Microsatellite Simple Sequence Repeat Markers Research Articles

Assessment the genetic diversity of common bean Phaseolus vulgaris collection by microsatellite SSR markers

Common bean plants (Phaseolus vulgaris L.) are the most important edible beans for their high nutritional value as an important source of dietary protein. However, in spite of the importance of this crop species, its genetics has not been fully characterized. Advances in molecular biology techniques have provided the basis for uncovering virtually unlimited numbers of DNA markers. Polymerase Chain Reaction (PCR) -based markers are more convenient and accurate determination of the genetic relationships. The utility of PCR-DNA based marker is generally determined by the technology that is used to reveal DNA-based polymorphism between and within different organisms. Thus, the present investigation aimed to assess the genetic variability among the different varieties of common bean based on the genetic distances that obtained by simple sequence repeat (SSR) or microsatellite techniques. SSR-DNA markers will identify closely related genotypes of different varieties of common bean. In the present study, a total of eleven bean varieties, nine of P. vulgaris L., one of Phaseolus coccineus, and one of Phaseolus lunatus namely: Bean CORA, Judia cilena, Diamant, palati, Distinction, Contender, Fagiolo Nano, Ambra, Bronco, Merit, Lima bean were selected SSR markers that were relatively more efficient in detecting similarities among Pharsalus genotypes studied with similarities up to 95%. SSR profiling provides useful information on the level of polymorphism and genetic diversity in common bean. Key words: Phaseolus vulgaris L., common bean, polymerase chain reaction, dietary protein.

Sequence‐characterized amplified region and simple sequence repeat markers for identifying the major quantitative trait locus responsible for seedling resistance to downy mildew in Chinese cabbage (Brassica rapa ssp. pekinensis)

With 1 figure and 2 tablesAbstractDowny mildew caused by the oomycete Hyaloperonospora parasitica Constant. (Pers. Ex Fr.) is a serious threat to Brassicaceae family. Previously, a major quantitative trait locus (QTL) for seedling resistance (BrDW) and its flanking markers, K14‐1030 and phosphoglucomutase, were identified in the Chinese cabbage. In order to establish the marker‐assisted selection (MAS) technique, K14‐1030 was successfully converted into a sequence‐characterized amplified region marker SCK14‐825, and a bacterial artificial chromosome (BAC) with sequence homology to K14‐1030 was identified. On the basis of the homologous and the linked BAC sequences, two microsatellite simple sequence repeat markers, kbrb058m10‐1 and kbrb006c05‐2, were designed and mapped on the confidence intervals of BrDW. These three markers could explain the QTL effect to a considerable extent and yield relatively high selection accuracy, which would be helpful in MAS for breeding downy mildew‐resistant Brassica rapa ssp. pekinensis varieties.

A flexible quantitative methodology for the analysis of gene-flow between conventionally bred maize populations using microsatellite markers.

Previous studies of gene-flow in agriculture have used a range of physical and biochemical markers, including transgenes. However, physical and biochemical markers are not available for all commercial varieties, and transgenes are difficult to use when trying to estimate gene flow in the field where the use of transgenes is often restricted. Here, we demonstrate the use of simple sequence repeat microsatellite markers (SSRs) to study gene flow in maize. Developing the first quantitative analysis of pooled SSR samples resulted in a high sampling efficiency which minimised the use of resources and greatly enhanced the possibility of hybrid detection. We were able to quantitatively distinguish hybrids in pools of ten samples from non-hybrid parental lines in all of the 24 pair-wise combinations of commercial varieties tested. The technique was used to determine gene flow in field studies, from which a simple model describing gene flow in maize was developed.

The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis

The utility of RFLP (restriction fragment length polymorphism), RAPD (random-amplified polymorphic DNA), AFLP (amplified fragment length polymorphism) and SSR (simple sequence repeat, microsatellite) markers in soybean germplasm analysis was determined by evaluating information content (expected heterozygosity), number of loci simultaneously analyzed per experiment (multiplex ratio) and effectiveness in assessing relationships between accessions. SSR markers have the highest expected heterozygosity (0.60), while AFLP markers have the highest effective multiplex ratio (19). A single parameter, defined as the marker index, which is the product of expected heterozygosity and multiplex ratio, may be used to evaluate overall utility of a marker system. A comparison of genetic similarity matrices revealed that, if the comparison involved both cultivated (Glycine max) and wild soybean (Glycine soja) accessions, estimates based on RFLPs, AFLPs and SSRs are highly correlated, indicating congruence between these assays. However, correlations of RAPD marker data with those obtained using other marker systems were lower. This is because RAPDs produce higher estimates of interspecific similarities. If the comparisons involvedG. max only, then overall correlations between marker systems are significantly lower. WithinG. max, RAPD and AFLP similarity estimates are more closely correlated than those involving other marker systems.