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Title: The genetics of life history traits in the fungus Neurospora crassa
Abstract: The study of life histories is fundamental to understanding why some organisms live for a very short time while others live for a long time, why some produce thousands of offspring while others produce one, or why some need a mate to reproduce while others can do it on their own. The life histories of many animals and plants are well known because we can easily walk into a forest or field and measure them. Fungi, on the other hand, are hard to find and see even though they occur most everywhere in great numbers. In the three chapters of this dissertation, I uncover key aspects of the life history of the genetic model Neurospora crassa, a filamentous fungus.
First, I present a novel algorithm for the design of crossing experiments, which test the reproductive abilities of individuals. The algorithm identifies a set of individuals (a “crossing-set”) from a larger pool of potential crossing-sets by maximizing the diversity of traits of interest, for example, maximizing the range of genetic and geographic distances between individuals included in the crossing-set.
Second, I use the algorithm to select strains for a mating experiment designed to test for maternal effects—the impact of the mother’s phenotype on the offspring’s phenotype—across sexual reproduction in N. crassa. I measured offspring phenotypes from crosses of all possible pairs of 22 wild-isolated strains. Crosses encompassed reciprocals of 11 mating-type “A” and 11 mating-type “a” strains. After controlling for the genetic and geographic distances between strains in any individual cross, I found strong evidence for maternal control of perithecia (sporocarp) production, as well as maternal effects on spore numbers and spore germination. However, both parents exert equal influence on the percentage of spores that are pigmented, and size of pigmented spores. This experiment is proof of maternal effects in a fungus, an unprecedented discovery.
Third, I compared the sexual spore viability data from the maternal effects experiment to asexual spore viability data I gathered for the same strains. I found a striking trade-off between the viabilities of sexual and asexual spores. I used genome-wide polymorphism data to determine the genetic basis of this trade-off and identified 36 single nucleotide polymorphisms (SNPs) significantly associated with both traits. All 36 of the identified SNPs exhibit antagonistic pleiotropy—they have opposing effects on sexual and asexual spore viability. Some of these SNPs occur in well-characterized genes involved in sexual reproduction, asexual reproduction, or both. Using the entire dataset of over 50,000 genome-wide SNPs, I show a negative correlation between effects SNPs on sexual and asexual viability across the entire N. crassa genome. These results suggest that a life history trade-off between sexual and asexual spore viabilities drives a large portion of the genetic variation in the N. crassa genome.