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Associated marker locus information, particularly the homoeologue-specific markers, offers a new resource for forage legume research to enable genetic analysis and improvement of this forage and grassland species.
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In other species, integration of independent mapping populations has enhanced genetic resolution and provided comprehensive relational locus information for disparate marker and population resources [ 32].
The second method (Method B) makes use of the marker information at only the most polymorphic marker locus for individuals with an unknown linkage phase.
For that, the core sequence of the marker locus (64 bp) was aligned towards the available genome sequence information to order the position of the markers on the scaffolds.
On the one hand, reference-free (anonymous) scans are carried out without information on the physical genomic position of a marker locus.
Furthermore, allelic variation at a candidate marker locus can be partially or completely masked by the presence of paralogous sequences, reducing the information content of such a marker.
The investigation of linkage between a quantitative trait and a marker locus.
Haseman, J. K. & Elston, R. C. The investigation of linkage between a quantitative trait and a marker locus.
In SPA, a QTL was confirmed if the phenotype was associated with a marker locus at P < 0.005, or with two adjacent marker loci at P < 0.01.
Locus information.
In this method, IBD probabilities are calculated for a fictitious locus A in the middle of a marker interval, where information is used from the markers on either side of this locus A. In our case, locus A is positioned at the marker locus in the middle of each marker interval.
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