Phenotypic constraints on crop improvement and the domestication of novel crops

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Crop domestication and improvement requires novel and important traits to be visible to the farmer and breeder and for selection to enhance these. This means that genetic, physiological, morphological or biochemical linkage of traits will play a profound role in ability to select for advantageous phenotypes. Selection on two linked positive traits will proceed quickly (e.g. larger seeds and larger fruits), whereas selection of a positive trait linked to a negative trait (larger plant have bigger seeds but fall over in the wind and rain) will generate conflicting selection, delaying or preventing trait improvement. In a scenario of climate change, it is increasingly urgent to breed resilient and productive crops, and even consider the potential value of currently underutilised crops with lower yield but climate resilience. In this project, the student will use QTL mapping to resolve the genetic basis of trait linkage, combined with analyses investigate the correlational structure and covariance of phenotypic traits (including traits known to be of agronomic value) to determine the sign and magnitude of linkage. This will be estimated for two crop progenitors (the progenitors of tomato and eggplant), i.e. where domestication has occurred, and two closely-related never-domesticated crop-wild relatives, i.e. where domestication could theoretically have taken place but did not. This systems level apporoach will identify differences in trait integration between the progenitors and never-domesticated species to test the hypothesis that trait linkage and integration plays a role in 'domesticability'. Population genetics approaches will compare diversity in the four species at candidate loci (domestication genes and the surrounding genomic region), and to model the possible outcomes of selection strategies aiming at uncoupling negative and positive traits. The results will have broad impact in terms of agriculture, climate change resilience, and understanding the fundamentals of how species evolve and diverge.