We have developed a locus-specific DNA target preparation method for highly multiplexed single nucleotide polymorphism (SNP) genotyping called MARA (Multiplexed Anchored Runoff Amplification). The approach uses a single primer per SNP in conjunction with restriction enzyme digested, adapter-ligated human genomic DNA. Each primer is composed of common sequence at the 5' end followed by locus-spe...

The application of commercially available microsatellite primers, developed for genomic analysis of the laboratory rat (Rattus norvegicus) and laboratory mouse (Mus musculus), to the genotyping of wild rodents provides a rapid and inexpensive alternative to cloning, sequencing and synthesizing species-specific primers de novo. The effort required to identify a useful panel of heterologous (inte...

UNLABELLED PREMISE OF THE STUDY The first microsatellite primers were developed for Callerya speciosa, an important traditional medicinal plant with island-mainland distributions in China, to further investigate its genetic variability and population structure. • METHODS AND RESULTS The microsatellite-containing sequences were selected from a cDNA library of C. speciosa. In total, 58 prime...

With the aim to increase the number of functional markers in resource poor crop like cultivated peanut (Arachis hypogaea), large numbers of available expressed sequence tags (ESTs) in the public databases, were employed for the development of novel EST derived simple sequence repeat (SSR) markers. From 16424 unigenes, 2784 (16.95%) SSRs containing unigenes having 3373 SSR motifs were identified...

Recent declines in costs accelerated sequencing of many species with large genomes, including hexaploid wheat (Triticum aestivum L.). Although the draft sequence of bread wheat is known, it is still one of the major challenges to developlocus specific primers suitable to be used in marker assisted selection procedures, due to the high homology of the three genomes. In this study we describe an ...

Random amplified polymorphic DNA (RAPD) bands that distinguish Meloidogyne hapla and M. chitwoodi from each other, and from other root-knot nematode species, were identified using a series of random octamer primers. The species-specific amplified DNA fragments were cloned and sequenced, and then the sequences were used to design 20-mer primer pairs that specifically amplified a DNA fragment fro...

SUMMARY PriSM is a set of algorithms designed to select and match degenerate primer pairs for the amplification of viral genomes. The design of panels of hundreds of primer pairs takes just hours using this program, compared with days using a manual approach. PriSM allows for rapid in silico optimization of primers for downstream applications such as sequencing. As a validation, PriSM was used ...

Ulmus pumila is an elm species, non-native to the USA that hybridizes with Ulmus rubra. In order to study the genetic structure and hybridization patterns between these two elm species, we developed 15 primer pairs for microsatellite loci in U. rubra and tested their cross-amplification in U. pumila. All 15 primers amplified in both species, 11 of which possessed species-specific alleles. Eight...

Ulmus chenmoui (Ulmaceae) is an endangered tree found on Langya Mountain, eastern China. To better understand the population genetics of U. chenmoui and conserve the species, we developed microsatellite markers. Using a suppression-polymerase chain reaction technique, 74 compound microsatellite primer pairs were designed. Twelve microsatellite markers were polymorphic in 39 individuals, and the...

Fusarium is a large and diverse genus of fungi of great agricultural and economic importance, containing many plant pathogens and mycotoxin producers. To date, high-throughput sequencing of Fusarium communities has been limited by the lack of genus-specific primers targeting regions with high discriminatory power at the species level. In the present study, we evaluated two Fusarium-specific pri...