In my F2 population for disease resistance study, the Mendelian segregation ratio showed 1:2:1. PCR amplification was done by two SSR markers, both were confirmed well fit to 1:2:1. But why the susceptible and resistant lines both (phenotypes) were in heterozygous type genotypes?
some times your marker far(distance) from gene, than gene will be in the receive form phenotypically. Better you select more marker for screening.
all the best.
As Rizwana wrote, your marker seem to be too far away from the R-gene. Therefore it does not predict the phenotype very well. If you konw in which region of the chromosome the R-gene and marker are located you should try to find markers, that are closer to your R-gene. By this you should get a better prediction of your marker for the phenotype.
Thank a lot Rizwana Begum Syed Nabi and Stephan Schie
My another questions is, could it be a partial resistance? Because QTL results for two flanking markers (including above marker) showed partial dominance (D-0.21)?
Also I have sequenced 3 cultivars ( Parent 1 resistant, P2 susceptible and Parent P3 susceptible) for the primer and the Results appeared the gene of interest (above primer in photo) was matched but only for reverse complement in all Three Cultivars (75-85%).
I would redesign the primers and repeat the analysis with the new primers. All markers on the chromosome near to the R-Gene should be linked, this does not mean, that you have a QTL.
The segregation of 1:2:1 indicates a monogenic dominant R-gene. I would try to find a marker between both flanking markers to see whether it better fits to the phenotype. The better marker and phenotype correlate, the closer you get with your marker. By this correlation you see into which direction of your markers the R-gene is located. By this you see in which region you should search for new/better markers.
May be you need to grow them for a few more generations to get homozygous plants
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