- Hello, and welcome to the Northern Lights Tour of Wednesday Night @ the Lab.  My name is Sara Richie.  I'm the Family Living educator here at the UW-Extension in Oneida County.  I would like to introduce our speaker, Dr.  Jeffrey Endelman.  Dr.  Endelman was raised in Houston, Texas.  He is now a faculty member at the University of Wisconsin-Madison in the Department of Horticulture, and he is also the lead researcher for the potato breeding program at UW-Madison which operates out of the Rhinelander Agricultural Research Station, also known as the UW Lelah Starks Potato Breeding Farm.  He will enlighten you today with Potato Breeding in the North Woods, where (potato) babies come from.   (applause)  - Great, thank you for the introduction, and it's a pleasure to be here. 

 As you just heard, I live and work in Madison but come up to Rhinelander quite often for my work in the potato breeding program.  So it's a pleasure to be here to be part of this lecture series in the Northern Lights Tour.  I'm hoping that this is a potato-friendly crowd.  How many of you like to eat potatoes or potato products? Everyone is raising their hand, that's great.  Me too, especially now that I have this job.  It's become sort of a, you don't feel bad about eating potatoes, it's just a great part of your job.  And by the end of this lecture, I'm hoping that I'll tell you a bit more about where do the varieties that you're eating, where do they come from? And what are some of the new molecular technologies that we're using to expedite that breeding process.   So to begin, let's make sure we're all on the same page in terms of understanding just the diversity of potatoes.   These represent the six main market categories that potatoes are traded in, in North America.  There are two categories of russet potatoes. 

 Russet refers to the brown texture of the skin.  There are two categories of round white potatoes.  There's a yellow skin, yellow flesh potato, and then there's a red skin with a white flesh potato.  And these are just the main market categories.  There's also just an incredible diversity of different colors and shapes, like fingerlings and purple with white patches around the eyes, in this example.  So these we can include in the general category of specialty potatoes.   And all of these different categories are part of the UW breeding program.  Now coming back to the main market categories, I mentioned there were two types of round white potatoes and two types of russets.  And the difference between these is how they're used.  So we have some round white potatoes that have certain characteristics that make them very well-suited to making potato chips. 

 We call that a processing use.  In particular, they have a high amount of starch content, which is good for frying.  And then we have some other round white potatoes which have a lower starch content, and they don't store as well.  And they're used for fresh market applications which could be everything else.  It could be boiling, roasting, baking, even.  So, those are the two different market uses of a round white potato.  And the same dichotomy exists for the russet potatoes.  We have some russet potatoes which are specialized that they make really good french fries.  That's a processing application.  And then there are other russet potatoes which are specialized for fresh market uses, like making a baked potato or a mashed potato, for example. 

 And initially, we may not be clear about which of these end uses a particular potato is best-suited for just based on looking at it.  But over a period of years and evaluation, we learn which of these market end-uses it's best-suited for.   Now, those are market categories.  Those are not varieties.  I want to make sure we understand what is meant by the word variety.  Because within a market category, there are many different varieties.  And a variety, in this case, refers to a genetically unique entity.  You are all probably familiar with the concept of the plant variety from apples, because in this country and all over the world, we buy apples by variety name.  So if you go to the store and you look for a Gala or a Pink Lady or a Granny Smith, these are distinct varieties.  And the genetics of a Granny Smith apple is the same in the U. 

S.  as it is in Australia and in Europe.   Within each of the potato market categories, we also have varieties.  But they're, for the most part, transparent to you as the consumer.  That's by design.  So when you go to the grocery store and you buy a red potato, there could be three or four different varieties that could be sold as a red potato in the grocery store.  And the same goes for when you have a bag of potato chips, many different varieties could have been used to make that potato chip.  Here's just an example of three of the varieties that have been released by the University of Wisconsin in the round white potato chipping category over the last 50 years.  So one of the earliest varieties developed by this program was called Superior, released in 1962.   That was a good variety. 

