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Simple sequence repeat (SSR) markers are widely used in plant genetics and breeding. However, there are many SSR markers that do not reveal polymorphism in cotton. Traditional SSR genotyping methods only provide information on product sizes. This leaves many marker polymorphism undetected, thus, lowering the utility of SSRs. In the present study, monomorphic SSRs between two mapping parents, 'Emian22' and 3-79, were subjected to single-strand conformation polymorphism (SSCP) analysis to reveal polymorphism. Of the 4194 monomorphic SSR primer pairs, 158 pairs (3.77%) showed polymorphism and revealed 174 polymorphic loci. Sequence analysis showed that the differences in PCR products between the mapping parents were solely due to base transition or transversion, which was in agreement with SSCP principles. SSCP also revealed SSRs with motifs of AT/TA and GAA/CTT were more polymorphic in dinucleotides and trinucleotides, respectively. Genetic mapping integrated 160 loci into our interspecific BC1 linkage map, 5 of which associated with QTLs related to cotton fiber quality. The technique discussed in the present study enables us to detect polymorphism of monomorphic SSRs, and increase the utilization efficiency of the existing SSR primers. [ABSTRACT FROM AUTHOR]

Sorghum is a potential energy crop thanks to its high biomass productivity and low input. Biomass yield in sorghum is defined by height and maturity. To develop molecular breeding tools for genetic improvement of these two traits, we have identified simple sequence repeat markers linked to height and maturity using a pool-based association mapping technique. The sorghum mini core collection was evaluated across five environments for height and maturity. Seven tall and seven short accessions were selected based on their height in all environments. Likewise, six early- and 10 late-maturing accessions were selected mostly based on their maturity in two post-rainy seasons. Two additional height pools were constructed based on phenotypes in one environment. The three pairs of pools were screened with 703 SSR markers and 39 polymorphic markers were confirmed by individual genotyping. Association mapping of the 39 markers with 242 accessions from the mini core collection identified five markers associated with maturity or height. All were clustered on chromosomes 6, 9, and 10 with previously mapped height and maturity markers or QTLs. One marker associated with both height and maturity was 84 kb from recently cloned Ma1. These markers will lay a foundation for identifying additional height and maturity genes in sorghum. [ABSTRACT FROM AUTHOR]

Traditionally, macrophyte density has been considered the primary factor affecting the large dissolved oxygen fluctuations in the Bow River. After a major flood event scoured macrophytes in 2005, and subsequently changed river dynamics, the City of Calgary needed to update their predictive computer model for water quality to reflect the new conditions, which led to this study. A 2006 aquatic vegetation survey was also completed to assess post-flood conditions. The survey found that the average macrophyte dry weight was much lower (28 g/m2 ± 100 (p = 0.05)) than the historic average of 241 g/m2 ± 29, while the average periphyton chlorophyll-a concentration was higher (343 mg/m2 ± 71) than the historic average (158 mg/m2 ± 17)). Dissolved oxygen (DO) fluctuations were similar to pre-flood levels despite changes in the dominant vegetation. Using the results of this survey, the significant and previously unrecognized effects of periphyton diurnal processes on DO concentrations in the Bow River were identified and the Bow River water quality model (BRWQM) was recalibrated to reflect these findings. Adjustments were made to the BRWQM’s periphyton submodel to account for the more dominant role played by these organisms in river processes, and a competitive shading factor between macrophytes and periphyton was also introduced to more accurately model the species' competition for available sunlight. This newly calibrated and validated version of BRWQM was tested and found capable of predicting the occurrence of low DO concentrations in the Bow River and can provide a useful tool for forecasting the water quality effects of the city's planned wastewater infrastructure expansion. [ABSTRACT FROM AUTHOR]