Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids

BACKGROUND: Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. RESULTS: Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. CONCLUSIONS: The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD-based association studies. The MADCE method therefore enables researchers to tackle many of the genotyping problems that arise when performing mapping, pedigree, and association studies in allopolyploids. We discuss the merits of MADCE in comparison to other marker systems in polyploids, including SNPs, and how MADCE could aid in the development of SNP markers in allopolyploids

Effects of hand orientation on motor imagery - event related potentials suggest kinesthetic motor imagery to solve the hand laterality judgment task

Motor imagery (MI) refers to the process of imagining the execution of a specific motor action without actually producing an overt movement. Two forms of MI have been distinguished: visual MI and kinesthetic MI. To distinguish between these forms of MI we employed an event related potential (ERP) study to measure interference effects induced by hand orientation manipulations in a hand laterality judgement task. We hypothesized that this manipulation should only affect kinesthetic MI but not visual MI. The ERPs elicited by rotated hand stimuli contained the classic rotation related negativity (RRN) with respect to palm view stimuli. We observed that laterally rotated stimuli led to a more marked RRN than medially rotated stimuli. This RRN effect was observed when participants had their hands positioned in either a straight (control) or an inward rotated posture, but not when their hands were positioned in an outward rotated posture. Posture effects on the ERP-RRN have not previously been studied. Apparently, a congruent hand posture (hands positioned in an outward rotated fashion) facilitates the judgement of the otherwise more demanding laterally rotated hand stimuli. These ERP findings support a kinesthetic interpretation of MI involved in solving the hand laterality judgement task. The RRN may be used as a non-invasive marker for kinesthetic MI and seems useful in revealing the covert behavior of MI in e.g. rehabilitation programs

Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids

Abstract Background Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. Results Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. Conclusions The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD-based association studies. The MADCE method therefore enables researchers to tackle many of the genotyping problems that arise when performing mapping, pedigree, and association studies in allopolyploids. We discuss the merits of MADCE in comparison to other marker systems in polyploids, including SNPs, and how MADCE could aid in the development of SNP markers in allopolyploids.</p

Figure 5 shows the results for the hand posture outward rotated condition.

<p>The upper panels show the grand average ERPs to back view stimuli (upper left panel) and palm view stimuli (upper right panel). Grand averages to medially rotated hand stimuli are depicted in dotted lines, grand average ERPs to laterally rotated hand stimuli are depicted in solid lines. The selected RRN window is highlighted by a white area between 400-450 ms after stimulus presentation (t=0). Consecutive RRN mean amplitude values (in µV) with error bars are depicted in the bar graphs below. On the lower left, RRNs to back view stimuli are depicted whereas on the lower right, RRNs to palm view stimuli are depicted.</p

DEVELOPMENTAL MEDICINE &amp; CHILD NEUROLOGY Children with unilateral cerebral palsy show diminished implicit motor imagery with the affected hand

ERP Event-related potentials HLJ Hand laterality judgement RRN Rotation-related negativity AIM Motor imagery refers to the mental simulation of a motor action without producing an overt movement. Implicit motor imagery can be regarded as a first-person kinesthetic perceptual judgement, and addresses the capacity to engage into the manipulation of one&apos;s body schema. In this study, we examined whether children with unilateral cerebral palsy (CP) are able to engage in implicit motor imagery. METHOD A modified version of the hand laterality judgment task was employed. Erroneous responses, reaction times, and event-related potentials from the electroencephalograph were analysed. RESULTS In 13 children with typical development (mean age 10y 7mo, SD 1y 2mo; seven male, six female), we observed the classic rotation direction effect. Specifically, when comparing outward rotated with inward rotated hand pictures, decreased accuracy and increased response times were observed. Event-related potentials analyses of the electroencephalogram revealed a more marked N1 and an enhanced rotation-related negativity. INTERPRETATION These findings suggest that an implicit motor imagery strategy was used to solve the task. However, in 10 children with unilateral CP (mean age 10y 7mo, SD 2y 5mo; five male, five female), these effects were observed only when the less-affected hand was involved. This observation suggests that children with CP could benefit from visual training strategies. Cerebral palsy (CP) describes a group of permanent disorders of movement and posture that are attributed to non-progressive disturbances that occurred in the developing fetal or infant brain

Figure 1a

<div><p>Figure 1a shows the 8 different hand stimuli that were randomly presented during the experiment. Coding of the 8 different stimuli: RBM right hand, back view, medially rotated; RBL, right hand, back view, laterally rotated; LBM left hand, back view, medially rotated; LBL, left hand, back view, laterally rotated; RPM right hand, palm view, medially rotated; RPL, right hand, palm view, laterally rotated; LPM left hand, palm view, medially rotated; LPL, left hand, palm view, laterally rotated;</p> <p>Figure 1b shows a graphic description of the three different hand posture conditions.</p> <p>Figure 1c depicts the presentation order within a trial.</p></div

Figure 4 shows the results for the hand posture inward rotated condition.

<p>The upper panels show the grand average ERPs to back view stimuli (upper left panel) and palm view stimuli (upper right panel). Grand averages to medially rotated hand stimuli are depicted in dotted lines, grand average ERPs to laterally rotated hand stimuli are depicted in solid lines. The selected RRN window is highlighted by a white area between 400-450 ms after stimulus presentation (t=0). Consecutive RRN mean amplitude values (in µV) with error bars are depicted in the bar graphs below. On the lower left, RRNs to back view stimuli are depicted whereas on the lower right, RRNs to palm view stimuli are depicted.</p

Figure 3 shows the results for the control hand posture condition.

<p>The upper panels show the grand average ERPs to back view stimuli (upper left panel) and palm view stimuli (upper right panel). Grand averages to medially rotated hand stimuli are depicted in dotted lines, grand average ERPs to laterally rotated hand stimuli are depicted in solid lines. The selected RRN window is highlighted by a white area between 400-450 ms after stimulus presentation (t=0). Consecutive RRN mean amplitude values (in µV) with error bars are depicted in the bar graphs below. On the lower left, RRNs to back view stimuli are depicted whereas on the lower right, RRNs to palm view stimuli are depicted.</p