Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR), and they are typically composed of 1–6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS) can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS in rice breeding programs aimed at improving blast resistance in this species. We also discuss the various advantages, disadvantages and uses of microsatellite markers relative to other molecular marker types.

We used 40 ± 5 nm gold nanoparticles (GNPs) as colorimetric sensor to visually detect swine-specific conserved sequence and nucleotide mismatch in PCR-amplified and non-amplified mitochondrial DNA mixtures to authenticate species. Colloidal GNPs changed color from pinkish-red to gray-purple in 2 mM PBS. Visually observed results were clearly reflected by the dramatic reduction of surface plasmon resonance peak at 530 nm and the appearance of new features in the 620-800 nm regions in their absorption spectra. The particles were stabilized against salt-induced aggregation upon the adsorption of single-stranded DNA. The PCR products, without any additional processing, were hybridized with a 17-base probe prior to exposure to GNPs. At a critical annealing temperature (55 °C) that differentiated matched and mismatched base pairing, the probe was hybridized to pig PCR product and dehybridized from the deer product. The dehybridized probe stuck to GNPs to prevent them from salt-induced aggregation and retained their characteristic red color. Hybridization of a 27-nucleotide probe to swine mitochondrial DNA identified them in pork-venison, pork-shad and venison-shad binary admixtures, eliminating the need of PCR amplification. Thus the assay was applied to authenticate species both in PCR-amplified and non-amplified heterogeneous biological samples. The results were determined visually and validated by absorption spectroscopy. The entire assay (hybridization plus visual detection) was performed in less than 10 min. The LOD (for genomic DNA) of the assay was 6 µg ml(-1) swine DNA in mixed meat samples. We believe the assay can be applied for species assignment in food analysis, mismatch detection in genetic screening and homology studies between closely related species.

Calcium carbonate and its polymorphs from cockle shells (Anadara granosa) and commercial calcium carbonate were characterised using a variable pressure scanning electron microscopes (VPSEM), a transmission electron microscope (TEM), an energy dispersive Xray analyser (EDX), X-ray diffraction (XRD) and Fourier transmission infrared spectroscopy (FT-IR). Cubic-like calcite crystals of commercial calcium carbonate and rod-like aragonite crystals of cockle shell powders were observed by both SEM and TEM. The EDX results showed that the cockle shells contained more calcium and carbon than the commercial calcium carbonate, whereas the commercial calcium carbonate contained more oxygen than the cockle shells. FT-IR analyses revealed the presence of carbonate groups in both the cockle shells and the commercial calcium carbonate. FT-IR analyses also showed the presence of aragonite in the cockle shells and calcite in the commercial calcium carbonate. XRD analyses showed that the cockle shells powder contained aragonite, whereas the commercial calcium carbonate contained calcite. The cockle shells powder was formed with good quality calcium carbonate and contained calcium carbonate in the aragonite phase.

We visually identify pork adulteration in beef and chicken meatball preparations using 20 nm gold nanoparticles (GNPs) as colorimetric sensors. Meatball is a popular food in certain Asian and European countries. Verification of pork adulteration in meatball is necessary to meet the Halal and Kosher food standards. Twenty nm GNPs change color from pinkish-red to graypurple, and their absorption peak at 525 nm is red-shifted by 30-50 nm in 3 mM phosphate buffer saline (PBS). Adsorption of single-stranded DNA protects the particles against salt-induced aggregation. Mixing and annealing of a 25-nucleotide (nt) single-stranded (ss) DNA probe with denatured DNA of different meatballs differentiated well between perfectly matched and mismatch hybridization at a critical annealing temperature. The probes become available in nonpork DNA containing vials due to mismatches and interact with GNPs to protect them from salt-induced aggregation. Whereas, all the pork containing vials, either in pure and mixed forms, consumed the probes totally by perfect hybridization and turned into grey, indicating aggregation. This is clearly reflected by a well-defined red-shift of the absorption peak and significantly increased absorbance in 550-800 nm regimes. This label-free low-cost assay should find applications in food analysis, genetic screening, and homology studies.

We report a simple, novel and low-cost method for the synthesis of aragonite nanoparticles from cockle shells. Aragonite is one of the least abundant biogenic polymorphs of calcium carbonate and is widely used as a biomaterial for the repair of fractured bone, development of advanced drug delivery systems, and tissue scaffolds. The method involves a simple mechanical grinding of the micron-sized cockle shell powders in the presence of a non-toxic and non-hazardous biomineralization catalyst, dodecyl dimethyl betaine (BS-12). The method produces rod-shaped aragonite particles with a diameter of 20 ± 5 nm with good reproducibility and without any additional impurities. This was confirmed by a combined analysis of variable pressure scanning electron microscopy (VPSEM), transmission electron microscopy (TEM), Fourier transmission infrared spectroscopy (FTIR), thermogravimetric analyzer (TGA), X-ray diffraction spectroscopy (XRD) and energy dispersive X-ray analyser (EDX). The method should find potential applications in industry for the large scale synthesis of aragonite nanoparticles from a low cost but abundant natural resource such as cockle shells.