Suppose we have located a specific gene on its related chromosome and will subsequently want to determine the inheritance of this gene before crossing.
Hi Ali,
first of all, it is not clear what you mean by "inheritance of a specific gene":
1) do you wish to know the "Mendelian" segregation ratios of the gene in subsequent generations?
2) do you want to estimate the expected value of the offspring for the phenotype affected by the specific gene?
3) something else?
If 1), you may want to predict carriers of specific alleles of the gene using SNP data: there are published method for this task (e.g. S. Li, H. Wang, A. Smith, B. Zhang, X. Zhang, G. Schoch, et al. Predicting multiallelic genes using unphased and flanking single nucleotide polymorphisms. Genetic Epidemiology, 35(2):85–92, 2011). Or pedigree + markers (e.g. Pirola, Y., Della Vedova, G., Bonizzoni, P., Stella, A., and Biscarini, F. (2013). “Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes,” in Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB’13). New York, NY: ACM, 9 pages.)
If 2), the field of genomic predictions for traits of interest in plants, human and animals has expanded vastly over the last few years. You may have a look at my work on sugar beets, for instance. But there are several papers on most plant and animal species, + humans (mainly disease traits, but not only)
3) I wait for additional details :-)
Hope this helps,
filippo
Hello Dr. Biscarini
I'm so glad to see a helpful comment from an expert on this topic.
In fact, I mean that when we find a gene or a marker linked to this gene in a plant by molecular techniques, how we can predict the presence of this gene in progenies of a distinct crossing? For example, using marker assisted selection we indicate that a Lilium plant has a resistance gene. In a breeding program we will cross this accession to another distinct accession of Lilium. Is it possible to predict the inheritability of this gene in the next generations? What about its expression in progenies?
Can we guarantee the presence and expression of resistance gene in Lilium progenies resulted from two distinct parent?
Thank you
1. If you found a tightly-linked molecular marker to the specific resistance gene, you can use this marker to predict which plants of the progeny will have this resistance gene. You can predict it, because most likely this marker will co-segregate with the resistance gene.
2. You cannot guarantee all the offspring from the two parental lines will have this resistance gene, unless the resistant parent is homozygous for this resistance allele, ex R/R. (R/R x -/- = all R/-, if diploid)
Dear Dr. Yuan-Yeu Yau
Thank you very much for your helpful comment.
I suppose a situation where we will not cross the parents.
For example, we have a resistant cultivar and decide to suggest it as a parent in crossing programs. Based on our resistant cultivar, can we choose the other parent to achieve successful types of crossing that result in resistant progenies which show target trait?
Hi Ali,
Yes, you can make cross. For example, you have a resistant cultivar 'A', and you can cross this cultivar 'A' to an elite cultivar 'B' (which has many good traits). After you cross 'A' with 'B', you get offspring. Next, you have to screen the offspring with the 'resistant' gene, AND you need to initiate a backcross program (backcross selected offspring back to the elite 'B' line) to restore the 'B' line genome makeup. In general, it will take several runs of backcrossing to restore B line genome makeup, and minimize the 'linkage drag' around the resistant gene.
Dear Dr. Yuan-Yeu Yau
I know that we can do this. I just want to be sure that is there a way to guarantee the appearance of target trait in phenotype before crossing.
Does the parent selection affect the appearance of target trait in phenotype? If yes, how can we predict this effect prior to crossing?
Hi Ali,
I am not sure that I completely follow your question. But, if you want to have a 'good trait' to be inherited into the progeny, the parental line(s) should possess this trait (ie. the gene(s) to control this trait). If you want to 'guarantee' the good trait to be inherited into some of the offspring, the parents should be pre-selected with those traits (by screening specific alleles or biomarkers associated with the specific traits).
Hello Dr. Yau,
Of course, I benefit by your comments.
Thank you very much for your time and consideration.
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