Tag Archive | selective breeding

Is Transformation Really that Different from Backcrossing?

GUEST POST: Benjamin Edge

Benjamin Edge (@edgeben) is a former wheat breeder for Pioneer Hi-Bred, International, a DuPont Company, and for Clemson University. He has released 10 PVP protected wheat varieties and is a co-inventor of record for 5 wheat variety patents. He has taught classes in plant breeding, biology, and computer technology.

Transformation, the insertion of genes into an organism through the use of a ‘gene gun’ or a bacterial vector, is a tool used by plant breeders to introduce new traits to a crop when there is not enough readily useful variation present in the crop they are trying to improve. Transformation results in what we commonly refer to as genetically modified organisms, or GMOs. While some consider this a risky technology,  transformation is actually very similar in effect to what conventional breeders do when they find a gene of interest in a wild relative, and use backcrossing to incorporate that gene into an adapted variety.

Backcrossing is a VERY effective tool of conventional plant breeders (Briggs and Knowles, 1977). Once you find a trait you are interested in, you can move that trait from a wild relative (closely related species) or from any member of the species you are working with into an adapted variety with great repeatability (reproduced or repeated easily). Backcrossing is used when you have a well adapted variety, say plant A, with high yield, large seeds, and strong stems, but with some weakness, such as susceptibility to a disease. If you find a plant, say plant B, with disease resistance, but poor yield, small seeds, and weak stems, you can use backcrossing to incorporate that disease resistance trait into plant A, what we call introgression of the trait.

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Contemporary Selective Breeding. Plant Edition.

vegetables

In an effort to address the naivete and sentimentality that people have about agriculture, we continue our look at contemporary selective breeding. After looking at the state of the art of dairy cow breeding, I thought we’d take a look at some recent articles about the state of the art in non-GMO plant breeding.

In Scientific American, Ferris Jabr takes a long and careful look at a new breed of plant um, breeders. Clocking in at nearly 5000 words, it’s thorough and lively primer on the subject of selective breeding. You’ll be doing yourself a favor to read the whole thing.

The story starts with the arrival of some seeds from habaneros that mutated in such away that they produced little to no capsaicin. Michael Mazourek started crossing them with other plants to try to create a pepper that had a habenero’s subtle, smoky flavor without the brutal and distracting heat. By running the genome of the plant and isolating the alleles responsible for the traits he was seeking he was able to skip step of waiting for plants to produce fruit to test if they were expressing those traits.

Mazourek belongs to a new generation of plant breeders who combine traditional farming with rapid genetic analysis to create more flavorful, colorful, shapely and nutritious fruits and vegetables. These modern plant breeders are not genetic engineers; in most cases they do not directly manipulate plant DNA in the lab. Rather, they sequence the genomes of many different kinds of plants to build databases that link various versions of genes—known as alleles—to distinct traits. Then, they peek inside juvenile plants to examine the alleles that are already there before choosing which ones to grow in the field and how best to mate one plant with another. In some cases breeders can even analyze the genetic profiles of individual seeds and subsequently select which to sow and which to disregard, saving them a great deal of time and labor.

Plant breeders have, of course, always used the best tools available to them. But in the last 10 years or so they have been able to approach their work in completely new ways in part because genetic sequencing technology is becoming so fast and cheap. “There’s been a radical change in the tools we use,” says Jim Myers of Oregon State University, who has been a plant breeder for more than 20 years and recently created an eggplant-purple tomato. “What is most exciting to me, and what I never thought I would be doing, is going in and looking at candidate genes for traits. As the price of sequencing continues to drop, it will become more and more routine to do sequences for every individual population of plants you’re working with.”

