Hi,
I'm constructing genetic maps for one hybrid population, which is a F1 population derived from a cross between two species (Miscanthus sinensis X Miscanthus sacchariflourus). Both parents are diploids (2X=38).
By using pseudo-testcross strategy, I successfully got 19 LGs for each parent. Female map was constructed using makers segregating as "lmxll", and male map was constructed using markers segregating as "nnxnp".
However, when constructed the composite map using all markers, I got 29 LGs, and only 9 LGs contain segregating markers from both parents (lmxll, nnxnp, hkxhk), while the remaining 20 LGs only contain marker which segregate in either of the parents (exclusively lmxll, or nnxnp).
I'm thinking that maybe this is because two parents represent two species, they do have distinct different genetic background, and two paired homologous chromosomes in hybrids have distinct genetic backgrounds. In addition, this population is F1, no cross-overs yet occurred between homologous chromosomes. Therefore, linkage groups were produced separately for two homologous chromosomes which are distinct from each other. While for the chromosomes that are similar in both parents, LGs from both parents can be resolved into an integrated one.
I don't know whether my explanation is right or not.
Does anyone have experiences with this kind of problem? Any possible explanations are welcomed.
You might want to try the R package LPmerge,
Hope this helps
Pablo
You need markers segregating in both parents to make a composite map- i.e. hkxhk markers, or (depending upon the marker platform and segregation) you need to re-code your lmxll and nnxnp markers to efxeg or abxcd markers. You shouldn't be able to form bona-fide linkage groups with only lmxll or nnxnp markers as (as you say) there are no crossovers between your two parents in the 'F1' progeny that you have used to build your map.
Thanks Richard, I think your suggestion is right. In my population, two parents are two species, so among 4000 SNPs, ~1600 are segregating in female parent, ~2400 are segregating in male parent, and only 17 are heterozygous (hkxhk) in both parents. Anchor markers that are heterozygous in both parents are needed to link two parental maps.
Hello Hongxu Dong,
I am trying to develop a composite map for one hybrid population like you tried 3 years ago. Just like you I have two heterozygous parents of roses that are themselves interspecific hybrids. The construction of separate maps wasn't a problem but whenever i try to use markers segegrating in both parents (abxab) so a mix of aaxab, abxaa and abxab, I find that the linkage groups containing the 3 kind of markers are way too long (5553cM ??) compared to the normal size known and other linkage groups contain like you only markers segregating in the one of the parents.
The only difference I have with you is that Out of almost 6000 markers I have around 400 that are abxab (coded hkxhk in JoinMap). So I thought that this would be enough to integrate no ? But I still have the same problem than you ...
Did you find any explanation ? Did you get to have your composite map afterall ?
Your help would be grately appreciated because there is no forum about problems like this in JoinMap version 4.1 or any version at all actually.
Best regards,
- Badges
- Science topic
- Similar topics
- Geoscience
- Cartography
- Mapping