Microsatellites are the choice of markers in many non model organisms for linkage map construction. I am working on a non model fish species and developed around 140 informative markers in order to perform linkage analysis. But the problem I am facing is that a large junk of markers were not assigned to any linkage group. Due to this reason, I am not able to get a complete linkage map of that particular species. Could anybody kindly help me to solve the problem?
You don't need an F2 cross. Mapping programs like Outmap, OneMap, or JoinMap can easily handle an F1 population IF you have enough progeny. From my experience with pine species and SSR markers, 75 progeny is the minimum, 100 is better, 200+ better yet for resolution of correct order at ~2 cM distances. Also, with too few progeny linkage phase cannot be accurately inferred from F1 progeny and parental genotypes alone. One way around this is with genotype information from the four grandparents in addition to the two parents (a 3-generation pedigree), which would allow you to determine phase a priori. On the issue of an incomplete linkage map, you simply need more segregating markers. Depending on the polidy, number of chromosomes and genome size (cM length), you may need close to 300-400 segregating marker for >90% map coverage.
Dear Arjun,
We need a bit more infor on this. Are you mapping in a single F1 family between two outbred parents? In general an F1 is not ideal for linkage mapping becasue many markers will not be informative for recombinations. An F2 is much better. Alternatively you could have multiple half-sib or full-sib families.
The problem is that any mapping population is only useful for the markers that segregate within that population. that's why for outbred species, it may be better to have mutiple families so that markers that do not segregate in one paprent, may be segregating in another parent.
Buit I do not know enough about your target species? Is it outbred?
How many fish in your F1?
How did you select the microsats etc?
Hi Arjun,
Follow this link which I hope can lead you to a solution regarding your concern. http://hub.africabiosciences.org/
You don't need an F2 cross. Mapping programs like Outmap, OneMap, or JoinMap can easily handle an F1 population IF you have enough progeny. From my experience with pine species and SSR markers, 75 progeny is the minimum, 100 is better, 200+ better yet for resolution of correct order at ~2 cM distances. Also, with too few progeny linkage phase cannot be accurately inferred from F1 progeny and parental genotypes alone. One way around this is with genotype information from the four grandparents in addition to the two parents (a 3-generation pedigree), which would allow you to determine phase a priori. On the issue of an incomplete linkage map, you simply need more segregating markers. Depending on the polidy, number of chromosomes and genome size (cM length), you may need close to 300-400 segregating marker for >90% map coverage.
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