 It is probably best known for having extremely good internal quality.  If you cut open the potato, it doesn't tend to discolor during storage.  You don't find hollow spaces, which are some of the defects that we find in potato varieties.  These defects they're often, they're pulled out before they get to you as a consumer, but we see them when they come out of the field.  So Superior was well-known for having a superior quality from the internal defect perspective.  But it didn't make the best potato chip, especially when stored at cold temperatures for many months, right? Think about how potatoes work.  We grow them during the season, we harvest them in the fall, and then they have to go into storage because we want to eat potatoes throughout the entire winter and spring.  And part of the physiological response of the potato to being stored at cold temperatures is that it accumulates sugars.  The starches are broken down into sugars which leads to dark-colored chips when fried, and that was one of the weaknesses of Superior.  In 1990 a replacement for Superior came along called Snowden, which was at the time one of the best examples of the potato variety that could store in cold temperatures for a long time and still produce a nice light-colored chip. 

 A more recent example would be Nicolet, just released a couple years ago.  Again, also in this potato chip category.   Anyone recognize the theme here for the names of these three varieties? Superior, Snowden, Nicolet?  You can call it out if you. . .  - Snowden Lake.  - Snowden Lake? Okay, so Snowden Lake is the lake just east of Rhinelander, which is actually adjacent to the research farm where these varieties were developed.  Superior, we all know what Superior is, right? A town and a lake.  Nicolet, named after an explorer in this region and also contributed his name to Nicolet College and Nicolet National Forest.  So you see the theme of geographical landmarks from the North Woods showing up in our potato varieties. 

 It's a way of honoring the fact that the Rhinelander area has been really important to potato breeding over this past 75 years.   Sometimes differentiating these round white varieties can be tricky, even for people who are experienced in this business.  And sometimes they don't show their true colors until you actually let them sprout.  So here's a photograph comparing side-by-side what the Snowden potato looks like compared to the Nicolet potato when the sprouts form at the eyes of the tubers.  In fact, this characteristic is required for registering all new potato varieties.  You can see, even if looking at the potato, you might have a hard time telling them apart.  You can see that the sprouts on the Nicolet have a nice purple color to them, compared to Snowden.  This characteristic of tubers from potato tubers to sprout is really important for how they're used agriculturally.  We'll come back to that shortly.  So, now for the question I think you're all dying to know, which is, where do new potato varieties come from? Well, they have mothers and fathers, just like humans do. 

 And the matchmaker here is the potato breeder.  As a breeder, your, one of the most important jobs is actually trying to find the right combinations, trying to pick the mother, the two parents to put together to find the right combination of traits in the offspring.   Unlike humans, potatoes are hermaphroditic, meaning that they have both the male and the female sexes in one plant.  Here's a photo of the greenhouse at the Rhinelander Research Station where we raise potatoes in pots specifically for the purpose of producing flowers so we can make cross-pollination between them.  So if you look at a potato flower, you'll see the yellow portion, which is the pollen-producing stamens, and then in the center of that is the pistil, which is the female part.  And potatoes can self-pollinate.  So you can have the mother and father be the same individual, and sometimes we actually do that.  More commonly, we will cross-pollinate them, taking the pollen from one variety and touching it to the pistil of the other variety to try and cross-fertilize them.   What happens after you cross-pollinate? Well, the flowers are fertilized, and they develop into fruits.  So maybe some of you have never seen a potato fruit before. 

 It should probably remind you of a small green tomato, right, because potatoes and tomatoes are closely-related.  They're both members of the nightshade family.  And within each one of these potato fruits can be hundreds of true seeds.  Here's a picture of an example of true seeds, and we preface the word seed with true because the tubers can also be used like a seed.  That's how commercial crops are planted.  So we have to be careful when we talk about a true seed versus seed, normally to a potato farmer would be a cut piece of potato.  That's where the sprouting of the potato tuber becomes important for agriculture.  Let's see, some other observations here.  So these seeds from one fruit, they're siblings.  They have the same parents and they resemble each other, both genetically and in terms of their observable traits. 

 And that resemblance is actually used when we do some of our analyses in the breeding program.  Now, any one of those seeds has the potential to become a new variety, but it's a long shot.  People quibble about what the true odds are.  I put in here about one in 100,000 seeds probably has what it takes to become a variety.  Some might argue it's closer to one in a million.  It depends on your perspective.  But the point is that very few of these seeds have what it takes to become the top spud.  Hopefully the cultural reference is not lost on this audience.  I grew up watching Top Gun, the movie, first in English and then in German when I was in high school.  So it's a big favorite of mine. 

