Breeding Workshop: trials, selections, breeding methods

Variety Trials: breeding to see what works (and what doesn't)

Jim Myers extolled the benefits of on-farm trials in his pre-conference workshop. It turns out that with participatory plant breeding, a cooperative arrangement that appeals to my grassroots heart, the variety trial is central to understanding and developing a new crop for a particular area. Myers held up a copy of an old AFES variety trial publication as an example of the kind of information breeders need to know and develop. He explained that it was important for:

• getting to know the crop
• expanding market potential, attracting new customers
• addressing crop stresses
• identifying organic info
• on-farm variety trials for vegetables, herbs, etc. (Here Myers talked about a publication from the Organic Seed Alliance that he authored about creating on-farm experimental designs for useful variety trials. The OSA has many helpful publications on everything from policy to seed production, worksheets and webinars.)

There are two basic trial methods, the observation trial and the replicated trial.

Observation trials are okay for evaluating disease resistance or discrete traits (color growth, habit, fruit size and shape, earliness), productivity, and adaptation to the locale. An example might be planting one-row plots of 10-30 feet. Observation trials are repeated over years in the same place.

Replication trials remove variation casused by differences in the local environment & provide repeated measures. They require randomization, such as in the variety's placement within the plot.

Siting a trial: get as uniform a section as possible. Consider soils, wind direction, even elevation, shade, moisture/wet or dry spots.

Traits to evaluate depend upon intended use and kind of crop: processing, fresh market, home garden/

On-farm trials in their simplest form: plant several varieties side by side and keep notes. This requires planning!

On-farm trials II:
Arrange among a group of farmers to grow an extended set of varieties, each grower grows a set on their farm. The advantage here is that a broader set can be looked, but it requires not only more planning but also coordination, and it should include a common variety to serve as a yardstick. Varietal performance may be affected by differences in location and cultural practices, too.

NOVIC (or, see the Northern Organic Vegetable Improvement Collaborative)

Mother Daughter Experimental Design: this is a statistical plot design that maximizes the amount of information obtained from diverse environments.

mother site: complete randomized block design with at least three replications
daughter sites: single replicates on at least three collaborating farms

Where to find the genetic variation?

From commercial sources:

• seed catalogs
• Native Seed Search
• Seed Savers Exchange

Exchange with other growers:

• seed swaps
• community seed banks/libraries/sanctuaries

USDA-NPGS (GRIN):

• Plant introduction collection (not a catalog: up to you to maintain seed or accession acquired)
• NSL # is storage of last resort, very hard to get
• PVP; has to be deposited in GRIN, but not available until patent runs out
• Tomato Genetic Resource Collection (genetic stocks housed at UC Davis, regular tomatoes housed at Geneva, New York)

Methods of recombination:

• natural crossing
• artificial 
• selection methods: mass selection, half-sib selection, bulk breeding, pedigree selection, single-seed descent, backcross breeding

Myers went into detail about each of these, but in particular the methods of selection. The technical aspects of the workshop were impressive and I will leave them aside, as the detail was considerable, but for those who are interested in pursuing breeding vegetable varieties, he recommended a few books, among them:

Breed Your Own Vegetable Varieties: The Gardener's Guide to Plant Breeding and Seed Saving, by Carol Deppe.

The Organic Seed Grower:  A Farmer's Guide to Vegetable Seed Production, by John Navazio.

There is also a book he co-edited but did not mention, Organic Crop Breeding.

Conference Workshop: On tomatoes and breeding lines: purple, yellow, rose

Jim Myers has worked on several species and varieties, but lately has caused a stir in the gardening world for his work with the Indigo Rose purple tomato, released by Oregon State University in 2012. To tomato lovers like me, this is pretty exciting, as it represents a new range of color and antioxidants available in these delicious fruit. But Myers was here to tell us about breeding vegetables in general. (Tomatoes, one of the most popular garden plants, are largely self-pollinating.)

