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.
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.