 And why is so hard to make the cut? Because there are a lot of different characteristics that are necessary to be commercially successful.  And I've grouped some of these characteristics into three different themes.  One is the appearance of the potato.  So it has a certain size and shape, color, the depth of the eyes, the quality of the skin, how textured it is or how shiny, those are all appearances.  And let's face it, we shop for potatoes largely with our eyes, just like we do a lot of other produce.  So they have to look good.  But then they also have to be productive, so that they can actually be profitable for farmers to grow them.  So they need to have yield.  They need to produce the right number of tubers per plant.  We call that tuber set. 

 They have to mature and die at the right time, and not continue growing through November, when we're trying to actually harvest the potatoes.  They have to be resistant to diseases, and they have to store well and not sprout when we don't want them to.  So we want them to sprout when we plant them.  But we don't want them sprouting when they're sitting on the grocery shelves.  So these are all different productivity characteristics.  And finally, there's a range of culinary traits for which we're, I think just scratching the surface, really, in terms of our evaluation.  So we're looking at how much starch do they accumulate? What are the characteristics of that starch, from the textural perspective? What's the flavor notes of a potato? We know it doesn't want to be bitter, but can we actually accentuate the positive flavors? And there actually are very interesting flavors in more rare, or heirloom, and South American-cultivated potatoes.  And I mentioned already the importance of making french fries and potato chips, so there's certain processing characteristics there.  So how do we find out whether a potato has what it takes? We don't do it all in one year.  It's a many years, probably in excess of ten years, process. 

 It involves a lot of people and a lot of work.  So I wanted to walk you through some of the highlights of this process.  And it begins in what I'll call year zero, because I want to count the number one starting from the first year we plant it in the field.  And before we get to plant the seeds in the field, we have to actually plant them in a greenhouse.  So in greenhouses at the Rhinelander Research Station, every seed, true seed, will go into a pot.  And we have upwards of 10,000 square feet filled with tens and thousands of four-inch pots, each one containing a genetically-unique plant.  At the end of that season, we will harvest one mini-tuber from that four-inch pot.  And here's a photo just showing you something about what the undergroun-- The below-ground development of potato looks like.  One of the challenges of working on potatoes is that so much of what's important happens out-of-sight.  And I, especially as someone who's been working in potatoes for only two years now, it's still a learning process to understand the complexity of what's involved in forming tubers underground. 

 But a couple of things I will share with you at this point.  One is that potato tubers are not roots.  That is sometimes a misconception.  They are actually, anatomically speaking, stems.  They form at the end of underground stems called stolons.  The tips of these stolons swell and form potato tubers.   And, from here on out, after this year zero, we will always be propagating these potatoes by cutting up the tubers and using the property of the eye sprouting.  We only get to plant that true seed that first time.  And this process of propagating, or multiplying potatoes through tuber cuttings, is a type of clonal propagation.  Because everything we propagate will be genetically identical to that initial plant. 

  So our goal when we go to the first actual field year is to plant about 50,000 of these mini-tubers.  Each one, again, being genetically unique.  And we use a pretty old, but still very appropriate piece of technology, which is two-row planter.  Two people can sit on the back of this and drop potatoes down a chute into the soil, and it's covered up.  And it takes probably about a week to plant 50,000 potatoes, and about another week to harvest them at the end of the season.  Here's a photo showing some of the harvest equipment we have.  We have a variety of conveyors that will lift potatoes up onto a belt.  The soil is shaken through the holes in the chain, and the potatoes drop off the end back onto the ground.  And we walk through the field for about a week looking at the different varieties and trying to find nice clumps of potatoes where we see that the potatoes have the right appearance, so the shape, the appearance of the skin, and the right number of potatoes per individual plant.   Of the 50,000 we planted that first year, probably only about 1,000 will be selected to be further evaluated. 

 So that's about two percent.  That's a pretty strong cut that takes place after that first year.  In that second year, we will cut up the potatoes that we harvested from that first plant, and we will try and plant eight seed pieces, so we have an eight-foot long section of the field, all genetically identical plants.  At the end of that year, we will harvest them and lift them back onto the ground.  And again, walk through that field over a couple of days, picking up the potatoes that have the appearance that we're looking for.  And we will also start to now measure some of the properties of these potatoes during storage.  So we'll start to characterize their starch content.  We will fry them, if they're destined to be a potato-chipping variety, and look at how good of a potato chip do they make, etc.  Now these first two years, and the greenhouse year, they all occur at this Rhinelander Agriculture Research station.  And here's a very nice aerial photo showing Snowden Lake, which is east of here, and the farm, which is adjacent to Snowden Lake. 