Managing & selecting self-pollinated crops:

• one individual can represent variety, but more than one is better
• roguing and selection
• isolation distances

Maintaining stock seed:

• take 50-100 single plant selections from a finished variety
• grow as progeny rows, using say, 50 seeds from your plant selection
• inspect each plant for deviations, rogue off-type plants (roguing means weeding the rogues, the plants that don't conform to the type you are looking for)
• eliminate progeny rows with high frequency of off-types
• harvest by progeny row
• composite seed (mixed-up seed) from progeny rows to make up foundation seed
• grow every year or when regeneration of variety required

Roguing and selection

• source of off-types
• seed mixes
• outcrossing
• spontaneous mutation (can come off the same plant)

Examples of off-types

• ovals and strings in beans or peas
• plant / fruit / flower colors that don't match the variety
• growth habit
• pod fiber
• sterile off-types
• disease resistance (could be a good thing! or the off-type could show a lack of disease or pest resistance, and so not be so good)

Isolation distances

• depends on geography barriers, pollinators, prevailing winds
• can isolate in time as well as space
• no isolation needed between beans and peas (10-50 ft)
• isolation may be needed for: endive, escarole, lettuce; tomato and eggplant (10-50 ft)
• isolation required: peppers (75-100ft)

Myers also discussed the requirements for cross-pollinated crops and how they differ from self-pollinated crops. Cross-pollinators usually produce many small seeds, while self-pollinators usually produce a smaller amount of very large seeds (although this isn't a hard and fast rule). 

Managing & selecting cross-pollinated crops

• many individuals to prevent inbreeding
• maintenance
• isolation distances

maintaining stock seed:

• keep population sizes large: below 30-50 plants inbreeding depression will occur (plants will become weakened due to lack of sufficient genetic variety)
• grow variety in extreme isolation (caged production ensures isolation where land is limited)
• continuous mass selection (trimming extremes in variation)

Isolation distances:

• depends on geography barriers, pollinators, prevailing winds
• is the crop insect or wind pollinated?
• can isolate in time as well space (two weeks is offten enough time)
• Cole crops, mustard greens, radish, kale, turnips, cucurbits, scarlet runner beans, onions, carrots, celery, chicory: .5-2 mi
• sweet corn: 66-1,320 ft
• table beet & chard: 1-2- mi (same color) 1.5-3 if different color, 3-5 mile if different types
• spinach .5-3 miles

Unripe Indigo Rose tomato, an open-pollinated variety incorporating anthocyanins in the skin of its ripe fruit and released by Oregon State University. For more on the variety, see OSU's FAQ page. This and other, similar tomatoes are now available from many seed companies.

Tomatoes

Tomatoes have three growth habits, controlled by a single gene: determinate, indeterminate, and semi-determinate. For example, Micro Tom is a tiny variety about 8" tall developed using regular breeding methods, which grows no taller. This is a determinate variety. An indeterminate is the norm for tomatoes, and is the vining ever-growing habit that most tomatoes will exhibit. A semi-determinate will fall somewhere in between. One attendee showed quite a bit of interest in the idea of breeding a northern-adapted variety from a small tomato such as Micro Tom.

Kurt Wold, another of the attendees at the conference and owner of Pingo Farm and Zone 1 Grown seed company, has many Russian varieties. He suggested that these cold-weather, short-season, early tomatoes make a good place from which to start breeding for Alaska's needs. He also has a small determinate variety, which would be better to start from than Micro Tom, he said, as it is already adapted to a northern climate. Myers agreed: starting with a variety that already has some of the characteristics you want will save a lot of time.

Cooperative breeding projects

In concluding his workshop, Myers asked his audience if there were any cooperative breeding projects in which people might be interested in participating. The local turnip breeding project already has a lot of adherents, and several more signed up during the conference, but others expressed interest in tomatoes, sweet or flour corn, and fava beans.

CES will set up a listserve to notify members about participatory plant breeding efforts/inquiries. For more information, contact Steve Seefeldt, CES agriculture agent for the Fairbanks area. (474-2423)

At the 2014 Sustainable Agriculture Conference: Plant Breeding Workshop

This year's SARE conference, officially the 10th annual Alaska Sustainable Agriculture Conference, hosted by CES, is being held at the Wedgewood Visitor's Center in Fairbanks. The conferences start with a pre-conference workshop day, usually one full-day workshop and one or two half-day workshops. This year's workshops included one on plant breeding and one on record keeping and taxes for agricultural businesses.

I'm at the second half of the preconference workshop on participatory plant breeding, taught by Jim Myers of Oregon State University. We've been covering plant genetics and the difference between inbreeders (selfers) and outbreeders (crossers). It's a bit of an intense short course! I was taking notes earlier for this workshop, but lost them all on the laptop computer when I shut down for lunch. Lunch was pretty good, especially the potato chowder made from local potatoes! I went back for three helpings. (Several businesses contributed locally grown food to the lunch spread, including Basically Basil, Johnson's Family Farms, and several others. Unfortunately, I don't have the list. I'll post the company names here as I find out.)

