“Examining the Effects of Domestication on Recombination Landscape in Maize”
Maize and its wild progenitor, teosinte, are a valuable system for studying the process of crop domestication. Domestication of maize has led to drastic changes in its genetic architecture and phenotype, such as ears with many small, soft kernels and less branching. However, there is a lack of research studying how meiotic recombination has evolved over the course of domestication in maize. Recombination, the swapping of genetic material between separate parental chromosomes through crossovers (COs), is essential to generating genetic diversity in nature as it can create novel combinations of beneficial alleles and remove detrimental alleles from the gene pool. Understanding and predicting recombination in crops is key to breeding new optimized varieties of plants. This study investigated how recombination patterns in maize shifted throughout the process of domestication through comparing maize to teosinte, its wild progenitor, and to maize landraces, the early-domesticated form of modern maize. I wrote R scripts to map COs in all three plants and found that overall recombination patterns were conserved, but that all plants varied in fine-scale hotspot position and that landrace and maize were more like each other than teosinte. They shared more CO hotspots with each other than with teosinte, and their overall recombination rates were similar and higher than teosinte, which is consistent with previous findings in other crops that domestication increases recombination. I also wrote scripts to identify regions of major changes in recombination and examined the correlation between these regions and sites of other changes that could impact fine-scale changes in recombination, such as differentially methylated regions and selective sweeps. I found no relationship between differences in recombination and these other regions in the maize genome over the course of domestication, leaving an open question of what may lead to dynamic shifts in recombination landscape as a crop evolves.
This internship was an invaluable opportunity to become more familiar with the computational tools used in plant science research, something I had little experience with before this summer. I had known I wanted to go into plant science for some time, but my research project was a totally new side of it to me. Additionally, hearing what other interns were working on, attending the weekly seminars, and interacting with faculty and grad students, especially my mentor and PI, gave me an appreciation for the diversity of topics studied under plant science and made me well-prepared for grad school in the future.