The DNA tricks that gave us 100 different kinds of tomatoes

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Jun 17, 2020, 11:00 ET

COLD SPRING HARBOR, N.Y., June 17, 2020 /PRNewswire/ -- An expansive new analysis of genetic variation among tomatoes has uncovered 230,000 previously hidden large-scale differences in DNA between 100 different 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.

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/CSHL, 2020.

The study, a collaborative effort led by Cold Spring Harbor Laboratory (CSHL) Professor and Howard Hughes Medical Institute Investigator Zachary Lippman and Johns Hopkins University (JHU) Professor Michael Schatz, is the most comprehensive analysis 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 JHU, the University of Georgia, the Boyce Thompson Institute, and others, seized the opportunity to investigate.

Together, the group sequenced and compared the genomes of 100 different varieties of tomato, including robust varieties suitable for industrial agriculture, succulent heirlooms, and wild relatives of cultivated tomato.

To gain a better understanding of structural variants' role in diversity, the team showed that thousands of genes were changed by the structural variations. Then they used CRISPR—the genome editing tool that can make targeted changes in DNA—to show that duplication of a particular gene causes a plant's tomatoes to increase in size by about 30 percent. Investigating another variant, they tracked down a gene that contributes to a smoky flavor in some tomatoes. And in another set of experiments, the researchers uncovered a complex interaction involving four structural variants that eliminates a trade-off between a feature that simplifies tomato harvesting and another that reduces productivity.

Understanding how these and other structural variants influence tomatoes gives breeders new power to improve the properties of tomatoes, a $190 billion global industry, and shows how structural variants that can enhance breeding are likely hidden in the complex genomes of many other important crops, like corn, rice, and soybeans.

About Cold Spring Harbor Laboratory

Founded in 1890, Cold Spring Harbor Laboratory has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Home to eight Nobel Prize winners, the private, not-for-profit Laboratory employs 1,100 people including 600 scientists, students and technicians. For more information, visit www.cshl.edu.

About Johns Hopkins

Johns Hopkins is America's first research institution and a premier university and health system with campuses around the world.

SOURCE Cold Spring Harbor Laboratory