. . . In part to circumvent the controversy surrounding GMOs, fruit and vegetable breeders at both universities and private companies have been turning to an alternative way of modifying the food we eat: a sophisticated approach known as marker-assisted breeding that marries traditional plant breeding with rapidly improving tools for isolating and examining alleles and other sequences of DNA that serve as “markers” for specific traits. Although these tools are not brand-new, they are becoming faster, cheaper and more useful all the time. “The impact of genomics on plant breeding is almost beyond my comprehension,” says Shelley Jansky, a potato breeder who works for both the U.S. Department of Agriculture (USDA) and the University of Wisconsin–Madison. “To give an example: I had a grad student here five years ago who spent three years trying to identify DNA sequences associated with disease resistance. After hundreds of hours in the lab he ended up with 18 genetic markers. Now I have grad students who can get 8,000 markers for each of 200 individual plants within a matter of weeks. Progress has been exponential in last five years.”

. . . Mills can look for these markers in cantaloupe seeds before deciding which ones to plant thanks to a group of cooperative and largely autonomous robots, some of which are housed in Monsanto’s molecular breeding lab at its vegetable research and development headquarters in Woodland, Calif. First, a machine known as a seed chipper shaves off a small piece of a seed for DNA analysis, leaving the rest of the kernel unharmed and suitable for sowing in a greenhouse or field. Another robot extracts the DNA from that tiny bit of seed and adds the necessary molecules and enzymes to chemically glue fluorescent tags to the relevant genetic sequences, if they are there. Yet another machine amplifies the number of these glowing tags in order to measure the light they emit and determine whether a gene is present. Monsanto’s seed chippers can run 24 hours a day and the whole system can deliver results to breeders within two weeks.

This example from the article is striking in that it shows Monsanto actively helping out local (east coast) vegetable farmers.

Fresh broccoli consumed the same day it was harvested is completely different from typical supermarket fare, Bjorkman says—it’s tender, with a mellow vegetative flavor, a hint of honeysuckle and no sharp aftertaste. Trucking broccoli from California to other parts of the country requires storing the vegetable on ice in the dark for days. With no light, photosynthesis halts, which means that cells stop making sugars. Rapidly dropping temperatures rupture cell walls, irrevocably weakening the plant’s structure and diminishing its firmness. When the broccoli is thawed, various enzymes and molecules that escaped their cells bump into one another and trigger a sequence of chemical reactions, some of which degrade both nutritional and flavorful compounds. Giving farmers in the east broccoli they can grow and sell locally solves all these problems. In a separate effort to boost the nutritional value of broccoli, Monsanto released Beneforte broccoli, which has been bred to contain extra high levels of glucoraphanin, a compound that some evidence indicates may fight bacteria and cancer. You can find the florets at some Whole Foods and States Bros.

It’s telling that there seem to be no safety concerns for the random mutation not previously existing in nature in those habaneros that Michael Mazourek was sent. It’s a novel gene that hasn’t been field tested for environmental concerns, it hasn’t undergone composition analysis, or testing for allergens. If breeders using genetic engineering to move one single gene to express a well understood protein into a crop all those things and a decade of testing would be necessary. Go figure.

A recent piece by Nova was about genetic engineering, but again, I thought the most interesting part was it’s portrayal of how specific and directed contemporary breeding is.

De Jong produced the plants in the same old, laborious way that his father did before him. He collected pollen from a plant that produces potatoes that fry as potato chips should and then sprinkled the pollen on the flower of a potato plant that resists viruses. If the resulting potatoes bear their parents’ finest features—and none of the bad ones—De Jong will bury them in the ground next year and test their mettle against a common potato virus. If they survive—and are good for frying and eating—he and his team will repeat this for 13 years to ensure that problematic genes did not creep in during the initial cross.

Each year, the chance of failure is high. Potatoes that resist viruses, for example, often have genes that make them taste bitter. Others turn an unappetizing shade of brown when fried. If anything like that happens, De Jong will have to start from scratch. Tedious as it is, he loves the work. Kicking up dirt in the furrows that cascade along the hillsides of upstate New York, he says, “I’m never stressed in the potato fields.”

De Jong has some serious cred in the agriculture world. Not only was his father a potato breeder, he’s also descended from a long line of farmers. The potato farmers he works with appreciate this deeply, along with his commitment to the age-old craft of producing new potato varieties through selective breeding. They even advocated on his behalf during his hiring and when he was up for tenure at Cornell, a school with a long history of agriculture research. “All of our farmers like Walter,” says Melanie Wickham, the executive secretary of the Empire State Growers organization in Stanley, New York. Often, he’s in the fields in a big hat, she says. Other times “you’ll see him in the grocery store, looking over the potatoes.”