Fortunately, Myers gave us all a CD with the full notes from his Horticulture 433 class, which is what he condensed part of his workshop from. It describes various systems of classification, from frost or cold tolerance, optimum temperature range, parts used for food, cultural groups, and botanical classification. There's 187 pages' worth of information on specific vegetables. It makes me want to cackle aloud.

Okay, so back to the notes I took from the workshop.

Myers gave us a short overview of the history of genetics and breeding in general, and how Gregor Mendel and his famous pea experiments were rediscovered in the early 1900s. We reviewed dominant and recessive genes, homozygosity and heterozygosity, and terms like allele and locus. Quite intense, as I said, and I won't go into the full details here (I can't remember them all, for one thing), but I'll explain a few things we went over.

In genetics, plants can be divided into those that have evolved such that they require no or very few crossing with other plants to maintain fertility and vigor (inbreeders or self-breeders, selfers for short), and those that do require it (out breeders or out crossers).

Inbreeders include:

• tomatoes
• eggplants
• most peppers
• beans (but not Scarlet Runner beans) (Fava beans are in between an inbreeder and an outbreeder, so one can use a small stock but not as small as true inbreeders.)
• peas 
• lettuces

Selfing a plant that is an F1 hybrid is a way to stabilize a variety for release. "F1" means the first generation between the cross between two distinct parents. Your hybrid starts out completely heterozygous (mixed genes of all sorts of traits). To make the plant breed true, or stabilize, breeders typically self 5 to 6 generations.

Nightshade family flowers in general have a higher percent of outcrossing, but still maintain selfing. Tomatoes may vary: some tomatoes have a style that sticks out beyond the flower (wild types), which will lend them to outcrossing.

Outcrossers include:

• mustards & brassicas, arugula
• melons & cucumbers, curcubits
• mustards have a sporophytic incompatibility: chemical self-pollination prevention
• corn (each seed has an individual silk down which pollen may travel)
• artichokes, daisies, sunflowers
• carrots, Queen Anne's Lace (protrandry: wind pollination)
• chenopod flowers
• onion family flowers: protrandry, vegetative bulblets (walking onions or Egyptian garlic also)

The Food Policy Conference: computers and workshops

I was having significant computer problems while in Portland (the laptop kept conking out) and the hotel computer wouldn't let me have more than one window open at a time. Very frustrating. However, now I am back and with excellent connectivity, so I can tell you all about the conference and easily link to the pertinent websites!

On the way down and back, I was reading Gary Paul Nabhan's book, Where Our Food Comes From.

So, here's the workshops and sessions I went to:

• Food Policy Advocacy 101: short course. I took a ton of notes on this half-day course. There was much discussion on strategy: constituents, allies, opponents, and targets. They mentioned an organization called the Midwest Academy, which trains people on how to organize for social change. They discussed what each of these elements were in a strategic advocacy campaign (constituents: those people you directly represent; allies: those who are on the ground for you; opponents: those who don't like what you represent and will work against you; targets: the specific people who can give you what you want). They described coalitions and recruitment, and how good communications, personal relationships, clear roles and responsibilities, transparency and accountability, a broad reach, and consensus-building are all important to making a coalition that works. In coalitions, formalized agreements can really help keep things clear and accountable. They recommended coalition letters, a memorandum of understanding between organizations, and formal agreements and titles for individual volunteers who build that coalition and make it work.
  

Throughout the conference my role in the library seemed most relevant, even though I was down there on behalf of food and agriculture organizations. This was because much of what I heard about was community organizing—work engaging the public and getting them involved in policy issues that directly affect them. I was pretty astounded that hardly anyone there had heard of the idea of a seed library (more on this later).

• Regional networking with the Canadians: lots of joking around (very politely!) by an impressively savvy bunch of food activists who were NOT happy about Stephen Harper and his government's potential impact on food policy.
• Food systems planning: this wasn't what it was advertised to be, and I and several other participants left it feeling quite shortchanged. Still, it was interesting, and the People's Budget came up in discussion.
• Building diverse local food policy leadership: this was basically about being inclusive, avoiding discrimination and privileging, and using a nifty tool called an interrelationship diagram. This workshop was conducted by Kolu Zigbi, of the Jessie Smith Noyes Foundation, and Rodrigo Rodriguez of the Southwest Organizing Project. These two were dynamic, interesting speakers, and excellent workshop teachers.
  