  I'll explain a bit more in a few moments about why Rhinelander plays an important role in this early process of the selection.  But after the two years, we want to move from Rhinelander to a part of Wisconsin that is more representative of what commercial potato production environment would look like.  And the majority of potatoes in this state are grown in the area called the central sands.  It's in the center part of the state, and there's, in the town of Hancock, the university has a research farm.  And we spend years three and four growing these potatoes in ever-larger quantities and conducting more and more detailed evaluations.  One of the nice pieces of equipment that we have available at the Hancock Research Station is a grading machine, which has an X-ray machine hooked up to it.  So, the word grading refers to the process of storing potatoes based on their size and whether they are misshapen to throw out the culls.  And this grading machine has a conveyor belt.  You're looking down the conveyor in this photo, and in the middle of that conveyor there's an X-ray machine, which takes an image of every potato to give us both an estimate of the geometry of the potato, as well as an estimate of the weight of it, which makes for a very rich data set to select, again, which have the right characteristics.  If a variety makes it through years three and four, we now send it out to a national network of test sites. 

 One of the great things, I think, about the potato-breeding community is that it's still a very vibrant, public sector activity.  There are some private breeding programs, and hopefully we'll have more in the future.  But for now, it's still, most of the breeding is taking place at the universities.  And so we have trial sites from coast to coast.  And we send our material to these locations, and they send us their best varieties.  And so for two years, we accumulate multiple locations' worth of data.  10 states worth for the chipping varieties, and five states for the French fry varieties.   So at the end of this six-year process, we now have a pretty good idea of whether a new variety has some commercial potential.  And only probably a handful of the 50,000 that started out this process will make it to this stage of evaluation.  And now we're going to put these out into the commercial farmers' hands. 

 We've done pretty much all we can from the perspective of a university, small-scale testing.  We want to now test these varieties on larger acreage, under more realistic, commercial conditions.  And so, we partner with the University of Wisconsin has a certified seed program, as well as our industry partner, which is the Potato and Vegetable Growers Association for Wisconsin.  So together with the breeding program, we have this effort which we call SPUDPRO.  It should have been called Top Spud, but anyways, it was called SPUDPRO, which involved an additional three to four years of testing and seed propagation.  And if a new variety succeeds at that point, it can actually finally get a name and be published.  So like the name Nicolet, that potato was tested for more than 10 years under the designation W2133-1.   So the potato, we don't give names to 50,000 potatoes, as you can imagine.  They just exist as numbers until such time that we think they actually have a potential to be commercially successful, and then they get a name.  Well, I've been promising that I would talk more about why is Rhinelander such an important part of the breeding program? Why am I here from Madison talking about potato breeding at this lecture series? Some of you may know that there are actually two University potato farms in the Rhinelander area, and they often get confused by people who are aren't familiar with what's going on on these two farms. 

 The one I've been talking about thus far is the farm east of town on Highway C, which we call the Rhinelander Agricultural Research Station.  There's also a farm on Highway K, west of town, which is run by the Wisconsin Certified Seed Potato Program.  They don't develop new varieties, they take varieties that we develop and they maintain them in a virus-free condition and produce virus-free potatoes for growers to grow, potato growers to grow.  So they work in close cooperation, but the work that we do at the breeding farm takes about ten years and then we sort of hand it off to the other farm to take it from there.  So, why are these two farms in Rhinelander? Well to explain that, I want to talk a bit about the geography of Wisconsin.  This is a map of the soils of Wisconsin.  Many people don't realize that soils, just like plants and animals, can be classified.  And in the top corner of this figure, you see the soil orders.  And the colors kind of represent different potential agricultural uses.  So, in light blue, it's an area, that's what we call the central sands. 

 It's classified as an entisol, which refers to a poorly-developed soil.  It doesn't have soil horizons.  So without irrigation, you really can't grow anything there.  But with irritation, you can grow high-quality potatoes and other vegetables.  So this is the center of the irrigated vegetable production for our state.  And you can see that Hancock is sort of on the eastern border of this geological area.  There are 63,000 acres of potatoes grown in Wisconsin every year, the majority of which, probably over 90 percent I would estimate, are in this Central Sands area.  Potato growers in this area, they are at the final step of the potato production chain, or supply chain.  Their role in the process is they get seed potatoes from a seed potato farmer, they plant them for one year, and then they sell their harvest to the grocery stores, to the french fry plants, the potato chip plants, etc.  So it's a one-and-done arrangement. 

