Analysis of wild tomatoes elucidates genetic basis underlying fruit traits

September 28, 2020

Domestication and subsequent intensive breeding of tomato had a major impact on fruit ripening and the myriad metabolic processes accompanying it. In result, modern tomato cultivars exhibit a range of archetypal fruit characteristics, including e.g. texture, size, aroma, pigmentation and flavor. At the same time, continuous selection through breeding resulted in reduced genetic diversity and recurrent elimination of significant fruit qualities, such as e.g. robustness of plants in drought stress or resistance to various pathogens.

In this study, the scientists utilized advanced genetic resources, together with multimodal molecular and phenotype profiling, to perform an integrative QTL analysis in tomato fruit. The population of interest included 580 introgression lines developed in the lab of Prof. Dani Zamir from the Hebrew University of Jerusalem. Each of these lines carries a small fragment of wild tomato Solanum pennellii in the background of a modern tomato cultivar M82. The team of Prof. Asaph Aharoni from the Weizmann Institute of Science performed a multimodal profiling of fruits from the whole population, including RNA sequencing, mass spectrometry-based metabolomics and pathogen sensitivity assays at different developmental stages. The resulting massive data resource was used in a multi-level QTL analysis and allowed Dr. Jedrzej Jakub Szymanski, head of the research group "Networking and Modelling" at IPK and former researcher in Prof. Aharoni´s lab, to draw causal links between genetic sequence variation, quantitative changes in gene expression and metabolite levels, and changes of complex phenotypic traits.

From hundreds of identified interactions the team picked several interesting candidates. "We focused on the impact of S. pennellii genes on human nutrition-associated secondary (specialized) metabolites and fruit resistance to pathogens, two very contrasting biochemical traits in the wild and domesticated tomato species", says Dr. Szymanski. The research team identified and characterized an enzymatic step in the predicted pathway wherein α-tomatine, the fundamental anti-nutritional and defense alkaloid present in green tomato fruits, is converted to esculeosides and lycoperosides during fruit ripening. "This chemical shift is probably important for reducing the bitterness provided by α-tomatine and/or countering temporal needs for defensive fruit metabolites", says Dr. Szymanski. Furthermore, loci and genes associated with the accumulation of health-promoting flavonoids in the fruit skin tissue were delineated. Observed changes in gene expression and metabolism, e.g. accumulation of defense metabolites, also affected complex phenotypes, such as pathogen resistance. "In our study, we observed that increased resistance of fruits to a common fungal pathogen B. cinerea was reflected on multiple levels of cellular complexity - variation in gene sequence, gene expression, accumulation of specific metabolites. Networking these elements reveal mechanisms leading from changes on the molecular level to macroscopic effects relevant for plant survival and its commertial value", says Dr. Szymanski.

The large dataset generated in the study is a unique resource for the research community. "While we were able to characterize in depth only a few candidate genes and metabolites, the dataset can potentially be mined for tens, if not hundreds, more candidates and could be integrated with the wealth of published phenomics data available for the same introgression lines", says Dr. Szymanski.

Exploring the trajectory from wild to cultivated fruit is indispensable for a comprehensive understanding of fruit metabolism and the impact of human selection on both positive and negative fruit quality traits. "We anticipate that the genotype-phenotype associations inferred through this study will be a significant contribution to the current molecular breeding efforts to counter the recurrent elimination of key fruit quality traits such as flavor and pathogen resistance."
-end-


Leibniz Institute of Plant Genetics and Crop Plant Research

Related Science Articles from Brightsurf:

75 science societies urge the education department to base Title IX sexual harassment regulations on evidence and science
The American Educational Research Association (AERA) and the American Association for the Advancement of Science (AAAS) today led 75 scientific societies in submitting comments on the US Department of Education's proposed changes to Title IX regulations.

Science/Science Careers' survey ranks top biotech, biopharma, and pharma employers
The Science and Science Careers' 2018 annual Top Employers Survey polled employees in the biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers in these industries as well as their driving characteristics.

Science in the palm of your hand: How citizen science transforms passive learners
Citizen science projects can engage even children who previously were not interested in science.

Applied science may yield more translational research publications than basic science
While translational research can happen at any stage of the research process, a recent investigation of behavioral and social science research awards granted by the NIH between 2008 and 2014 revealed that applied science yielded a higher volume of translational research publications than basic science, according to a study published May 9, 2018 in the open-access journal PLOS ONE by Xueying Han from the Science and Technology Policy Institute, USA, and colleagues.

Prominent academics, including Salk's Thomas Albright, call for more science in forensic science
Six scientists who recently served on the National Commission on Forensic Science are calling on the scientific community at large to advocate for increased research and financial support of forensic science as well as the introduction of empirical testing requirements to ensure the validity of outcomes.

World Science Forum 2017 Jordan issues Science for Peace Declaration
On behalf of the coordinating organizations responsible for delivering the World Science Forum Jordan, the concluding Science for Peace Declaration issued at the Dead Sea represents a global call for action to science and society to build a future that promises greater equality, security and opportunity for all, and in which science plays an increasingly prominent role as an enabler of fair and sustainable development.

PETA science group promotes animal-free science at society of toxicology conference
The PETA International Science Consortium Ltd. is presenting two posters on animal-free methods for testing inhalation toxicity at the 56th annual Society of Toxicology (SOT) meeting March 12 to 16, 2017, in Baltimore, Maryland.

Citizen Science in the Digital Age: Rhetoric, Science and Public Engagement
James Wynn's timely investigation highlights scientific studies grounded in publicly gathered data and probes the rhetoric these studies employ.

Science/Science Careers' survey ranks top biotech, pharma, and biopharma employers
The Science and Science Careers' 2016 annual Top Employers Survey polled employees in the biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers in these industries as well as their driving characteristics.

Three natural science professors win TJ Park Science Fellowship
Professor Jung-Min Kee (Department of Chemistry, UNIST), Professor Kyudong Choi (Department of Mathematical Sciences, UNIST), and Professor Kwanpyo Kim (Department of Physics, UNIST) are the recipients of the Cheong-Am (TJ Park) Science Fellowship of the year 2016.

Read More: Science News and Science Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.