Table 1 The nine scenarios between two linked loci in the clonal F1 population for estimating the recombination frequency
ScenarioMarker CategoryRecombination Frequency
Locus 1Locus 2rFrMr
1I (ABCD)I (ABCD)
2I (ABCD)II (A = B)
3I (ABCD)III (C = D)
4I (ABCD)IV (AB = CD)1/2√1/2√
5II (A = B)II (A = B)
6II (A = B)IV(AB = CD)
7III (C = D)III (C = D)
8III (C = D)IV (AB = CD)
9IV (AB = CD)IV (AB = CD)
  • The symbol √ is used to indicate that recombination frequency rF, rM, or r could be estimated, and 1/2 is used to indicate that only half of the observed samples are used in estimating recombination frequency. When one marker is category II and the other one marker is category III, recombination frequency between them cannot be estimated and therefore it is not included.