i am working on groundnut SSR markers and i want to know the information about co -dominant markers and its usage and at the same how it will be beneficial in identifying polymorphism between plants of single genotype
Co dominant markers can differentiate alleles of same gene.. SSR is one best example that determines allelic variation in population that can help differentiation of genotypes in population.
Let's say you are working on a plant trait with 2 alleles, one is 'wild-type' (A) and one is 'mutation form (a)'. So, there are 3 possible genotypes: AA, Aa and aa. Co-dominant markers are when you do PCR, you can see both bands for A and a on a gel. Therefore, for AA and aa plants, you will see only one band, and for Aa plant you can see TWO bands. The advantage of this is: that you can distinguish AA from Aa plants by genotyping.
In a very straight froward sentence you can write the co-dominant markers are those which can distinguish between homozygote and heterozygote plants and it follows the genotypic ratio like for F2 segregation involving single gene it should show the ratio 1:2:1 where as dominant markers will show phenotypic ration i.e. 3:1 where single gene is involved. RFLP, SSR, STS, STMS etc are co-dominant markers and RAPD, ISSR, AFLP, DAF etc are dominant markers.
@ Arup Kumar : Sir, I feel stumbled for these words ":dominant markers will show phenotypic ration i.e. 3:1" . Merging the concept of Phenotypes with Genotype (DNA) will make it wrong. In very simple words "A Co-dominant maker simply differentiate 2 alleles of a gene in given locus but a dominant marker can not". Relating with phenotype will crumble the imaginations of banding pattern.
Concept of Dominant Allele suppressing the phenotype of weaker allele is the phenotypic ratio of 3:1. It does not mean the AA will have same banding pattern as Aa. If that is the case, AA, Aa, aA, aa all will have same band.
Dear Dr. Vimarsh Gowda,
I wrote all those words for the understanding of Dr. Siva. The band sharing may from any parent i.e. either male or female donor in case of dominant marker. I did not explain it in terms of genetics I explained it for a layman as I take regular classes for students who don't understand even allele.. Anyway thank you very much.
Codominant markers will clearly show bands for homozygous dominant like AA, homozygous receive- aa and heterozygous state- Aa, after running your PCR. Dominant markers will not show all the allelic patterns in a genotype- (like AA, aa, and Aa), the result is not exhaustive or detailed.
@ Arup Kumar Mukherjee and Vimarsh Gowda : Sir can you please explain in F2 population how the ratio of 3:1 came for the dominant marker when it can detect only one allele of a gene. why cant it be 3:0? Please explain the principle behind dominant markers...
please tell me what makes Co domain marker distinguish between heterozygous and homozygous alleles.
Just imagine you have a band of 350 bp size for parent A and another fragment of 200 bp for parent B. If you cross between AxB and then selfing then in F2 you will have AA having 300 bp band AB both 300 and 200 bp band (2 nos) and BB having 200 bp bands only. Now if you have dominant marker it will show either of A type or B type band but if you take co-dominant marker it can distinguish between A type, B type and AB type clearly giving a segregation ratio of 1:2:1. Whereas dominants will give 2:1 ratio.
To understand meaning of codominance, lets take an example of flower color in Four o'clock plant. Crossing of Red (RR) and White (rr) flower result in flower having Pink (Rr) color.
Now, knowing this information we can identify heterozygous (Rr) plant just by looking at the color of flower. We need not to go for any other assay. This is how codominant nature can be easily used to differentiate between homozygous (RR/rr) and heterozygous (Rr) plants.
Now, in case of molecular marker like SSR (which is codominant), it produces single band for homozygous and two bands for heterozygous (As explained by Arup Kumar Mukherjee). Point to note here is we can identify heterozygous plant by looking only at the gel picture (showing two bands parallel to pink color of flower). Thats how codominance nature of SSR can be used for this differentiation.
@ Abhishek Pandey: lets suppose an Ssr is polymorphic for p1(100bp) and p2 (50bp). P1 and p2 produces single band bcz they have respective size allele on both the homologous chromosomes.
In case of f1 where one chromosome is from p1 and another from p2, it amplifies theses two alleles, 100 bp n 50 bp, from homologous chromosomes. Thats why it produces two bands. Dats how it distinguishes between homozygous and heterozygous plants.
Plz see illustration.
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