Thousands of years ago, people in South America began domesticating Solanum pimpinellifolium, a weedy plant with small, intensely flavored fruit. Over time, the plant evolved into S. lycopersicum - the modern cultivated tomato.
Although today's tomatoes are larger and easier to farm compared with their wild ancestor, they also are less resistant to disease and environmental stresses like drought and salty soil.
Researchers from Boyce Thompson Institute, led byZhangjun Fei, created a high-quality reference genome for S. pimpinellifolium and discovered sections of the genome that underlie fruit flavor, size and ripening, stress tolerance and disease resistance.The results were publishedinNature Communicationson November 16.
"This reference genome will allow researchers and plant breeders to improve traits like fruit quality and stress tolerance in the tomato," said Fei, "for example, by helping them discover new genes in the modern tomato as well as by reintroducing genes from S. pimpinellifolium that were lost over time as S. lycopersicum was domesticated."
Fei is a BTI faculty member and co-corresponding author on the paper, as well as an adjunct professor in Cornell University's School of Integrative Plant Science (SIPS).
Although other groups had previously sequenced S. pimpinellifolium, Fei said this reference genome is more complete and accurate, thanks in part to cutting-edge sequencing technologies that are able to read very long pieces of DNA.
"Older sequencing technologies that read short pieces of DNA can identify mutations at the single-base level," said Shan Wu, a postdoctoral scientist in Fei's lab and co-corresponding author on the paper. "But they aren't good at finding structural variants, like insertions, deletions, inversions or duplications of large chunks of DNA."
"Many known traits of the tomato are caused by structural variants, so that is why we focused on them," Fei said. "Structural variants also are understudied because they are more difficult to identify."
Fei's group compared their S. pimpinellifolium reference genome to that of the cultivated tomato, called Heinz 1706, and found more than 92,000 structural variants.
The researchers then combed thetomato pan-genome, a database with the genomes of more than 725 cultivated and closely related wild tomatoes, and discovered structural variants related to many important traits. For example, the modern cultivated tomato has some genomic deletions that reduce their levels of lycopene, a red pigment with nutritional value, and an insertion that reduces their sucrose content.
Jim Giovannoni, BTI faculty member and co-author of the study, notes that many consumers are disappointed in the quality and flavor of modern production tomatoes because past breeding efforts ignored those traits in favor of performance and yield.
"Identification of the additional genetic diversity captured in the S. pimpinellifolium genome provides breeders with opportunities to bring some of these important features back to store-bought tomatoes," said Giovannoni, who is also an adjunct professor in SIPS and a scientist with the U.S. Department of Agriculture's Agricultural Research Service.
The researchers found many other structural variants that could be of interest to plant breeders, including variants in numerous disease-resistance genes and in genes involved in fruit size, ripening, hormonal regulation, metabolism, and the development of flowers, seeds and leaves.
The group also found structural variants associated with regulating the expression of genes involved in the biosynthesis of lipids in fruit skin, which could help improve the fruit's post-harvest performance.
"So much genetic diversity was lost during tomato domestication," Fei said. "These data could help bring some of that diversity back and result in tomatoes that taste better, are more nutritious and more resilient."
Reference: Wang X, Gao L, Jiao C, et al. Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. Nature Communications. 2020;11(1):5817. doi:10.1038/s41467-020-19682-0.
This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.
