Abstract
Marker segregation distortion is a natural phenomenon. Severely distorted markers are usually excluded in the construction of linkage maps. We investigated the effect of marker segregation distortion on linkage map construction and quantitative trait locus (QTL) mapping. A total of 519 recombinant inbred lines of soybean from orthogonal and reciprocal crosses between LSZZH and NN493-1 were genotyped by specific length amplified fragment markers and seed linoleic acid content was measured in three environments. As a result, twenty linkage groups were constructed with 11,846 markers, including 1513 (12.77%) significantly distorted markers, on 20 chromosomes, and the map length was 2475.86 cM with an average marker-interval of 0.21 cM. The inclusion of distorted markers in the analysis was shown to not only improve the grouping of the markers from the same chromosomes, and the consistency of linkage maps with genome, but also increase genome coverage by markers. Combining genotypic data from both orthogonal and reciprocal crosses decreased the proportion of distorted markers and then improved the quality of linkage maps. Validation of the linkage maps was confirmed by the high collinearity between positions of markers in the soybean reference genome and in linkage maps and by the high consistency of 24 QTL regions in this study compared with the previously reported QTLs and lipid metabolism related genes. Additionally, linkage maps that include distorted markers could add more information to the outputs from QTL mapping. These results provide important information for linkage mapping, gene cloning and marker-assisted selection in soybean.
Highlights
To validate the effectiveness of constructed linkage maps in this study, we evaluated the quality of the linkage maps, and detected quantitative trait locus (QTL) for seed linoleic acid content in soybean
After clustering of the reads with their reference, a total of 418,100 SLAF labels were obtained from all the recombinant inbred lines (RILs) and two parents
A total of 11,846 SLAF markers in all the RILs were mapped onto 20 chromosomes with an average markerinterval of 0.21 cM
Summary
Many studies on linkage map construction in soybean have been reported. The linkage maps were constructed using morphology and isoenzyme markers, e.g., the first soybean genetic map was constructed by 57 classical markers (Palmer and Kilen 1987). With the development of more advanced technologies, molecular markers have been used to construct linkage maps. These markers have the potential to “saturate” the genome and this increases the probability of QTL detection (Keim et al 1990).
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