Genome Project Update: December 2018

December 20, 2018, Novogene, the lab sequencing the RNA (gene expression) dahlia leaf material collected in summer 2018, has finished their quality checking analysis.  We now have millions of data points from each of 15 species dahlias (including 3 different sources (seed collected in different Mexican states) of D. coccinea and 2 sources of D. sorensenii, the proposed parents of modern cultivars).  We also have samples from 5 types of cultivars:  pairs of samples from two different named cultivars with the same floral form.  From previous work we have an RNA analysis of one modern day, single dahlia for an 11th comparison. Currently, postdoc Alex Harkness who is an expert in phylogenetic reconstruction and analysis of evolutionary plant history will work (pro bono) on the new data with programs and tests to address the origin of the modern dahlia.  Question 1:  How close are modern cultivars to each other; if very close, then all modern dahlias have the same wild species parent(s)?  Question 2:  Do modern dahlias share significant sequence similarity to D. coccinea, or D. sorensenii, or both?   Or, perhaps we will be surprised and identify a different wild species as the likely progenitor or hypothesize a “missing” species as a more likely parent. These analyses should either actually answer our questions, or point us to which additional species we need to collect. 
If we haven’t yet found the parents of modern day dahlias, Dr. Walbot would need to make more trips to Mexico to collect more species dahlia seed from natural populations (not botanical gardens where cross-hybridization is common).  In discussing this with Stanford University Prof. Rodolfo Dirzo, who helped collect in both Morelos and Queretáro, one approach would be to offer a stipend (~ $1000) to the top botany group in Mexican states known to have “missing link” species that we want to analyze.  The Mexico botanists would spend mid-September to mid-October finding, tagging, and acquiring GPS co-ordinates for field specimens of these species; this bio-prospecting is necessary because historic herbarium specimens indicate approximate locations (such as 3 km on Calle XYZ from town ABC) rather than GPS co-ordinates of the plant.  Then in late October – early November, Prof. Dirzo and Walbot could fly to Mexican cities to collect seeds using the GPS coordinates and the help of the Mexican collaborators.  The clade (group of species closest to modern dahlia) has about 14 species altogether, and we have data on 7 of them.   
There is a family tree of species dahlias that was put together 20 years ago based on hundreds of characters. With the new information from Novogene, Alex Harkness will construct a more accurate “tree” of the 15 species sampled.  Because of new RNA sequencing equipment and a smaller price tag to do the sequencing work, we are able to do a more accurate family tree with millions of characters for each species.   There are sufficient data to address how closely related modern cultivars are to each other and whether they express the same genes in immature leaves.  We will be able to see if their genetic makeup has change dramatically or not so much over the last hundreds of years. 
In short here is what we are trying to do:    
  1. Find the parents of modern day dahlias. That has not been done yet by scientists! 
  2. Make a more accurate “Dahlia Family Tree” or phylogeny. This would be new as an accurate “tree” based on many characters does not exist for the group.
  3. Compare species dahlias with modern day dahlias to see how diverse they are or how much they have changed over the last 300 years. This has never been done. For those interested in crossing species dahlias with modern dahlias, knowledge of where “genetic diversity” occurs can guide which types to cross.   
  4. Once the parents or parent of the modern day dahlia is found, a DNA high quality assembled genome of one of the parents will be made at a cost of $30,000.  This high quality sequence of the dahlia has never been done before. Information from the DNA sequencing will stimulate scientific research on the dahlia and make it possible for the dahlia to be included in scientific experiments done on commercial flower crops like sunflowers, a close relative. 
  5. From sequenced examples of 11 modern dahlias, we can see how “diverse” the genetic material is in breeding types we analyzed:  formal decoratives, informal decoratives, balls, anemones and singles.  Do some floral forms have more promise in developing additional dahlia cultivars? 
  6. ADS can evaluate whether sequencing additional floral forms is warranted.  The cost would be about $300 per sample x 2 cultivars of each floral form = $600 for a floral form.  Including two floral forms provides a test of whether each floral form is really a “clear type” based on DNA evidence, much like a paternity test for human family trees.  
Dr. Walbot, as well as Tim Culbertson and Prof. Rodolfo Dirzo are very grateful for travel support from ADS to participate in the adventure of collecting dahlia seed in the native habitats of Mexico and are all thrilled to be part of this project.