Detecting and mapping repulsion-phase linkage in polyploids with polysomicinheritance

It has been suggested that ratios of coupling to repulsion-phase linked mar kers can be used to distinguish between allopolyploids and autopolyploids, because repulsion-phase linkages are much more difficult to detect in autop olyploids with polysomic inheritance than allopolyploids with disomic inher itance. In this report, we analyze the segregation pattern of repulsion-pha se linked markers in polyploids without complete preferential pairing. The observed repulsion-phase recombination fraction (R) in such polyploids is c omposed of a fraction due to crossing-over (R-c) and another fraction due t o independent assortment (R-i). R-i is the minimum distance that can be det ected between repulsion-phase linked markers. Because Ri is high in autopol yploids (0.3373, 0.4000, 0.4286 and 0.4444) for autopolyploids of 2n=4x. 6x . 8x and 10x), large population sizes are required to reliably detect repul sion linkages. In addition, the default linkage used in mapping-programs mu st be greater than the corresponding R-i to determine whether a polyploid i s a true autopolyploid. Unfortunately, much lower default linkages than the R(i)s have been used in recent polyploid studies to determine polyploid ty pe, and markers have been incorporated into polyploid maps based on the R v alues. Herein. we describe how mapping repulsion linkages can result in spu rious results. and present methods to accurately detect the degree of prefe rential pairing in polyploids using repulsion linkage analysis.