Understanding Quantitative Trait Loci with the Help of Tomatoes

How do geneticists pin down the handful of genes behind a complex trait like the mass of a tomato? Traits like these are shaped by so many genes, and blurred by so much environmental noise, that any single one seems to vanish into a smooth continuum. This video tells the story of the 1988 study by Paterson and Lander that found a way through, mapping the quantitative trait loci (QTLs) behind fruit mass, pH, and soluble solid concentration in tomatoes. Rather than chase each gene directly, they tracked restriction fragment length polymorphisms (RFLPs), harmless DNA markers scattered across the genome, using how often a marker's genotype lined up with a change in phenotype to triangulate the real QTL nearby. With 70 markers across all twelve chromosomes and interval mapping to weigh how likely a QTL was at each point, they located and measured the effect of fourteen QTLs across the three traits. The real trick was the markers themselves: older morphological markers were too scarce to cover the genome, while these #RFLP polymorphisms were everywhere, making Lander's maximum likelihood methods feasible for the first time. That breakthrough in #QTLmapping jump-started genetic maps for crops like wheat and sugarcane, and today single nucleotide polymorphism markers carry the same logic into the study of human disease. Who'd have thought the humble #tomato would play such a role in unravelling the mysteries of genetics? Creator: John Saxon References Anderson J, Stack R, Liu S, Waldron B, Fjeld A, Coyne C, Moreno-Sevilla B, Fetch J, Song Q, Cregan P, et al. 2001. DNA markers for Fusarium head blight resistance QTLs in two wheat populations. Theor Appl Genet 102:1164–1168. https://doi.org/10.1007/s001220000509 Lander ES, Botstein D. 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121(1):185–199. https://doi.org/10.1093/genetics/121.... Lander ES, Green P. 1987. Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci U S A 84(8):2363–2367. https://doi.org/10.1073/pnas.84.8.2363 Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD. 1988. Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335(6192):721–726. https://doi.org/10.1038/335721a0 Singh R, Singh S, Tiwari D, Srivastava S, Singh S, Sharma M, Singh R, Mohapatra T, Singh N. 2012. Genetic mapping and QTL analysis for sugar yield-related traits in sugarcane. Euphytica 191:333–353. https://doi.org/10.1007/s10681-012-08... Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB. 1992. High density molecular linkage maps of the tomato and potato genomes. Genetics 132(4):1141–1160. https://doi.org/10.1093/genetics/132.... Wellcome Trust Case Control Consortium. 2007. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447(7145):661–678. https://doi.org/10.1038/nature05911