De Jong has been working with farmers long enough to know that our food supply is never more than a step ahead of devastating insect infestations and disease. Selective breeders like De Jong work hard to develop resistant crops, but farmers still have to turn to chemical pesticides, some of which are toxic to human health and the environment. De Jong enjoys dabbing pollen from plant-to-plant the old-fashioned way, but he knows that selective breeding can only do so much.
seedlings

So while De Jong still devotes most of his time to honing his craft, he has recently begun to experiment in an entirely different way, with genetic engineering. To him, genetic engineering represents a far more exact way to produce new varieties, rather than simply scrambling the potato genome’s 39,000 genes the way traditional breeding does. By inserting a specific fungus-defeating gene into a tasty potato, for example, De Jong knows he could offer farmers a product that requires fewer pesticides.

“We want to make food production truly sustainable,” De Jong says, “and right now I cannot pretend that it is.”

. . . I first encountered De Jong on April 4, when he sat on a panel about GMOs in New York City hosted by the advocacy groups GMO Free NY and the Wagner Food Policy Alliance. The modest awkwardness that endears him to farmers didn’t charm the audience. As De Jong explained how scientists create GMOs, they began to murmur, lost amidst De Jong’s scientific jargon and meandering delivery.

De Jong did, however, liven up during a discussion in which Jean Halloran, a member of the panel from the Consumer’s Union, suggested that farmers in the developing world could ditch pesticides, not use GMOs, and increase yields. “We favor a knowledge-based approach rather than a chemical-based approach to increasing production,” Halloran had said.

De Jong did not find this solution realistic and asked, “Do you want to be the African farmer who has to apply insecticide every week—really nasty stuff—without protective equipment?” The question hung in the air for a second, and the panelist beside him repeated the no-chemical mantra.

Weeks later, De Jong tells me the panel opened his eyes. He was shocked at how people who don’t live near farms feel entitled to advise farmers, especially on environmental matters. “There is a romantic notion of environmentalism, and then there is actual environmentalism,” De Jong says. “Farmers are very conscious of the environment. They want to hand off their operation to their kids and their kids’ kids, so they maintain the land the best they can while doing what they need to do in order to sell their harvest,” he says. “My guess is that the majority of people who are anti-GM live in cities and have no idea what stewardship of the land entails.”

“I find it so tragic that, by and large, crop biotechnologists and farmers want to reduce their pesticide use, and yet the method we think is most sustainable and environmentally friendly has been dismissed out of hand.” He pauses as he recalls the event and says, “There is no scientific justification for it—it is just as if there is a high priest who decided, ‘Thou shalt not be GMO.’ ”

DeJong is very clear about the traits his potatoes are going to end up with. He’s going to get to where wants to go. What he doesn’t understand is why he shouldn’t just skip to the good part.

P.S. Wired has an interesting piece on the vegetables that Monsanto has developed using these techniques. I’ve been using those BellaFina peppers for some time with out realizing they were a Monsanto product. They are great. Cheap and convenient. I used one pepper at a time, mostly in my morning eggs.

Sources:
Creating Tastier and Healthier Fruits and Veggies with a Modern Alternative to GMOs
Ferris Jabr | Scientific American | 24 January 2014

GMOs May Feed the World Using Fewer Pesticides
Amy Maxmen | PBS | 24 July 2013

Monsanto Is Going Organic in a Quest for the Perfect Veggie
Ben Paynter | Wired | 21 January 2014

Contemporary Selective Breeding. Cow Edition.

Ed Yong has a fascinating post about a new evolutionary biology study on cow milk and the differences for male and female offspring. If you are interested in animal husbandry and/or evolutionary biology it’s an interesting read especially if you follow through with the links, especially this one.

For the purposes of this blog, I’d like to underline something that Ed’s post alludes to but doesn’t call out specifically.

