BackgroundPigeonpea [Cajanus cajan (L.) Millsp.] is an important legume crop of rainfed agriculture. Despite of concerted research efforts directed to pigeonpea improvement, stagnated productivity of pigeonpea during last several decades may be accounted to prevalence of various biotic and abiotic constraints and the situation is exacerbated by availability of inadequate genomic resources to undertake any molecular breeding programme for accelerated crop improvement. With the objective of enhancing genomic resources for pigeonpea, this study reports for the first time, large scale development of SSR markers from BAC-end sequences and their subsequent use for genetic mapping and hybridity testing in pigeonpea.ResultsA set of 88,860 BAC (bacterial artificial chromosome)-end sequences (BESs) were generated after constructing two BAC libraries by using HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes. Clustering based on sequence identity of BESs yielded a set of >52K non-redundant sequences, comprising 35 Mbp or >4% of the pigeonpea genome. These sequences were analyzed to develop annotation lists and subdivide the BESs into genome fractions (e.g., genes, retroelements, transpons and non-annotated sequences). Parallel analysis of BESs for microsatellites or simple sequence repeats (SSRs) identified 18,149 SSRs, from which a set of 6,212 SSRs were selected for further analysis. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, we identified 842 polymorphic SSR markers that will have utility in pigeonpea improvement. Based on these markers, the first SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. Utility of developed SSR markers was also demonstrated by identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment in commercial hybrid breeding programme.ConclusionIn summary, while BAC libraries and BESs should be useful for genomics studies, BES-SSR markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in pigeonpea.

Surface- and tip-enhanced Raman spectroscopy (SERS and TERS) techniques exhibit highly localized chemical sensitivity, making them ideal for studying chemical reactions, including processes at catalytic surfaces. Catalyst structures, adsorbates, and reaction intermediates can be observed in low quantities at hot spots where electromagnetic fields are the strongest, providing ample opportunities to elucidate reaction mechanisms. Moreover, under ideal measurement conditions, it can even be used to trigger chemical reactions. However, factors such as substrate instability and insufficient signal enhancement still limit the applicability of SERS and TERS in the field of catalysis. By the use of sophisticated colloidal synthesis methods and advanced techniques, such as shell-isolated nanoparticle-enhanced Raman spectroscopy, these challenges could be overcome.

Chemical mapping of a photocatalytic reaction with nanoscale spatial resolution is demonstrated for the first time using tip-enhanced Raman spectroscopy (TERS). An ultrathin alumina film applied to the Ag-coated TERS tip blocks catalytic interference whilst maintaining near-field electromagnetic enhancement, thus enabling spectroscopic imaging of catalytic activity on nanostructured Ag surfaces.