An international team of researchers, led by scientists at Michigan State University and the University of California, Davis, has used the power of genomics to reveal the evolutionary origins of the cultivated strawberry and deciphered the genetic code of this highly coveted fruit. The genetic code empowers scientists by pinpointing genes and other features along each of the chromosomes—a genetic road map with physical addresses, analogous to GPS coordinates on a map.
Until now, little has been known about the evolutionary origins of the cultivated garden strawberry (Fragaria x ananassa). Whereas most species, including humans, are diploid with two copies of the genome (the genetic material of an organism) – one copy from each parent. Strawberry is an octoploid, with eight complete copies of the genome that were contributed by multiple, distinct parental species.
In a new study published in Nature Genetics, researchers now unveil how the strawberry became an octoploid, as well as the genetics that determine important fruit quality traits. What researchers uncovered is a complex evolutionary history that started long ago on opposite sides of the world.
The sequencing and analysis of the cultivated strawberry genome, exposing a wealth of new information about its origin and traits, is the product of an international team supported by Michigan State University (MSU) AgBioResearch, the University of California, Davis (UC Davis), the United States Department of Agriculture, the California Strawberry Commission and the National Science Foundation. Patrick Edger (MSU) and Steven Knapp (UC Davis) serve as co-corresponding authors for this manuscript titled, “Origin and evolution of the octoploid strawberry genome.”
“For the first time, analysis of the genome enabled us to identify all four extant relatives of the diploid species that sequentially hybridized to create the octoploid strawberry,” Edger said. “It’s a rich history that spans the globe, ultimately culminating in the fruit so many enjoy today.”
These four diploid species are native to Europe, Asia and North America, but the wild octoploids are almost exclusively distributed across the Americas. The results presented in the paper suggest a series of intermediate polyploids, tetraploid (four copies) and hexaploid (six copies) that formed in Asia, prior to the octoploid event that occurred in North America, involving the hexaploid and a diploid species endemic to Canada and the United States. This makes the strawberry relatively unique as one of only three high-value fruit crops native to the continent.
Breeders began propagating these octoploids around 300 years ago. Since then, they have been used around the world to further enhance variety development. However, Edger hypothesized that — as with several other polyploids — an unbalanced expression of traits contributed by each diploid parental species, called subgenome dominance, would likely also be present in the octoploid strawberry. He was right.
“We uncovered that one of the subgenomes (parental species) in the octoploid is largely controlling fruit quality and disease resistance traits,” Edger said. “Knowing this, as well having identified the genes controlling various target traits, will be helpful in guiding and accelerating future breeding efforts in this important fruit crop.”
The genomic discoveries provided by this study will advance the trait selection process, bringing about a more precise method of breeding for this important worldwide crop. The genome will enable studies that were previously unthinkable in strawberry, and will be a catalyst for tackling difficult breeding and genetics questions.
“Without the genome we were flying blind,” Knapp said. “I remember the first time I saw a visualization of the assembled genome, which went from a complex jumble of DNA molecules (170 billion nucleotides) to an organized and ordered string of 830 million base pairs. That was a special moment that changed everything for us in strawberry.”
Knapp said that, historically, scientists studying complex biological phenomena in strawberry have tended to focus on diploid relatives because of the complexity of the octoploid, even though genetic analyses in the octoploid are actually straightforward once one has a good road map.
“We have been on a crusade to shift the focus in the basic research community to the commercially important octoploid,” Knapp said. “The wild octoploid ancestors, together with cultivated strawberry, provide a wellspring of natural genetic diversity to support biological and agricultural research.”
Traditional breeding has been highly successful in strawberry, yielding outstanding modern cultivars that have been the catalyst for expanding production worldwide. As with other crops, many challenges remain that will require breeders to continually redesign cultivars and introduce genes from wild species and other exotic sources to meet new challenges. The genome is an essential vehicle for applying predictive, genome-informed approaches in strawberry breeding and cultivar development.
For the U.S., improved varieties could provide a boon to an already-thriving business. The U.S. is the global leader in strawberry production, a yield comprising roughly one-third of the world’s total. In 2016, the country produced more than 1.5 million tons.