Molecular Plant Breeding & Data Analysis: Methods & Applications (Part 1)

[@mariamazalamsimuko6911]

Thank you for this lecture. Very helpful!

[@SethMurray]

Questions from one of the attendees and my quick (not checked for typos) answers: 2) Difference between LD mapping and QTL mapping? same for Association mapping and GWA? LD mapping essentially is another older name for Genome Wide Association Studies (GWA / GWAS). You discover Quantitative Trait Nucleotides which are essentially SNPs with higher resolution than Quantitative Trait Loci (QTL), but most people still call them QTL. I prefer using QTL just for linkage mapping to distinguish it from GWAS. I think you will find every example in between in the literature. 3) BLUP or Mean, which is better to use for QTL mapping with F2 population, or which one is better? You cannot use either unless you have a clonal crop because F2’s are not replicated or “immortalized” to combine replicates of. 4) How to do the analysis if we have many environments, Environment by environment or combined? I suggest doing it all ways and comparing the results. Combining them through complex models (getting genotype BLUPs) and environment by environment (still using BLUPs) 5) Data must be prepared trait by trait with genotypic data before to start QTL analysis, or can we put all the pheno traits together? If not, why? I don’t understand your question, sounds like an issue specific to the software you are using. 6) How to transformation the markers physical position to CM in genome? Depends on your crop and the resources available. This is not something I have personally done in the last 12 years so you should find someone else to answer. 7) For which trait is good to check the QTL? can we check for qualitative trait? This question does not make sense to me as written. If I was to guess I think you mean to confirm that your map is correct? And for that a highly heritable simple / Mendelian trait like seed color is best in my opinion. 8) If we want to consider the heritability, which trait can we identify the QTL? (high H² or low?) It depends on so many things. If you have no heritability than you will not find QTL. If you have high heritability you will still find less QTL than heritability would suggest (search literature for missing heritability problem). 9) Which of LOD can we use or consider for QTL identification? Not a question with a simple answer. What are your goals? What type of mapping are you doing? 10) What is transgressive segregation? Variation that exceed that of the parents. For example if you cross a parent that is 100cm tall by another that is 100cm tall, the progeny could easily range from 50cm to 150cm. This is because although the two parents are the same height, it is different combinations of loci that then get reshuffled

[@blaisemvny7909]

Thank you for this Lecture! I learned a lot from it.

[@peacealiru4177]

Thank you for sharing your knowledge , i learned a lot too

[@sogximunia]

Great lecture

[@MohamedAhmed-wg3ed]

Thank you so much ❤

[@pedrochavez526]

Hola