The DNA tricks that gave us 100 different kinds of Tomatoes
Tomatoes come in many sizes, colors, and flavors. CSHL Professor Zach Lippman, JHU Professor Mike Schatz, and colleagues around the world described the genetic underpinnings of 100 different types of tomatoes, including those in this photograph. Credit: Lippman lab.
An expansive new analysis of genetic variation among tomatoes has uncovered 230,000 previously hidden large-scale differences in DNA between varieties. As tomato plants evolved, segments of DNA were deleted, duplicated, or rearranged. These genomic “structural variations” underpin the vast diversity among tomatoes, changing flavors, altering yield, and shaping other important traits.
The study, a collaborative effort led by Cold Spring Harbor Laboratory Professor and Howard Hughes Medical Institute investigator Zachary Lippman and Johns Hopkins University (JHU) Professor Michael Schatz, is the most comprehensive analysis to date of structural genome variation for a major crop. Breeders and scientists will be able to apply the information to breed or engineer new, more desirable plants with greater efficiency.
Large-scale differences between genomes, known collectively as structural variants, are likely responsible for a wide range of plant features that breeders care about, but these elements have been notoriously difficult to study, leaving much of the genetic origins of tomato diversity unexplained, says Xingang Wang, a postdoctoral researcher in Lippman’s lab. New DNA sequencing technology along with powerful new genome editing technology has recently made structural variants easier to detect and study how they affect crop traits. Lippman’s team, in collaboration with scientists at Johns Hopkins University, the University of Georgia, the Boyce Thompson Institute, and others, seized the opportunity to investigate. Lippman notes,
“There was a whole massive amount of natural genetic variation that we were blind to. The only way to get at it was through this new technology. And there were already quite a few examples in the literature of how some of that hidden—what we call structural variation—was important. It was probably being grossly underestimated in terms of its importance. So we really just needed to walk through that door. And the only way to do it was to do it at scale with a hundred different genomes.”
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Original article written by: Jennifer Michalowski, Science Writer