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The pervasive usage of this marker set has led to the development of functional assays based on multiplex PCR and multi-color capillary gel electrophoresis.
Furthermore, a high-resolution association map created using a high-density marker set has the potential to unravel stress-associated genetic variability in a genome [ 10].
Several linkage maps of various sizes, marker sources and completeness are available, however, no integrated map and marker set has explored consistency of linkage analysis among unrelated mapping populations.
Furthermore, we have used a case only study design, which for a given sample size and marker set, has been suggested by others to be more powerful than a case control study design (reviewed in Montana et.al [ 42]).
The noted weaknesses in the use of solely performance indicators for marker discovery, without considering the stability of the proposed marker set, has been raised in the literature [ 34] and is in congruence with the findings of this study.
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We analyzed the banding patterns in the most widely adopted sugarcane bioethanol strains and in several indigenous yeast contaminants, and found that our marker set had very good discriminatory power.
Power analysis indicated that our microsatellite marker set had an acceptable type I error rate (а = 0.051) and a 100% power to detect GST ≥ 0.008 based on sample sizes from our 2011 collection.
The marker with the minimum SSW/SSB was selected if more than one marker or marker set had the same training accuracy, where SSW and SSB indicate the within-population and between-population sum of squares for genotypic values or gene expression levels, respectively.
Data for these marker sets have been submitted to the CottonGen SNP database (http://www.cottongen.org).org
Two recent studies, examining larger cohorts and using denser marker sets, have been more successful.
Finally, haplotype block and haplotype-tagging SNP analyses have been suggested to only be reliable when markers are dense, otherwise marker sets have considerable loss of information[ 50].
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