Selecting and Importing Carrot Roots for Breeding

Posted on Monday, 16 March 2020 under The Bauta Family Initiative on Canadian Seed Security

Chris Thoreau
March 2020

This March I joined USDA carrot breeder Dr. Phil Simon and his crew from University of Madison-Wisconsin in Southern California to dig and evaluate some 700 plots of carrot trials as part of his USDA-ARS carrot breeding program. This is the second time I have participated in these trials and it was another great learning experience.

While my first visit was purely a learning opportunity, this second visit was much more involved as I was selecting a collection of red carrot roots to import back into Canada for a breeding project here in BC with FarmFolk CityFolk and the Centre for Sustainable Food Systems at UBC Farm with support from Organic Seed Alliance.

Building on the work of the BC Seed Trials and Canadian Organic Variety Improvement project (CANOVI), these carrot roots will go to the FarmFolk CityFolk Education and Research Seed Farm for a new breeding project focused on red carrots. Simultaneously, seed from each of these varieties will be planted in trials at FFCF Seed Farm in Abbotsford, UBC Farm in Vancouver, as well as at Wisbey Veggies and Forstbauer Family Natural Food Farm – both in Chilliwack.

So these are the two topics of this post:

  1. Importing carrots into Canada
  2. Selecting carrots for breeding

Let’s start with the import process…

Part I – The Import Process

I started the import process in January by researching what I needed to know to get carrot roots from the United States into Canada. I used two main resources to do this:

  1. Canadian Food Inspection Agency (CFIA)
  2. United States Department of Agriculture (USDA)

The CFIA was my main source of information since the import of plant material into Canada has some restrictions. Even though the roots are leaving the US, this is not considered an export process. The distinction here is that it is more important for the importing country to protect itself from contaminated imports than it is for the exporting country to prevent contaminated exports, though both parties take responsibility in the process through the issuing of the phytosanitary certificate with guidance from the importing country.

The main CFIA document I referred to for carrot root import information was D-08-04: Plant Protection Import Requirements for Plants and Plant Parts for Planting which states in Section 4.1 Plants with roots, without soil, which states:

  • A Permit to Import is not required unless specified in directive D-94-14. In this case, the importer must obtain the Permit to Import prior to importation.
  • The USDA must issue a Phytosanitary Certificate, which must accompany the consignment. Additional declarations attesting to freedom from regulated pests, including soil-borne pests (see Section 3.9.2), may be required depending on the commodity and state of origin.

As a note, Directive D-94-14 is nowhere to be found.

So, at this point, I know I will need a USDA-issued Phytosanitary Certificate. In following up with the CFIA to confirm these details they further referred me to their Automated Import Reference System (AIRS). The AIRS system is a reference system for importers to verify the requirements they need when importing items into Canada. It is also the system that Canada Border Services Agency (CBSA) uses to verify import requirements. The system takes you step by step through import details to ensure you are properly informed. In my case, this is how it looked for carrot roots for planting:

  • HS Description: 060290

– 06 Live trees and other plants; bulbs, roots and the like; cut flowers and ornamental foliage
– 02 Other live plants (including their roots), cuttings and slips; mushroom spawn.
– 90 Other

  • OGD Extension: 002430

– 0024 Other rooted propagative material – greenhouse plants
– 30 Carrots (with tops only) – vegetable transplants (Daucus spp.)

  • Origin: UCA

– US United States
– UCA California

  • Destination: BC

– BC British Columbia

  • End Use: 05

– 05 Propagation (growing or sowing)

  • Miscellaneous: 034

– 034 Without soil, related matter or growing media

All of the information above has an effect on import requirements since different destinations, places of origin, and end uses will result in different import requirements.

In checking the AIRS system for carrot roots I confirmed the details from Directive 84-04, but also learned that carrots, coming from California, require the additional declaration:

The material was produced and prepared for export in accordance with the conditions of entry specified in Quarantine Directive 82-01 of February 1, 1982.”


The soil originated in an area in which, on the basis of official surveys, Meloidogyne chitwoodi does not occur.”

M. chitwoodi is the Columbia root-knot nematode which has a presence in both California and in BC and is a known carrot pest.

Once I had this information I got in touch with the USDA to find out what I needed to do in order to get a phytosanitary certificate issued. I found the USDA Animal and Plant Health Inspection Service website which states:

The United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine (USDA-APHIS-PPQ) provides phytosanitary certification of both U.S. and foreign-origin agricultural commodities. The export program does not require certification of any U.S. exports, but rather provides certification of commodities as a service to U.S. exporters.

I got in touch with the contact listed for Imperial County, where I would be importing the roots from and they connected me with the Imperial County Agricultural Commissioner, which confirmed with me they are the authority issuing the phytosanitary certificate and would be available to do an inspection of the roots when I was ready. I informed them of my travel dates and kept them updated with my plans to ensure there were no last-minute issues regarding root inspection.

