This folder contains Brian Yandell’s presentation for the January 2017 Plant Breeding Network and Tools as a Driving Force for Better Economy Symposium in Bangkok, Thailand. The talk is divided into multiple segments with plenty of time for open discussion. Source material to reproduce the talk can be found at https://github.com/byandell/PlantSysGen.
- Introduction [PDF | HTML] (32 pages)
- Quantitative Trait Loci (QTL) [PDF | HTML] (43)
- Association Mapping [PDF | HTML] (24)
- Genome-Wide Selection [PDF | HTML] (12)
- Multiple Traits [PDF | HTML] (18)
- Systems Genetics Tools [PDF | HTML] (14)
Extra Material:
references
- A Guide to QTL Mapping with R/qtl: book by Karl W. Broman & Śaunak Sen
- Broman KW (2001) Review of statistical methods for QTL mapping in experimental crosses. Lab Animal 30:44–52. (review for non-statisticians)
- Endelman JB (2011) Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP. Plant Genome 4: 250-255. doi:10.3835/plantgenome2011.08.0024 (presentation of rrBLUP ideas)
- Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits Sinauer Associates, Sunderland, MA, ch. 15. (chapter on QTL mapping)
- Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199. (the seminal paper)
- Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971. (LOD thresholds by permutation tests)
Strickberger MW (1985) Genetics, 3rd edition. Macmillan, New York, ch. 11. (old but excellent general genetics textbook with a very interesting discussion of epistasis)
Yandell System Genetics References