Read the original post:
Bringing Back Tomato's Genetic Diversity That Was Lost in Domestication - Technology Networks
- Age-related genetic changes in the blood associated with poor cancer prognosis - Medical Xpress - April 24th, 2025
- Parts of our DNA may evolve much faster than previously thought - The University of Utah - April 24th, 2025
- It runs in the family: the importance of genetics in pneumothorax - The BMJ - April 24th, 2025
- Inferring past demography and genetic adaptation in Spain using the GCAT cohort - Nature - April 24th, 2025
- Answers to a 160-year-old riddle about the genetics of Mendels pea traits - Nature - April 24th, 2025
- Towards a genetic obesity risk score in a single-center study of children and adolescents with obesity - Nature - April 24th, 2025
- Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa - Nature - April 24th, 2025
- Study highlights critical diversity gap in psychiatric genomics research - Medical Xpress - April 24th, 2025
- Daily briefing: Potato pangenome reveals the complex genetics of the humble spud - Nature - April 24th, 2025
- Genetic diversity and adaptability of native sheep breeds from different climatic zones - Nature - April 24th, 2025
- Ginkgo Automation Partners with Aura Genetics to Accelerate Direct-to-Consumer Testing and Innovation - PR Newswire - April 24th, 2025
- Why Sarepta Therapeutics And Other Genetics Stocks Just Got A Sizable Boost - Investor's Business Daily - April 24th, 2025
- Why White Blood Cells were used to study genetic past and future of Indians - India Today - April 24th, 2025
- Association between plausible genetic factors and weight loss from GLP1-RA and bariatric surgery - Nature - April 24th, 2025
- Recent habitat modification of a tropical dry forest hotspot drives population genetic divergence in the Mexican leaf frog: a landscape genetics... - April 24th, 2025
- Barney's Farm Partners with Backpackboyz on Groundbreaking Cannabis Genetics Project - Ganjapreneur - Ganjapreneur - April 24th, 2025
- U.S. Preimplantation Genetic Testing Market Witness the Highest Growth Globally in Coming Years 2025-2034 - openPR.com - April 24th, 2025
- Exploring the implications of case selection methods for psychiatric molecular genetic studies - Nature - April 24th, 2025
- Genetic susceptibility to schizophrenia through neuroinflammatory pathways associated with retinal thinness - Nature - April 24th, 2025
- Who Were the Carthaginians? Ancient DNA Study Reveals a Stunning Answer - Haaretz - April 24th, 2025
- Genetics - National Geographic Society - March 28th, 2025
- Genetics: Introduction, law of inheritance and Sex Determination - BYJU'S - March 28th, 2025
- Genetics, ecology and evolution of phage satellites - Nature.com - March 28th, 2025
- As a geneticist, I will not mourn 23andMe and its jumble of useless health information | Adam Rutherford - The Guardian - March 28th, 2025
- Rare loss-of-function variants in HECTD2 and AKAP11 confer risk of bipolar disorder - Nature.com - March 28th, 2025
- With 23andMe filing for bankruptcy, what happens to consumers genetic data? - The Conversation Indonesia - March 28th, 2025
- A genetic tree as a movie: Moving beyond the still portrait of ancestry - Phys.org - March 28th, 2025
- Genetic mutations linked to Marek's disease in chickens identified - Phys.org - March 28th, 2025
- 23andMe is looking to sell customers genetic data. Heres how to delete it - CNN - March 28th, 2025
- Horses Pulled Off a Genetic Trick Only Viruses Were Thought to Use - SciTechDaily - March 28th, 2025
- CONSUMER ALERT: Warning 23AndMe Customers That Their Private Genetic Data May Be at Risk - Office of the Attorney General for the District of Columbia - March 28th, 2025
- A new study reveals the genetic change that made horses so athletic - KUOW News and Information - March 28th, 2025
- "Mystery ancestors" gave humans 20% of our current DNA, but who were they? - Earth.com - March 28th, 2025
- Correcting the Mutation Behind a Genetic Eye Disease - The Scientist - March 28th, 2025
- Your DNA is safe here: The AncestryDNA Genetic Test Kit is only $39 now - New York Post - March 28th, 2025
- 23andMe Is Bankrupt. Heres What You Need to Know About Your Genetic Data. - The Wall Street Journal - March 28th, 2025
- Commentary: 23andMe files for bankruptcy, putting its hoard of personal health information at risk - Los Angeles Times - March 28th, 2025
- DNA Microscopy Creates 3D Maps of Life From the Inside Out - SciTechDaily - March 28th, 2025
- Eugenics Must Be Included in Genetics Curriculum: Prof - Mirage News - March 28th, 2025
- 11-minute video on human genetics can make people more accepting of others, reveals new study - Hindustan Times - February 24th, 2025
- Advancing Cancer Genetic Testing to Improve Prevention and Patient Treatment - The Scientist - February 24th, 2025