Upon this confirmation I also sent the Agricultural Commissioner the details of my AIRS inquiry to ensure the conditions could be met; in other words – confirming there was no presence of M. chitwoodi in Imperial county. I sent a copy of my original AIRS report as well as highlighting the specific “Additional Declaration” in my emails – which I did twice. The office did confirm by email that everything was OK with the conditions on the certificate.

However, that was not quite the case. Leading up to the root inspection everything was fairly smooth until I took the roots for inspection and was shown the draft phyto certificate they made up – which did not contain the required Additional Declaration, the need for which I had confirmed twice via email. The challenge here was that there was no official record of M. chitwoodi in the area as it was not a pest in the county.

Here, I will make a long story short as we spent a few hours trying to determine whether the carrots qualified for the phyto based on the required declaration I referred to above:

The material was produced and prepared for export in accordance with the conditions of entry specified in Quarantine Directive 82-01 of February 1, 1982.”


The soil originated in an area in which, on the basis of official surveys, Meloidogyne chitwoodi does not occur.”

In this case, because there were no official surveys to validate the second statement we had to find conditions to meet the conditions of the first statement. In reviewing Directive 82-01, the following statement validated the issuing of the certificate:

2. A) b) All other areas in California are considered to be outside of both the designated regulated and quarantine areas and regulated commodities originating from this area are exempt from these import requirements.

Had this statement not been there then I would not have been able to get the certificate.

So, after all this and one-day delay, I was issued the certificate with the required declaration and was ready to bring the carrot roots home!

The main issue here that complicated things was that I had been poorly informed by my contact at the Agricultural Commissioner’s Office who did not carry out their due diligence in ensuring that the conditions in the AIRS report were able to be met. Had there been any concern I would simply have contacted the USDA site where the carrots were growing and had them do a field test for M. chitwoodi to validate the field being pest free.

So the lesson here is in taking as many steps as possible to ensure the conditions of the phyto certificate can be met and to get written confirmation where possible. To have done all this work to prepare and select the carrots then not be able to get the certificate for import would have been very disappointing.

Once the certificate is issued you are ready for import. The certificate must accompany the roots, whether you are importing them yourself or sending them via courier. I would further recommend including the CFIA AIRS report with the certificate as well – this simplified things for me at the airport back in Vancouver (which was a bit distracted by COVID-19 when I arrived!).

To ship the carrots I bought a cooler and some ice packs to keep them cool during shipping, which I did myself as I was flying back to Vancouver and the cooler became a “checked bag”. Ironically, the cooler did not make it onto my flight so the carrots did not arrive in Vancouver until a day after I did! But the cooler did its job and kept the carrots cold and the carrots made it back early the next day.

The roots will now stay in cold storage for about a month to ensure they are properly vernalized to trigger bolting when they are planted.

So in summary, here is the import process:

  1. Use the CFIA AIRS system to determine import requirements, including the issuing of an import permit (not required in this case), a phytosanitary certificate, and any additional declarations that may be required.
  2. Research any additional declarations to ensure they are not prohibitive and document your research
  3. Contact the USDA to find a local office to inform them of your import needs and to set up an appointment to conduct a root inspection and issue the phytosanitary certificate.
    – I set up my appointment to be at the USDA site where I harvested the carrots from, but I ended up taking the roots to the office for inspection which was probably the easier choice for a small volume of roots
  4. Share with the inspecting office the additional declarations, if any, and get written, documented verification that the declarations can be met and make other arrangements for testing of this if required in lieu of any existing verification
  5. Take roots for inspection and secure phytosanitary certificate
  6. Pack roots in cooler with ice packs to keep them cool and ship them off! Be sure the certificate is with the roots when you arrive back in Canada.

Part II – Selecting Roots

So, now the question is – what are these roots we are bringing back to Canada and why are we going through so much trouble to import them? Let’s cover that next…

Introduction and Overview

Many growers, both organic and conventional, have an interest in growing red carrots for market but are constrained by three main factors:

  1. Bolting – red carrots tend to bolt (go to seed) quickly, making it hard to time harvests for fresh roots
  2. Flavour – red carrots are notoriously bland
  3. Nematode susceptibility – red carrots are generally susceptible to nematode damage

Phil Simon has been making crosses between red carrots and orange carrots to improve flavour while also selecting plants that are later bolters. With this work he has been collaborating with Organic Seed Alliance through the Carrot Improvement for Organic Agriculture (CIOA) project which is doing similar breeding for organic systems. As of yet, not as much work is being done on nematode resistance.