For decades, the dairy industry has used data to supercharge the humble black-and-white Holstein cow into a milk-producing machine. Across the US, thousands of dairy farmers keep assiduous records about how much milk their cows produce, and the volume and composition of that milk. All of this information feeds into mathematical models that predict the total amount of milk a cow makes over its lifetime. Farmers use this information every day to decide how to care for and breed their animals. As a result, cows today make four times more milk than they did in the 1940s.

. . . Either way, Hinde’s results have implications for the dairy industry. If they wanted to, dairy managers could ensure that most of the calves they breed are females, but they’d need to separate semen by sex to do so. In the past, some people have argued that this isn’t cost-effective, but it might be worth it if it leads to a 2.7 percent bump in milk production.

I think a lot of the conversation around food in this country (and around the world) is hamstrung by the naive, sentimental and sometimes schizophrenic vision many people have of agriculture.

Ed Yong’s post alludes to two things.

First. Modern selective breeding is much more specific and sophisticated than most people realize. In the last hundred plus years, selective breeding has produced much more substantial changes in domesticated animals and crops than people realize. Many amateur ‘critics’ of contemporary agriculture believe that selective breeding means farmers are just mating their healthiest males with their healthiest females in a parallel to survival of the fittest in nature. In their objection to genetic engineering they say that we should stick with our food the way it is, as nature intended. They seem to be completely unaware of how drastically we have engineered the genetics of domesticated plants and animals without recombinant DNA technology. They seem to be unaware that the market for bull semen goes back decades. They seem to be unaware that contemporary plant breeders use tissue cultures and genetic marker assisted breeding in their work. Selective breeding hasn’t been about capitalizing on serendipity for a long time. It works toward very clear, pre-defined goals.

Allow me to risk setting up a strawman argument. You can sometimes hear from the same quarters a pair of schizophrenic claims. In one context, people might say our health problems began 10,000 years ago with the introduction of agriculture and selective breeding. The claim is that humans haven’t been able to co-evolve to thrive on domesticated grains/wheat, as fast as we’ve been able to breed the grains for yield. The same has been said about cow’s milk. (The evidence though seems to go the other way on that count. Europeans actually evolved lactose tolerance very quickly.) In another context, the issue becomes that the (supposed) increase in chronic disease (allergies, autism, insert health problem du jour) in the last three decades must be caused by the rapid changes to agriculture in the last three decades. Our problems are either being caused by the Sumerians or Monsanto.

Where things can get really schizophrenic is when goalposts start getting moved as misinformation and misunderstanding is addressed. It’s about nutrition. No it’s about animal welfare. No it’s about food access and affordability. No, it’s about family farms. No it’s about the environment. I would argue that this stems from the fact that the pastoral sentimentality that drives so much of the current food conversation is really an aesthetic proposition. The arguments to defend that proposition shift as each is found wanting.

The second thing that Yong’s piece touches on is the positive environmental impact of contemporary breeding. I’ll let the Alexis Madrigal piece that he links to in his introduction make the case.

Dairy breeding is perfect for quantitative analysis. Pedigree records have been assiduously kept; relatively easy artificial insemination has helped centralized genetic information in a small number of key bulls since the 1960s; there are a relatively small and easily measurable number of traits — milk production, fat in the milk, protein in the milk, longevity, udder quality — that breeders want to optimize; each cow works for three or four years, which means that farmers invest thousands of dollars into each animal, so it’s worth it to get the best semen money can buy. The economics push breeders to use the genetics.

The bull market (heh) can be reduced to one key statistic, lifetime net merit, though there are many nuances that the single number cannot capture. Net merit denotes the likely additive value of a bull’s genetics. The number is actually denominated in dollars because it is an estimate of how much a bull’s genetic material will likely improve the revenue from a given cow. A very complicated equation weights all of the factors that go into dairy breeding and — voila — you come out with this single number. For example, a bull that could help a cow make an extra 1000 pounds of milk over her lifetime only gets an increase of $1 in net merit while a bull who will help that same cow produce a pound more protein will get $3.41 more in net merit. An increase of a single month of predicted productive life yields $35 more.