 Where do they get their seed potatoes from? They get them from farmers, potato farmers, in the Antigo area.  So we move a few notches north.  The Antigo area is actually on the northern border of probably what you would consider the prime agricultural soils of Wisconsin.  It's actually technically an alfisol.  So it has a nice soil profile, and it specializes in growing potatoes for seed purposes.  Although some of their harvest will also be sold for grocery store end-use.  Now a potato seed grower in the Antigo area, they actually will re-plant some of their harvest.  So they can sell some to the grocery stores, they can sell some to a farmer in the Central Sands area, and then they can keep some of their harvest back for themselves to re-plant.  But in order to keep it back for their own re-planting purposes, it has to meet very stringent requirements in terms of how much disease is present.  We'll talk more about disease in a moment. 

 But because of the mathematics of how potatoes can multiply, one acre of a potato farm in the Antigo area can provide enough seed for 10-15 acres of land in the Central Sands.  That's why you don't need more than 10 percent, probably, of the total area devoted to seed production to satisfy all of our commercial production in the Central Sands area.  Now these Antigo growers, after a couple of years their seed may no longer meet the requirements for the disease.  So, they have to get their seed from somewhere.  Where do you think they get their seed from?  Rhinelander.  So now you see Rhinelander is really at the head of this whole potato-supply chain process.  There are two farms in the Rhinelander area that are specialized in producing the seed for the seed-growers, okay.  And that's maybe a little hard to wrap your head around, But we call that nuclear seed, sometimes, to differentiate it.  They produce nuclear seed which they sell to a seed grower, who then sells it to the commercial grower.  And these two specialized farms, one is this UW farm on Highway K I mentioned earlier, and one is a private farm, which was known as Zeloski Farm for many years and now is called Eagle River Seed Farm. 

 So this process is something like a hot potato game.  That's the first thing I thought of when I learned about it.  The technical name is the limited generation system.  But it's a hot potato because, at every stage, you're only growing the potatoes for as many years as you can before they accumulate a certain amount of disease, and then you have to pass them on to farther down the supply chain, they get closer and closer to the end-use in the food system.  In any given location, though, they will only handle that seed for a limited number of generations.  Hence the name limited generation system.   And as I've been alluding to, one of the main reasons this limited generation system evolved over the past century is because of the pressure from diseases.  Because the potatoes are propagated clonally, by cutting, they can tend to accumulate viral diseases more easily than seed-propagated crops, like soybeans, or corn, for that matter.  One of the main diseases we struggle with is viruses, and these viruses are transmitted by aphids, primarily.  Here's a picture showing a green peach aphid, which is a very small insect, on a potato leaf. 

 And one of the main viruses that is probably the biggest source of economic losses for Wisconsin is called Potato Virus Y, or PVY, for short.  There's also a PVX.  They started using different letters of the alphabet.  So PVY does bad things to potatoes.  Here's a photo showing you a healthy potato plant next to an infected potato plant.  You can see the one on your left is stunted-looking, the leaves are wrinkly, versus the healthy plant has a smooth leaf and it's a more erect plant.  And this virus disease can also lead to not just fewer tubers, or less yield, it can also actually lead to rotting and necrosis of tubers, which reduces the-- Basically these have to be thrown away at this point.  So here's an example of some of the symptoms you can see on potato tubers.  So this limited generation system helps to prevent the virus from building up to unacceptable levels.  And it's based on this principle of geographic isolation. 

 Rhinelander is geographically isolated from Antigo, which is geographically isolated from the Central Sands.   So when I hear about Potato Virus Y, immediately my first thoughts are, what can I do as a potato breeder? And there are pesticides that we can use to manage viral diseases and many other diseases, but there are also genetic solutions.  It turns out that if we look beyond our cultivated North American potato, we can find resistances to almost any disease you can think of in potato.  We just have to go searching in the world's repository of potato germplasm, as it's called.   And potato varieties in the United States really just represent a fraction of that genetic diversity.  The most of it is in Latin America, which is where potatoes were first domesticated from the wild potatoes many thousands of years ago by the Native Americans.  Here's a map showing the distribution of wild potato species where the lighter colors represent regions of high diversity for potato wild relatives, and the main hot spots for diversity are really in the Andean mountains of Peru and neighboring countries.  And that's where it's believed that potatoes were first domesticated.  Research has shown that, although the center of diversity for potato is in the Andean mountains, it looks like, actually, the potatoes that we have in North America descend more directly from a group of potatoes that are cultivated in the southern part of Chile.  And they get the name Chilotanum. 

