Publicly available in the "Unsolved Mysteries" series of PLOS Biology: Controlling Size in Multicellular Organs: Focus on the Leaf

In Molecular Breeding:
Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley
R. K. Varshney, T. Thiel, T. Sretenovic-Rajicic, M. Baum, J. Valkoun, P. Guo, S. Grando, S. Ceccarelli and A. Graner
            Volume 22, Number 1 / August, 2008

Abstract:  A ‘core set’ of 28 simple sequence repeat (SSR) and 28 single nucleotide polymorphism (SNP) markers for barley was developed after screening six diverse genotypes (DGs) representing six countries (Afghanistan, Pakistan, Algeria, Egypt, Jordan and Syria) with 50 SSR and 50 SNP markers derived from expressed sequence tags (ESTs). The markers of the core set are single locus with very high quality amplifications, high polymorphism information content (PIC) and are distributed across the barley genome. PIC values for the selected SSR and SNP markers ranged between 0.32–0.72 (average 0.58) and 0.28–0.50 (average 0.42), respectively. To make the SNP genotyping cost effective, CAPS (cleaved amplified polymorphic sequence) and indel assays were developed for 23 markers and the remaining 5 SNP markers were optimized for pyrosequencing. A high coefficient of correlations (r = 0.96, P < 0.005) between the genetic similarity matrices of SSR and SNP genotyping data of the core set on diverse genotypes (DGs) and their similar groupings according to the geographical distribution in both SSR and SNP phenograms with high bootstrap values underline the utility and reliability of the core set. A comparative allelic and sequence diversity for SSR and SNP markers between the DGs and six elite parental genotypes (PGs) of mapping populations showed comparable diverse nature of two germplasm sets. However, unique SNPs and indels were observed in both germplasm sets providing more datapoints for analysing haplotypes in a better way for the corresponding SNP marker.

This month on the freely available Public Library of Science (PLOS - Biology), Gene Banks Pay Big Dividends to Agriculture, the Environment, and Human Welfare , by RC Johnson of USDA.

The US National Institute of Health (NIH) has begun a policy of requiring the authors of research reports that describe work supported by the NIH to deposit accepted manuscripts into PubMed Central (PMC), the NIH's public digital library of full-text articles, with the understanding that the articles will be freely available for all to view no later than 12 months after publication. See the free PLOS Biology article by co-founder Harold Varmus.

In Crop Science:
Marker-Assisted Selection in Plant Breeding: From Publications to Practice
Yunbi Xu and Jonathan H. Crouch
Crop Sci 48:391-407 (2008)

The volume of publications on the development and to a lesser extent the application of molecular markers in plant breeding has increased dramatically during the last decade. However, most of the publications result from investments from donors with a strategic science quality or biotech advocacy mandate leading to insufficient emphasis on applied value in plant breeding. Converting promising publications into practical applications requires the resolution of many logistical and genetical constraints that are rarely addressed in journal publications. This results in a high proportion of published markers failing at one or more of the translation steps from research arena to application domain. The rate of success is likely to increase due to developments in gene-based marker development, more efficient quantitative trait locus (QTL) mapping procedures, and lower cost genotyping systems. However, some fundamental issues remain to be resolved, particularly regarding complex traits, before marker-assisted selection realizes its full potential in public sector breeding programs. These include the development of high throughput precision phenotyping systems for QTL mapping, improved understanding of genotype by environment interaction and epistasis, and development of publicly available computational tools tailored to the needs of molecular breeding program