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It thus seems that a large excess of one germplasm type can confuse analysis by Structure.
The correspondence between the inbreds' assignment by MCLUST and STRUCTURE and the germplasm type information were compared.
With the maximum membership probability criterion, the assignment by STRUCTURE showed for 94.4% of the inbreds correspondence with the germplasm type information.
Therefore, some of the inbreds containing this haplotype can be readily used as donors for marker-assisted selection within their respective germplasm type, be it temperate or tropical.
Due to the fact that germplasm type information was in very good agreement with molecular marker information, sugar type and yield type inbreds were the basis for all further analyses.
MCLUST based on principal components, principal coordinates, or lapvectors had high correspondence with the germplasm type information as well as the assignment by STRUCTURE, which indicated that these methods might be alternatives to STRUCTURE for population structure analysis.
Similar(51)
Nevertheless, we observed a higher average MRD for all the inbreds than for that between two germplasm types.
The SNP classification does not indicate if it will or will not be a useful marker in other germplasm types.
A different degree of divergence between these two germplasm types was observed across the genome (Additional file 6).
Summary of line designations, generations and parental lines for the seven plant germplasm types utilized in this study.
The observation of distinct subgroups was further made possible by the occurrence of only few recombination events between the two germplasm types [ 8].
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