 Not very creative, but it conveys the right idea.  So, why do you think, given that when the Europeans first came to the Americas, and they would have seen potatoes all over their travels in Latin America, and they brought back potatoes from all over Latin America back to Europe.  But it was the ones from southern Chile that became the dominant type of potato in northern Europe.  Anyone want to guess, why might that be the case? What do you think is similar between southern Chile and northern Europe compared to, say, Peru and northern Europe?  Latitude.  Excellent.  The pattern of the seasons and the pattern of having long days in the summer and the short days in the winter, that's a pattern typical of temperate locations that are far from the equator.  And those signals from the sun are cues that actually potatoes respond to it, they govern whether they will flower, they govern whether they will even set potato tubers.  And so it was actually the building on hundreds of years of adaptation by the Native Americans in southern Chile, it was fairly easy to then adapt those varieties to northern Europe, compared to a very difficult time adapting the Peruvian varieties to northern Europe.  So that's sort of the mystery of where our potatoes came from.  And the North American potatoes came from Europe. 

 So they had to go across the Atlantic and back in order to end up here in the U. S.  There are actually a number of cultivated potatoes in Latin America that we have no analogs of here in the U. S.  and they have names like Stenotomum, and Phureja, and Andigena.  And there are also dozens of wild species.  And potato geneticists have been searching through these genetic resources for disease-resistance genes, and have found three different species or sub-species that contain resistance genes for this potato virus Y disease.  And they have been now cross-bred over the last 50 years into some of our North American varieties.  But it's still the case that most of our best North American varieties don't have resistance to this disease.  It's a process, it takes many decades to try and move these resistance genes from something like a cultivated potato in the Andes to something that would be commercially acceptable in the U. 

S. .  So we're still engaged in this process of trying to move these resistance genes into European-U. S.  varieties.  And what I want to tell you now about is how we can use some DNA technologies to facilitate that process.  The key idea here is what we call a genetic marker.  So to explain genetic markers, I want to tell you a little bit more about potato genetics.  Like human DNA, potato DNA is a chemical sequence of four different letters.   And these letters, A, T, C, G, they encode different properties in proteins and in the regulation of how the organism develops. 

 The DNA is organized as long molecules that are called chromosomes.  And the term we use for the complete sequence of all the DNA in an organism, or all of the chromosomes, would be the genome.  So here's a comparison of how the human genome compares with the potato genome.  There are approximately 3. 2 billion letters, or bases, in the human genome, which is about four times as many as in the potato genome, estimated to be around 850 million.  It's still a lot of DNA.  Humans have 23 pairs of chromosomes.  Potatoes have only 12 chromosomes, but they come in groups of four.  So this is one of the most confusing things about potato genetics when you first start working in it, if you've come from a crop like corn or soybeans.  Because, humans, like corn, soybeans, most animals, inherit one version of a gene from mom and one version of a gene from dad. 

 That's the pairing process.  Potatoes inherit two versions of a gene from mom and two versions of a gene from dad.  The technical term for this is autotetraploid.  You can hear the word tetra, the number four is present in that name.   So as a result of this tetraploid property, when I draw cartoons of potato genetics, I'm going to have four strands of DNA instead of just seeing two strands of DNA for every variety.  So here's a hypothetical case, I take Variety 1 as a mother, Variety 2 as a father, and I look at the DNA sequences, and, I find at this one position, there is some variation.  The other positions nearby, it's always the same across all four chromosomes in each variety.  But at this one position, there's a variant.  In some strands of DNA it's an A and some it's a T.  And you can represent that in a more concise way on the right just by saying this is a TAAA by TTAA. 