• Planning for the future of food: this was a presentation of four strategic action plans at four different levels, from neighborhood to city to county to state. The plans were Food for Growth, from Buffalo's West Side in New York state; Transforming the Oakland Food System (California); Multnomah Food Action Plan: Grow and Thrive 2025 (Multnomah County, Oregon); and the Michigan Good Food Charter.
• Accessing and using food data to support collaborative policy decisions: this was all about a great GIS mapping and database synthesis project by CARES. Really powerful tool, but only as good as the resource databases (which seem to be considerably out of date in Alaska, but this may change now that the 2010 Census is done).
• Local food systems: this was pretty frustrating until I finally deviated from the prescribed discussion points and asked people in our group what was working for them. Then the discussion took off like a rocket and I found out about all kinds of cool things: neighborhood cooperative chicken flocks, the growth in communal community gardens in Port Townsend (up from three to 25 in one year in a community of about 8,000), an eat local week program focused on a 100-mile diet in public schools, the part of the USDA’s SNAP that allows for purchasing of food plants (something new to many at the workshop including me, although it has been part of the program since 1973), a local theme garden with plants labeled in Latin (a Roman theme), a marketing co-op for urban farmers (Urban Abundance), rotating free tastings by vendors at a local farmers’ market, a food & market calendar created through a collaborative effort from many local health and food organizations and businesses, using faith-based and other community organizations to publicize information on local food, and so on.

Overall, the conference was great. I'm really glad I went.

At the Food Policy Conference: Neighborhood to Nation in Portland

I'm in Portland, Oregon, attending the Neighborhood to Nation Food Policy Conference, sponsored by the Community Food Security Coalition. A few Alaskans are here: Bob Mikol (TA for Craig Gerlach's Comparative Farming and Sustainable Food Systems class, among other things), Danny Consenstein (Alaska Farm Service Agency), Alli Harvey (with the Alaska Center for the Environment's Local Food project), Diane Peck (Alaska Department of Health and Social Services, Obesity Prevention and Chronic Disease Prevention), Rachel Garcia (intern with the Alaska Community Agriculture Association), Eleanor Wirts (UAF RAP grad student and musher), Johanna Herron (Alaska Farm to School), Mark Carper (UAA and the Alaska Food Policy Council), Kelsey Bearden (fellow student from Comparative Farming), Lisa Sadler-Hart (Sitka Local Foods Network), and myself (UAF School of Natural Resources & Agricultural Sciences, Ester Republic reporter and publisher, librarian, gardener, AK Food Policy Council member, Ester Community Association member, et cetera). I'm down here in large measure because of Gerlach, SNRAS dean Carol Lewis, and Diane Peck. There were others from Alaska, too (Danielle Giles, Nikos Pastos, and Ryan Zinn, but I didn't meet them--Zinn was a presenter, from the Fair World Project).

And I'm having a blast. This is a great group of people, a good 640 strong, from 46 states and DC, plus Ontario, Alberta, British Columbia, Manitoba, Quebec. I attended a short course (Food Policy Advocacy 101) this morning and the plenary gathering this afternoon. The plenary speakers were great, talking about poverty, food deserts, exploited food service and other food industry workers (did you know that the federal minimum wage is only $2.13 an hour? ridiculous!), community gardens, community organizing. Talk about inspiring people.

After the plenary session, we broke out into networking groups, and Eleanor and I went with the Canadians while the rest of the Alaskans networked with the Northwest region. THAT was interesting. We told them we were crashing their party, and they accepted us with good grace and not a few jokes ("I can see Alaska from my house!"). The stereotype of the polite Canadian was not actually blown, despite a not-very-serious attempt to dispel it ("Fuck off!" from one speaker and apparently frequent Facebook poster (not sure if this was a joke, actually) at an opportune and humorous moment of self-teasing about being all polite--I guess you had to be there, but the whole group laughed). There was much emphasis on relationships between people, talking about developing mutual trust and respect between food producers and others in the food system. I was struck by the quiet, polite, and respectful discourse, along with the deep level of political savvy and pronounced opinon concerning the recent majority government positioning of Steven Harper and his party in the Canadian federal government. Very different in approach and delivery than US types, but lots of zing and pow (quite politely phrased, though)!

I've met a lot of fascinating people with great projects and amazing accomplishments. One man, Raymond Figueroa, from New York City, is working with a community gardening project (Friends of Brook Park) taking on abandoned spaces and turning them into a way to give locals control over their food and a way to make a difference in their own lives, to bring dignity back.