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Genome-wide scan of the soybean genome using degenerate oligonucleotide primed PCR: an example for studying large complex genome structure

Content Provider	Springer Nature Link
Author	Van, Kyujung Kang, Yang Jae Shim, Sang Rea Lee, Suk Ha
Copyright Year	2012
Abstract	The availability of next generation sequencing instruments has made large-scale and genome-wide sequence analysis more feasible in a wild variety of species with large complex genomes, especially crops. This report suggested an approach for characterizing large complex genomes of less-studied/orphan crops. Degenerate oligonucleotide primed PCR (DOP-PCR) is a useful tool for the survey of genomes in less-studied/orphan crops, as prior sequence information is not necessary. Here, four different degenerate primers were redesigned from previously described DOP-PCR primers. The degeneracy of these primers was increased with the addition of two more ‘Ns’. The amplified DOP-PCR products from Sinpaldalkong 2, a soybean genotype, were applied to GS-FLX and the reads from Sinpaldalkong 2 were mapped against Williams 82 as a reference ( http://www.phytozome.net/soybean.php ), using the Burrows-Wheeler Aligner ( http://bio-bwa.sourceforge.net/ ). These results suggest the identification of 4 single nucleotide polymorphisms between Sinpaldalkong 2 and Williams 82 and recent duplication of the soybean genome. The sequenced reads were subsequently assembled into contigs by Newbler under default conditions. A total of 29 Sinpaldalkong 2 contigs exhibited 95% similarity and < E-100 when mega-blasted with Williams 82 reference sequences. These contigs were mapped to the soybean chromosomes and positioned as clusters within each chromosome. Most of the contigs also showed similarity with the Arabidopsis RNase H domain-containing protein, suggesting a potential way to study retrotransposons in less-studied/orphan crops. Using these modified DOP-PCR primers and GS-FLX, it is possible to obtain insight into the large complex genomes of less-studied/orphan crops.
Starting Page	467
Ending Page	474
Page Count	8
File Format	PDF
ISSN	19769571
Journal	Genes & Genomics
Volume Number	34
Issue Number	5
e-ISSN	20929293
Language	English
Publisher	The Genetics Society of Korea
Publisher Date	2012-08-31
Publisher Place	Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	DOP-PCR Genome duplication GS-FLX Less-studied/orphan crops Retrotransposons Soybean Human Genetics Plant Genetics & Genomics Microbial Genetics and Genomics Animal Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Biochemistry Molecular Biology

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