. . . One reason for the change in breeding emphasis is that our cows already produce tremendous amounts of milk relative to their forbears. In 1942, when my father was born, the average dairy cow produced less than 5,000 pounds of milk in its lifetime. Now, the average cow produces over 21,000 pounds of milk. At the same time, the number of dairy cows has decreased from a high of 25 million around the end of World War II to fewer than nine million today. This is an indisputable environmental win as fewer cows create less methane, a potent greenhouse gas, and require less land. . .

. . . While we may worry about the use of antibiotics to stimulate animal growth or the use of hormones to increase milk production by up to 25 percent, most of the increase in the pounds of milk an animal puts out over the pastoral days of yore come from the genetic changes that we’ve wrought within these animals. It doesn’t matter how the cow is raised — in an idyllic pasture or a feedlot — either way, the animal of 2012 is not the animal of 1940 or 1980 or even 2000. A group of USDA and University of Minnesota scientists calculated that 22 percent of the genome of Holstein cattle has been altered by human selection over the last 40 years.

In a sense that’s very real, information itself has transformed these animals. The information did not accomplish this feat on its own, of course. All of this technological and scientific change is occurring within the social context of American capitalism. Over the last few decades, the number of dairies has collapsed and the size of herds has increased. These larger operations are factory farms that are built to squeeze inefficiencies out of the system to generate profits. They benefit from economies of scale that allow them to bring in genomic specialists and use more expensive bull semen.

No matter how you apportion the praise or blame, the net effect is the same. Thousands of years of qualitative breeding on family-run farms begat cows producing a few thousand pounds of milk in their lifetimes; a mere 70 years of quantitative breeding optimized to suit corporate imperatives quadrupled what all previous civilization had accomplished. And the crazy thing is, we’re at the cusp of a new era in which genomic data starts to compress the cycle of trait improvement, accelerating our path towards the perfect milk-production machine, also known as the Holstein dairy cow.

ADDENDUM – 6 June 2015

Lastly, I think one of the things that becomes blindingly obvious from both pieces is how carefully all the input and health markers for these animals are recorded and monitored. The idea that the addition of biotech crops into their feed could be producing adverse health outcomes that have somehow evaded notice is preposterous. Unsurprisingly, when three decades of this data was reviewed, a complete absence of any problems was exactly what they found.

A new scientific review from the University of California, Davis, reports that the performance and health of food-producing animals consuming genetically engineered feed, first introduced 18 years ago, has been comparable to that of animals consuming non-GE feed.

The review study also found that scientific studies have detected no differences in the nutritional makeup of the meat, milk or other food products derived from animals that ate genetically engineered feed.

The review, led by UC Davis animal scientist Alison Van Eenennaam, examined nearly 30 years of livestock-feeding studies that represent more than 100 billion animals.

When it comes to the potential adverse effects that current biotech crops could have on birds or mammals, the argument that “We just don’t know” just doesn’t hold any water.


Study Of 1.5 Million Cows Shows Daughters Get More Milk Than Sons

Ed Yong | Phenomena | National Geographic | 23 January 2014

The Perfect Milk Machine: How Big Data Transformed the Dairy Industry
Alexis C. Madrigal | The Atlantic | 1 May 2012


An Evolutionary Whodunit: How Did Humans Develop Lactose Tolerance?

Helen Thompson | The Salt | NPR | 28 December 2012

10 Things You Didn’t Know About Bull Semen

Brian Cathcart | The Independent | 9 June 1996

Creating Tastier and Healthier Fruits and Veggies with a Modern Alternative to GMOs
Ferris Jabr | Scientific American | 23 January 2014

No sign of health or nutrition problems from GMO livestock feed, study finds
UC Davis | 25 September 2014

Prevalence and impacts of genetically engineered feedstuffs on livestock populations
Van Eenennaam and Young | Journal of Animal Science | 20 November 2014

Ferris Jabr | Scientific American | 23 January 2014