Organic Seed Alliance currently has two advanced lines that have improved resistance to bolting and fairly good flavour and are almost ready for release as finished varieties. Phil had many other later-generation red crosses showing promise. It is from these two pools of roots planted in Southern California that I was able to select from to bring back to Canada for breeding. With all of these varieties being quite similar we would be growing them as mixed populations in two separate cages to create two new unique populations that we can select towards creating a new variety. How we do this is still to be determined.

With this in mind, what I want to share here is how I selected the roots from each of the populations to bring back to Canada.

The Populations

There were two types of trial plots at the trial location:

  1. One-meter plots of crosses to be selected for further breeding
  2. Longer plots with larger populations of later generations meant for selection for bulking up seed production

I was able to select from both trials for roots to bring back to Canada. For the longer plots I made my selection from about 200 roots and narrowed them down to 40-60, depending on the population and what I liked. From the smaller plots took just three to five roots remaining after Phil had done his selections.

Step 1: Choosing characteristics

These were the four main characteristics I was looking for to determine which populations I would select roots from:

  1. Bolting resistance – selected from populations with low to no bolting in the field
  2. Colour – looking for a deep red colour
  3. Shape – looking for a slight taper with a blunt tip (nantes-type)
  4. Red core – avoiding any coloured cores

While the above characteristics were the main things I was selecting for, I also made selections based on the following:

  1. Single crowns
  2. Well-shaped crowns
  3. Colour and texture – no green or “rough” crowns
  4. Smooth skin/no lenticels
  5. No pest damage
  6. No funny shapes!
  7. No root hairs
Here is the starting population of carrot roots before selection

Here is the starting population of carrot roots before selection

Step 2: Selection for Crowns, Colour, and Shape

I started selection by removing anything with split crowns and any odd colours. In most cases this was not common, which is why I started with this. Then I moved onto removing roots with odd shapes, which was also a small number. You can see the variation in the original roots in the image here.

Step 3: Selecting for Blunt Tips & Smoothness

Selecting for a blunt tip was a primary selection criteria and here I removed anything that was too pointy or had a “whip” or “rat tail” at the root tip. This made a huge dent in the number of roots remaining.

I then removed roots with rough skins and excessive root hairs while simultaneously looking for traits I had already selected against and may have missed.

Here are the roots after selecting for bluntness and smoothness

Here are the roots after selecting for bluntness and smoothness

Step 4: Selecting for Ideal Crowns

From the remaining roots I then turned to the crowns to look more specifically for crowns that were not pinched or had a divot where moisture could gather. I also removed any crowns where the tops were too narrow or too wide. I simultaneously removed any with green shoulders or any roughness on the shoulders.

I then did another selection for bluntness again, being more picky this second time around.

Step 5: Red Cores

Knowing that all the roots had the blunt tips I was looking for, I then cut off the tips to look at the core. Here I was looking for solid red cores and selecting against white or yellow cores – for no other reason than consistency and because this was the dominant core trait.

Here are the roots after selecting for bluntness and smoothness

Here are the roots after selecting for bluntness and smoothness

Step 6: One Last Selection

After checking the cores I took one last look at crowns and smoothness in a final selection. Here is what one of the end populations looked like:

Step 7: Washing Roots

Because I was bringing the roots across the border I needed to wash them – a step one would usually avoid when storing carrots for seed production. I tried to do so quickly and gently to avoid damaging them and reducing their storage life

Step 8: Storage, Inspection, and Shipping

Once I finished with selections I placed the carrots in a labeled paper bag which then went into a plastic bag and into the cooler to prepare them for inspection and shipping.

Step 9, Pending: Tasting

While I could have done a tasting of roots then as well, I held off and we can do a tasting here in Canada before planting. This will be the last selection, removing anything with an unpleasant flavour.

What Happens Next?

I tried to be quite particular in my selections and hope I have returned to Canada with a good selection of roots for breeding. Three of the populations have about 40 to 50 roots each while some selections have just three to five roots as they came from smaller populations – and thus are not “ideal” selections, as you can see from the images.

The carrots are now in a cooler, vernalizing for a month, to ready them for planting to go to seed. Over the next few weeks we will decide how to mix these roots to create to new populations which will lead to two new varieties.

The roots will be planted into different mesh tents which isolates them from pollinators when they go to see and will allow us to create two distinct populations.

Complementary Trials

With the selected roots going to seed, we will also sow seed from each of the selections to observe how they perform in the Pacific Northwest – which has very different growing conditions than Southern California. If there is sufficient seed we will do early and late plantings to see how they perform at different times of the year and how resistant they are to bolting.

Ideally, we will do trials at the FFCF Seed Farm, UBC Farm, and up to two other farms in the region.

So this is the first of what may be many steps of breeding red carrots for organic agriculture in BC. We will continue to engage with Organic Seed Alliance and Phil Simon throughout the process to help keep us on track. Watch fro updates and field days in the coming months.