Research inequity in the plant sciences.

Do all plant biologists worldwide have equal access to novel methods, enabling them to be equally productive, publish, and receive credit for their research? Or does reduced access to cutting-edge techniques in countries with lower financial resources create an inequity for researchers located there? Such disparities and biases do exist within our discipline and must be addressed if we are to move forward as a more just society. Applications in Plant Sciences has taken steps to address this important issue of research inequity, as outlined below. We now call upon the entire botanical community-researchers, editors and reviewers, funding agencies, and publishers-to work together toward a more equitable environment for all researchers around the world.

An empirical review: Characteristics of plant microsatellite markers that confer higher levels of genetic variation.

During microsatellite marker development, researchers must choose from a pool of possible primer pairs to further test in their species of interest. In many cases, the goal is maximizing detectable levels of genetic variation. To guide researchers and determine which markers are associated with higher levels of genetic variation, we conducted a literature review based on 6782 genomic microsatellite markers published from 1997-2012. We examined relationships between heterozygosity (H e or H o) or allele number (A) with the following marker characteristics: repeat type, motif length, motif region, repeat frequency, and microsatellite size. Variation across taxonomic groups was also analyzed. There were significant differences between imperfect and perfect repeat types in A and H e. Dinucleotide motifs exhibited significantly higher A, H e, and H o than most other motifs. Repeat frequency and motif region were positively correlated with A, H e, and H o, but correlations with microsatellite size were minimal. Higher taxonomic groups were disproportionately represented in the literature and showed little consistency. In conclusion, researchers should carefully consider marker characteristics so they can be tailored to the desired application. If researchers aim to target high genetic variation, dinucleotide motif lengths with large repeat frequencies may be best.

An efficient technique for primer development and application that integrates fluorescent labeling and multiplex PCR.

PREMISE OF THE STUDY: Development of genetic markers can be costly and time-consuming, especially when multiple primer pairs are fluorescently labeled. This step was streamlined by combining two techniques in the same PCR reaction: (1) custom-labeling of primers by the investigator and (2) multiplexing multiple primers together in the same reaction. • METHODS AND RESULTS: This technique was successfully used to develop microsatellite markers in several plant species. Microsatellites amplified with this multiplexing process were identical to those generated from PCR using individual primer pairs and with traditional methods using a priori labeled fluorescent primers. Tests of PCR cycling programs revealed that conditions recommended for the commercial kit generated stronger fragment peaks than the previously recommended cycling protocol. • CONCLUSIONS: This technique is an efficient and economical way to fluorescently label multiple microsatellite primers in the same reaction. It is also applicable to other markers used in PCR amplification of genetic material.