Fig. 1.

Phase considerations and clustering strategy in a tetraploid. (a) The three phases considered for a pair of 2 × 0 markers, from left to right, ‘coupling’, ‘mixed’ and ‘repulsion’; (b) In the case of preferential pairing between homologues 1–2 and 3–4, we must consider two separate types of coupling phase, either coupling within preferential bivalents (left) or coupling between preferential bivalents (right). In the extreme case of an allotetraploid, this distinction could also be termed ‘subgenome-specific’ versus ‘subgenome-straddling’; (c) Simplex × nulliplex (1 × 0) markers (solid black dots) uniquely define homologous chromosomes and are initially clustered together. Higher-dosage marker types such as duplex × nulliplex (2 × 0) markers (dark grey) provide linkage associations between simplex × nulliplex homologues, helping to identify chromosomal linkage groups. Cross-parental markers such as simplex × simplex (1 × 1, light grey) can also link these groups together, leading to consistent linkage group numbering across parents