loci. Online Resource 1b documents the fact that adding DArT markers did not affect the previous high overall map quality, as measured by the average χ2 value.Fig. 2

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