Angiosperm systematics has progressed to the point where it is now expected that multiple, independent markers be used in phylogenetic studies. Universal primers for amplifying informative regions of the chloroplast genome are readily available, but in the faster-evolving nuclear genome it is challenging to discover priming sites that are conserved across distantly related taxa. With goals incl...

Retrotransposons are abundant in the genomes of plants. In the present study, inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers were developed for the cassava genome (Manihot esculenta Crantz). Four cassava cultivars (Fécula Branca, IPR-União, Olho Junto, and Tamboara, two samples per cultivar) were used to obtain IRAP ...

Eucommia ulmoides Oliver, the only extant species of Eucommiaceae, is a second-category state-protected endangered plant in China. Evaluation of genetic diversity among some intraspecific hybrid populations of E. ulmoides Oliver is vital for breeding programs and further conservation of this rare species. We studied the genetic diversity of 130 accessions from 13 E. ulmoides intraspecific hybri...

Anaerobic ammonia oxidizing (anammox) bacteria play an important role in transforming ammonium to nitrogen gas and contribute to fixed nitrogen losses in freshwater environments. Understanding the diversity and abundance of anammox bacteria requires reliable molecular tools, and these are not yet well established for these important Planctomycetes. To help validate PCR primers for the detection...

SUMMARY BEsTRF (Best Estimated T-RF) provides a standalone environment for analyzing primers-enzymes-gene section combinations used in terminal-restriction fragment length polymorphism (T-RFLP) for its optimal resolution. User-defined sequence databases of several hundred thousand DNA sequences can be explored and the resolution of user-specified sets of primers and restriction endonucleases ca...

Mango is one of the most commercially important fruit crops in tropical and subtropical regions. To increase the efficiency of breeding strategies, two EST-derived marker systems were developed in the present study using information from the mango fruit transcriptome. Using simple sequence repeats, 218 of 230 primer pairs showed stable amplification for 7 mango genotypes with amplicons ranging ...

PREMISE OF THE STUDY We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility. METHODS AND RESULTS We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the singl...

Evaluation of chloroplast DNA (cpDNA) diversity in wild relatives of crop brassicas is important for characterization of cytoplasm and also for population genetics/phylogeographic analyses. The former is useful for breeding programs involving wide hybridization and synthesis of alloplasmic lines, while the latter is important for formulating conservation strategies. Therefore, PCR-RFLP (Polymer...

PREMISE OF THE STUDY Chloroplast primers were developed from genomic data for the taxonomically challenging genus Castilleja. We further tested the broader utility of these primers across Orobanchaceae, identifying a core set of chloroplast primers amplifying across the clade. METHODS AND RESULTS Using a combination of three low-coverage Castilleja genomes and sequence data from 12 Castilleja...

Ion implantation, a new biophysically mutagenic technique, has shown great potential for crop breeding. To reveal the mutation effect of low-energy ion implantation on Baiyangdian red lotus, sequence-related amplified polymorphism markers were used to amplify and detect the DNA sequence differences in mutants induced by Fe(+) ion implantation. A total of 121 primer combinations were teste...