  So one copy of T crossed with two copies of T.   Now I'm hoping some of you remember learning about Mendel in your high school biology or college biology classes, right? If you do, you probably learned the fact that if I take a mother which is TA, and a father which is TA, the children, I expect 25 percent of the offspring to be TT, 25 percent to be AA, and 50 percent to be TA, like one of the parents.  So this is how the children can look different than either one of the parents.  They call this independent segregation of chromosomes.  Well, it gets more complicated with potatoes, because we have four versions that can re-combine.  So anyone want to take a stab? What do you think a TAAA by TTAA becomes? It's not easy to just do on the top of your head, don't worry.  This is how I torture my graduate students, it's a lot of fun.  So it turns out the statistics are this, that around eight percent of the children, the offspring, will have no copies of T, 42 percent will have one or two copies of T, and eight percent will have three copies of T.  So you can work out mathematically what all of these different ratios are, and that allows us to interpret our genetic data.   So the typical practical problem that we're trying to solve with these markers is the following, we have one variety which has good productivity, good yield, good marketability, but it's susceptible to this disease. 

 And we have another variety which just isn't quite good enough from a yield or marketability perspective, but it has the resistance genes.  So can we combine the best traits from both of these? So we have a susceptible and resistant parent, and we know because of this segregation property of chromosomes, some of the offspring will inherit the resistance gene and some will not.  Now we could take the time, and it may take a couple years, we could figure out which of these had that resistance gene by actually challenging them with the pathogen, but there's a faster way.  We can extract the DNA, and we can assay that one position in the genome and find out which ones have the resistance gene.  And I'll tell you two methods that we're using to do this.  Method 1 is a tried and true method, been around for decades, called gel electrophoresis.  The idea is that you'll take the DNA out of the, take the cells, break open the cells, take the DNA.  And then you will cut the DNA with certain enzymes in such a way that the fragments that result are different depending on whether it has that T or that A at that position.  The enzymes we'll try and cut right there, and if it's a T, it can cut it, if it's an A, it can't cut it.  That will lead to different size fragments, and we can now put those DNA fragments in a type of gel matrix, apply electric current, and the DNA moves with the smaller fragments moving faster than the bigger fragments. 

 And the result is this kind of a banding pattern that can be used to then diagnose what gene, what version of the gene is present.  So at the bottom, for example, in the yellow letters, the two bottommost lanes, as they're called, is a resistant with a three-band pattern and a susceptible with a two-band pattern.  It's kind of faint, but here's the three bands versus two bands.  And the top four are examples of new varieties that we didn't know what their status was until we ran this test.  And we learned that only one of the four had the resistance gene.  So this is one way that's fairly cost-effective if you know exactly what you're looking for.  The problem is that, in many cases, you don't necessarily know what you're looking for.  You're in the process of trying to discover where is the resistance gene? And to do that, you need hundreds, preferably thousands of these markers.  And that's a lot of gels, it used to take a graduate student four years to do that project.  Now we can do it in about two weeks. 

 And we do it using a type of microchip technology specialized for DNA.  It's a fluorescent array, and the same technology used to make computer chips can make a certain substrate to which we attach pieces of DNA that are complimentary to the potato genome.  And this chip fits in the, actually, many hundreds of those chips fit in the palm of your hand.  The potato array that we currently have is only about, I guess only about three years old now.  We have 12,000 of these genetic markers.  12,000 positions on the genome we can interrogate with one of these chips.  Our goal is to increase this to about 80,000 markers in the next several years.  If that seems like overkill, just remember, there are 850 million letters in the potato genome.  So, even with 80,000, we're talking about one-hundredth of a percent that we're actually assaying with this.  So it's sufficient for many applications, but still not sufficient for other applications. 

 Well let me now give you a short story about how we've used this potato chip to, by chip, I mean the microchip, to do some interesting genetic studies.  Here is a picture showing a population that was developed by my colleague, Shelley Jansky at the University of Wisconsin.  And what Dr.  Jansky did is she took a wild potato called M6, which produces these small, round, white potatoes.  They're small, like the size of a quarter or something.  And, then this other potato called DM, which produces more like a fingerling-type with a red skin.  She crossed those two and got something quite unusual.  She got a purple-skinned potato, which was mostly round, maybe a little bit oblong.  And then she took that purple-skinned potato, and she self-pollinated it, and she got what you see in that picture.  All those colors and shapes were present in the genes of that one purple potato that you see right there. 

 A remarkable example of how certain genetic properties can be masked.  And that's what we call 'recessive' genes.  And the goal of this genetic study was to try and uncover the genetics behind all these colors.  It wasn't just on the outside, you looked on the inside of these potatoes and you see some have white flesh, some have yellow flesh, some have a purple or red center part of the potato.  Just an amazing population.  Well, we took this, we took about 180 of these progeny.  We tested each one of them with this potato array and got thousands of DNA markers.  And now, we were able to actually do a statistical analysis at each one of those markers to find out, is that marker next to a gene for one of these color traits? And the results of this analysis can be displayed in this kind of a figure.  The vertical axis is the peaks there, the taller the peak, the higher the certainty that that position is linked to a gene for that trait.  And so what you're looking for are the mountains in this kind of analysis. 