- Environmental factors, lifestyle choices have greater impact on health than genes, study finds - ABC News - February 24th, 2025
- Study finds lifestyle, environment have greater impact on lifespan than genetics - CBS Boston - February 24th, 2025
- Safeguard repressor locks hepatocyte identity and blocks liver cancer - Nature.com - February 24th, 2025
- Mass spectrometry-based mapping of plasma protein QTLs in children and adolescents - Nature.com - February 24th, 2025
- The Avestagenome Project and TIGS Sign Strategic Alliance to Advance Research in Rare Genetic Disorders - The Tribune India - February 24th, 2025
- Researchers make breakthrough discovery after studying genetics of trees: 'There is a need for proactive conservation' - MSN - February 24th, 2025
- iPSCs and iPSC-derived cells as a model of human genetic and epigenetic variation - Nature.com - February 24th, 2025
- Beyond genetics: The biggest factors that influence health and aging - Earth.com - February 24th, 2025
- Genetic diversity and dietary adaptations of the Central Plains Han Chinese population in East Asia - Nature.com - February 24th, 2025
- How a uniquely human genetic tweak changed the voices of mice - NPR - February 24th, 2025
- Genetic evidence identifies a causal relationship between EBV infection and multiple myeloma risk - Nature.com - February 24th, 2025
- Genetic markers of early response to lurasidone in acute schizophrenia - Nature.com - February 24th, 2025
- Bupa to offer first genetic test for disease prediction in UK - The Times - February 24th, 2025
- Advancing Therapeutic Knowledge of Genetic Influence in ALS: Matthew B. Harms, MD - Neurology Live - February 24th, 2025
- Association of dietary carbohydrate ratio, caloric restriction, and genetic factors with breast cancer risk in a cohort study - Nature.com - February 24th, 2025
- Evaluation of polygenic scores for hypertrophic cardiomyopathy in the general population and across clinical settings - Nature.com - February 24th, 2025
- Familiar autism-linked genes emerge from first analysis of Latin American cohort - The Transmitter: Neuroscience News and Perspectives - February 24th, 2025
- Almost 90% of people would agree to genetic testing to tailor medication use, survey finds - Medical Xpress - February 24th, 2025
- Largest Genetic Study of Bipolar Disorder Identifies 298 Regions of the Genome That Increase Risk for the Condition - Mount Sinai - January 27th, 2025
- Study Sheds Light On The Origin Of Earth Lifes Genetic Code - Astrobiology News - January 27th, 2025
- Largest study on the genetics of bipolar disorder to date gives new insights into the underlying biology - Medical Xpress - January 27th, 2025
- Genetic Swiss Army Knife: New Tool For Gene Editing And Therapy - Forbes - January 27th, 2025
- Uhm Ji-won says the power of genetics is undeniable with Hyun Bin and Son Ye-jin's son - - January 27th, 2025
- Integrative proteogenomic analysis identifies COL6A3-derived endotrophin as a mediator of the effect of obesity on coronary artery disease -... - January 27th, 2025
- Genetic analysis reveals the genetic diversity and zoonotic potential of Streptococcus dysgalactiae isolates from sheep - Nature.com - January 27th, 2025
- Eight psychiatric disorders share the same genetic causes, study says - Medical Xpress - January 27th, 2025
- Exploring genetic associations and drug targets for mitochondrial proteins and schizophrenia risk - Nature.com - January 27th, 2025
- Predictive Genetic Testing and Consumer Genomics Market - GlobeNewswire - January 27th, 2025
- Evolution without sex: How mites have survived for millions of years - EurekAlert - January 27th, 2025
- Our Understanding of Rules that Produce Lifes Genetic Code May Require a Revision - DISCOVER Magazine - January 27th, 2025
- Personalized therapy for rare genetic diseases: Patient-derived organoids offer new hope - Medical Xpress - January 27th, 2025
- The One Thing That's More Important for Longevity Than Your Genes - Parade Magazine - January 27th, 2025
- Complete recombination map of the human genome created - Medical Xpress - January 27th, 2025
- Evidence of genetic determination of annual movement strategies in medium-sized raptors - Nature.com - January 27th, 2025
- Genetic study of Alaska red king crabs suggests species is more diverse and resilient to climate change - Global Seafood Alliance - January 27th, 2025
- Smartwatches reveal insights into psychiatric illnesses and genetic links - Medical Xpress - January 27th, 2025
- Unlocking the Blueprint of Human Life With a Revolutionary DNA Map - SciTechDaily - January 27th, 2025
- Largest Genetic Study of Bipolar Disorder Identifies Nearly 300 Risk-Associated Genome Regions - Inside Precision Medicine - January 27th, 2025
- Genetic Discrimination Is Coming for Us All - The Atlantic - November 16th, 2024