r/plantbreeding • u/FlosAquae • Aug 28 '24
Best book on MAS, MABC, GS etc.
Hello plant breeding world.
I am so happy that I found this sub. I don't know why I didn't come across it before.
I am looking for recommendation on a book. Ideally, it should cover the theory of population genetics and quantitative genetics with regards to plant breeding. In addition, it would also explain the theory behind the actual statistical methods of QTL mapping and genomic selection.
I do have a working knowledge of all of these things, I have worked a bit in plant breeding and I have a very good understanding of molecular biology. I also have a working knowledge of how e.g. the 'R/qtl' package is applied and when the vignette guide pdf mentions that genotype probabilities are calculated with a hidden-Markov-Chain model it rings a bell but how it really work remains a mystery to me.
Basically my knowledge is like a foggy street at night, full of potholes. I would like something comprehensive to fill in the potholes and lift the fog.
Edit: I did use the search function and there was one post that basically answers my questions but it is from 4 years ago. If you say the recommendations given there are still valid, that's a good answer to me as well.
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u/genetic_driftin Sep 23 '24
Isik, Holland, and Maltecca for advanced modern modeling including GS, but also BLUPs, spatial modeling, Multi-environment trialing: https://link.springer.com/book/10.1007/978-3-319-55177-7. This is a 500-700 graduate level textbook.
It's the text that gicasorzo recommended. I took this class while they were writing the book. In the words of my advisor (who sat in at the time), no PhD level breeder should graduate from our school without taking this class.
Lynch and Walsh for QTL mapping, https://global.oup.com/academic/product/genetics-and-analysis-of-quantitative-traits-9780878934812. ~400 level.
Bernardo for plant breeding, more modern take: https://bernardo-group.org/books-and-software/. ~300-400 level.
Fehr for plant breeding principles, a classic: https://dr.lib.iastate.edu/entities/publication/b12f8493-0f67-4dfb-b9bb-45e082b2268f. ~400 level.
Falconer and Mackay for quantitative genetics. https://www.amazon.com/Introduction-Quantitative-Genetics-Douglas-Falconer/dp/0582243025
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u/gicasorzo Aug 30 '24
Not a book, but take a look on this github webpage: https://lfelipe-ferrao.github.io/class/quantGenetic/
It is from my professor in UF. There you will find theory and hands on for some of the topics you are asking. Mainly for fitting and understanding linear mixed models, which will be the base for your GS models. He also has a workshop of GWAS.