 The horizontal axis is, the markers are laid out along the potato genome.  You can see the numbers one to 12 there.  The 12 chromosomes and each marker has its place.  And we discovered there are actually five genes involved in just the color properties, just whether you see red or purple skin and flesh takes five genes to completely determine that in this population.  Just think about how many genes are involved in the 20 other traits that we have to think about for breeding.  So you can see why it's, it can be a complicated business.  We like to give genes names.  So the R gene on chromosome two is the one that produces the red pigment.  The 'P' gene on chromosome 11 produces the purple pigment.  Neither the red pigment or the purple pigment can be expressed unless the D gene has a certain state. 

  It's called developer because it allows the pigment to develop in the potato.  The purple, we learned, is dominant over the red.  So if you have both a purple pigment and a red pigment, you'll tend to see purple.  So that's for the, that's the overall color.  What about the flesh? There are two genes that effect the flesh color.  They get symbols PF and PF2.  PF stands for pigmented flesh.  And both of these genes, we discovered, modulate how dark that flesh pigment is.   So what's the practical relevance of this study? I mean, it's a very interesting study to a geneticist, but it does have a practical relevance, because as I mentioned at the beginning, potatoes, to a large degree, the appearance is what sells potatoes.  And the dark red skin color is actually one of the most important traits that we focus on when we develop a new red-skin variety. 

 So now we actually understand the genetics of the intensity of that red color better than we used to, and we can hopefully target these genes to more efficiently develop red-skinned potatoes that actually retain their dark red skin color throughout the storage season.  Besides color, I would say one of the, probably second-most important traits in terms of appearance for a red-skinned potato is whether they keep their skin when you harvest them.  There's a premium for harvesting early in potatoes and in many other crops.  But the trade-off is that when the potato is harvested early, the skin hasn't had fully time to cement down onto the tuber.  So this skin-peeling characteristic is one of the, is important to study.  Here I'm just going to contrast for you, hopefully you can see this a little bit in this photo.  The top photo shows the number one red variety in Wisconsin, it's called Dark Red Norland, which, this was harvested just a few weeks ago on July 15, it's a very early harvest for potatoes, but some of our growers actually do that.  And remarkably, it had very good skin integrity.  Another variety, which we just released a couple years ago, it's called Red Endeavor, it has a number of advantages over Dark Red Norland, namely yield, shape, internal quality, but one thing it doesn't beat the Dark Red Norland in is the skin set.  You can maybe see here, sort of flecks of yellow or white which is the skin peeling off during that harvest. 

 So, this is one of my main priorities for the next several years is to try and breed a red-skin variety that can beat the Dark Red Norland for that early skin set.   All right, let me wrap things up here and just remind us that I've tried to give you an overview of how new potato varieties are developed.  It's a long process, takes many years and the work of a lot of people, and we're trying to use new technologies to make that process more efficient.  And I've given you some examples of how we can use genetic markers to do that.  The breeding program has a great history.  It's a real honor for me to be the leader now.  Over 75 years, and for most of that time, the Rhinelander Agriculture Research Station has been integral to that program.  And it continues to be really important today because of the geographic isolation and because of our facilities and staff, who have the institutional know-how to manage a breeding program.  So, with that, let me acknowledge those people here.  Many of them are in the audience. 

 There's really just a great group of people that I've had the privilege of working with in the last two years.  And if you have never been to the Rhinelander Agriculture Research Station, let me invite you now to our family day, which is on September 24th, open to the public, it's a chance to come, help us harvest potatoes both for the food pantry and take a few of the odd-balls home with you, 3:30 p. m. , I hope to see you there.  I have a website, if you're interested in the potato breeding program.  You can go to the website.  I have a blog that I try and update with some regularity.  So check it out.  And I want to close by acknowledging that we get a lot of financial support from several organizations, in particular the USDA, the College of Agriculture and Life Sciences for UW-Madison, and the Wisconsin Potato and Vegetable Growers Association.  Thanks for your attention. 

 (applause)   - Hello, and welcome to the Northern Lights Tour