Hi all I am working on cross pollinated crop of Jatropha Curcas. in this i want to map the QTLs for yield related traits, to this I have selected two inbred lines at self generation 6(S6) level and two heterozygous lines. Designed crosses like inbred X Inbred and Heterozygous X Inbred. The heterozygous lines are contrasting and geographically different and inbreeds are having les contrast and high homozygosis. So let me know which cross combination is good and what generation need to be mapped
https://www.wiley-vch.de/books/sample/3527311165_c01.pdf
this book can solve your query.
For inbred X inbred, F1s are are heterozygous, you need to self F1 to get a segregating F2 population. And you can accurately estimate linkage phase between markers.
For heterozygous X inbred, you will only get a population segregating for the heterozygous parent, because inbred parent is homozygous for all positions. Therefore you can only map QTLs that are segregating in the heterozygous parent.
You can also try heterozygous x heterozygous, and two-way pseudo-testcross strategy can be used to construct two parental maps. If there are enough bi-parental markers (i.e segregating in both lines), you can also get an integrated map. Then you can proceed to do QTL analysis.
For trees, two-way pseudo-testcross is maybe the best strategy considering the time spend.
Dear Hongxu Dong, As per the second point of your answer it would be good for me mapping of QTLs for only heterozygous parent, because I am using heterozygous parent is high yielding in contrast to that I selected low yield homozygous line. So please let me have your view on this.
In coming to third point, If we cross heterozygous X heterozygous, How we will track the segregation pattern which allele coming from which parent?
For heterozygous x heterozygous cross design, genotypes can be coded following JoinMap. For example, if the species is diploid, you will have three segregation types:
1. lmxll: locus heterozygous in the first parent. Possible segregating genotypes are lm, ll, and --, which is missing data. The segregating allele is coming from the first parent.
2. nnxnp: locus heterozygous in the second parent. Possible segregating genotypes are nn, np, and --, which is missing data. The segregating allele is coming from the second parent.
3. hkxhk: locus heterozygous in both parents. Possible segregating genotypes are hh, hk, kk and --, which is missing data. The segregating allele is coming from both parents.
If the species is tetraploid with disomic inheritance, you will have two more segregation types in addition to the three types mentioned above:
4. abxcd: locus heterozygous in both parents, four alleles. Possible segregating genotypes are ac, ad, bc, bd and --, which is missing data.
5. efxeg: locus heterozygous in both parents, three alleles. Possible segregating genotypes are ee, ef, eg, fg and --, which is missing data.
Anyway, there are several popular software for genetic map construction, like JoinMap, R/QTL, etc. You can read the manual, it has detailed explanations.
Hope this helps.
Dear Hongxu Dong, the segregation pattern you have for which generation and what is segregation ratio and my lines are diploid only.
As mentioned before by Hongxu Dong, heterozygous X heterozygous is a good solution and for a diploid you will have lm, ll, np, nn and heterozygous. You can map QTL with an F1 population using R or map/qtl.
Good luck!
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