Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers.

BMC Genomics
Antonio CabreraEsther van der Knaap

Abstract

Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studie...Continue Reading

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Citations

Feb 22, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hiroyuki FukuokaAkio Ohyama
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Methods Mentioned

BETA
PCR

Software Mentioned

BLASTX
Contig Assembly Program CAP3
Primer3
python contig
RosCOS
Python Contig Viewer
Sequencher

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