Prediction and analysis of spatial order in haploid chromosome complements

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Abstract
Bennett proposed a model that predicts a mean ordered arrangement of all the chromosomes in a simple haploid genome, based on associations of pairs of most similar long, and pairs of most similar short, chromosome arms. The model orders a complete simple haploid genome so that each chromosome is associated with 2 constant neighbors. A test of the model is described with 2 types of data obtained from the same reconstructed serially sectioned somatic metaphases examined in the EM. First, chromosome arm volumes were estimated and used to identify the chromosomes and to predict their mean spatial order. Secondly, centromere positions in 3 dimensions were established. In the species and hybrids used, all with 14 chromosomes, there are so many ways of positioning the chromosomes within haploid sets that a computer-aided analysis was developed. With use of only centromere identities and positions, the programs generated all possible orders of centromeres in haploid sets (where each centromere has 2 neighbors) and computed the sum of distnces between centromeres for each order within a cell. Orders were ranked in ascending sequence of sums of distances. Orders that ranked highest were taken as best. After results for replicate cells were pooled, orders were ranked from best to worst. A test of the predicted order was then made by finding its position on this summary. In all the 4 grasses [Aegilops umbellulata, Hordeum bulbosum, H. vulgare, Secale africanum] examined, the predicted order was among the 5% of orders judged best by the analysis. To demonstrate and confirm the predicted order in these grasses, only 7-10 reconstructed nuclei were required. Presumably this test is suitable for general application to other materials whose simple haploid genomes contain between 6 and about 10 biarmed chromosomes.