Improving Quantitative Trait Loci Mapping Resolution in Experimental Crosses by the Use of Genotypically Selected Samples

Department of Biology, University of North Carolina, Chapel Hill, 27599, USA.
Genetics (Impact Factor: 5.96). 06/2005; 170(1):401-8. DOI: 10.1534/genetics.104.033746
Source: PubMed


One of the key factors contributing to the success of a quantitative trait locus (QTL) mapping experiment is the precision with which QTL positions can be estimated. We show, using simulations, that QTL mapping precision for an experimental cross can be increased by the use of a genotypically selected sample of individuals rather than an unselected sample of the same size. Selection is performed using a previously described method that optimizes the complementarity of the crossover sites within the sample. Although the increase in precision is accompanied by a decrease in QTL detection power at markers distant from QTL, only a modest increase in marker density is needed to obtain equivalent power over the whole map. Selected samples also show a slight reduction in the number of false-positive QTL. We find that two features of selected samples independently contribute to these effects: an increase in the number of crossover sites and increased evenness in crossover spacing. We provide an empirical formula for crossover enrichment in selected samples that is useful in experimental design and data analysis. For QTL studies in which the phenotyping is more of a limiting factor than the generation of individuals and the scoring of genotypes, selective sampling is an attractive strategy for increasing genome-wide QTL map resolution.

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    • "The genetic maps for the five populations we evaluated had average map distances between adjacent markers ranging from 3.8 to 7.9 cM (Table 1). Xu et al. (2005) reported that marker density less than 10 cM between flanking markers containing QTLs greatly improved QTL detection power and precision of CIs. Most QTLs were identified within dense flanking marker intervals; the exceptions to this were QTLs on Gm05 and Gm06, which were near Satt681 and BARC-04481-08709 in the 93K×J population (Table 3). "
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    Theoretical and Applied Genetics 07/2015; 128(10). DOI:10.1007/s00122-015-2566-1 · 3.79 Impact Factor
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    • "This resource is useful across onion germplasm since the anchor markers used here have been tested in other mapping populations, allowing the linkage maps to be aligned for comparative mapping using the CMap tool [45] provided at[41]. The map was then used as a reference to select a subset of genotypes for bin mapping [46,47] to facilitate rapid marker screening and targeted map development. A set of 10 genotypes was identified for selective genotyping (bin mapping) using MapPop [32], providing an approximate bin length resolution of 8.8 cM. "
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    • "Using the high dense SNP information, we selected 164 informative markers on all chromosomes, except Y. Marker distances in genomic regions that differed between the two parental lines were below 10 Mb, which was about 5 cM (Additional file 3: Figure S1) [23]. A higher marker density would not lead to a higher mapping resolution in this pedigree [42]. Intervals larger than 10 Mb did not contain informative markers and thus could not add information to the linkage analysis. "
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