Analysis Of Natural Variation In Recombination In Maize
Meiotic recombination is a major source of genetic variation in plants. Understanding factors that affect the recombination rates in plants is important for general genetic studies on meiosis as well as for plant breeding efforts. To examine how maize evolution and domestication affected meiotic recombination genes, I examined evolution patterns in eleven genes controlling key recombination pathway steps in a diverse set of maize inbred lines and several teosinte accessions. Even though meiotic recombination genes generally exhibit high sequence conservation expected in a pathway controlling a key cellular process, I identified several different selection modes in the eleven genes. Adaptive evolution signatures were found in about half of the examined genes in maize. Interestingly, in Balsas teosinte, the closest wild relative of maize, different and fewer genes showed adaptive evolution patterns than in maize. Changes in relatively few amino acid residues were responsible for the adaptive evolution signatures in maize and teosintes. Through protein structure predictions, I found that several of the amino acid residues identified as targets of selection are likely to induce functional changes in their proteins. I hypothesize that the evolutionary changes in the recombination pathway may have contributed to the successful domestication of maize and its expansion to new cultivation areas. In another study to understand the factors that affect recombination rates in plants, I analyzed natural variation in crossover rates in maize during meiosis. I analyzed the numbers of chiasmata in thirteen randomly chosen parent inbreds lines from the NAM (nested association mapping) population. I hypothesized that genetic differences in the inbreds may affect the number of crossovers, which directly translates to natural variation in recombination frequency in these inbreds. After analyzing chiasmata numbers in maize, I found that the inbreds were significantly different from each other with respect to the average chiasma numbers per cell. These findings indicate that there are genetic regulatory elements in these inbreds, which lead to the observed differences in chiasma counts. It is possible to identify these regulatory elements and understand their mode of action, which in future, would enable the manipulation of recombination frequencies.
natural variation; recombination
McCouch, Susan Rutherford
Alani, Eric; Hua, Jian
Ph.D. of Plant Breeding
Doctor of Philosophy
dissertation or thesis