Oct 21, 2015

Breeding techniques will improve in the search for superior traits

As part of its Grow Ahead: The Future of Fruits & Vegetables series, Fruit Growers News questioned several fruit breeders about what their trade might look like 50 years or even 100 years from now, what fruit traits their future colleagues might be looking for and the breeding techniques they might use to find them.

The responses were numerous and wide-ranging. Edited (and sometimes paraphrased) versions are below.

John Clark, University of Arkansas. I continue to believe that the optimum selection of the diversity of characters needed in a successful variety must be identified by someone experienced and trained in the art of plant breeding. I don’t think breeders will be replaced with only molecular or other breeding methods used to develop varieties. The plant will continue to be evaluated in the environment in which it is to be grown; there are simply too many variables to account for otherwise.

However, methods used in plant breeding are rapidly changing. I have been enlightened in the value of molecular methods to increase precision and efficiency in breeding. My training and practice has been entirely in “classical” breeding, generally described as a system where plants with complementary traits are hybridized to create offspring with one or more characters improved, and occasionally improved enough to become a variety.

Our peach breeding program is incorporating molecular methods. I use molecular markers to more precisely choose parents in crossing. I use this information in addition to relying solely on looking at the tree or examining its parents. I can also discard a seedling at the small-plant stage of growth, by identifying plants that are susceptible to bacterial spot, soft-fruited or have other shortcomings – this all determined when the tree is 6-12 inches tall, not 3 or 4 years old.

Further, the characterization of genetic diversity using molecular methods will be more and more valuable to breeders. As we use molecular markers to identify traits present in material that might be in some other breeding program, or a germplasm repository, this can accelerate breeding progress. Genetic diversity remains the foundation of crop improvement, and anything that helps in identifying or expanding diversity will lead to more great discoveries.

In the next 50 years, new methods of creating diversity will be utilized. I hear a lot about “gene editing” these days, a method to more precisely alter genetic sequences, and one that does not use the older transformation methods that have created so much fear and concern. “Precision breeding” is talked about, again a category of genetic manipulation that is much different than transformation. There are multitudes of smart people working in this area. They will create new magic, and breeders will be able to utilize these new discoveries. But someone will still need to ease out in the sun, examine these genetic improvements, be able to spot the good ones and move them into growers’ hands as a new variety.

Quality will continue to move further up the line as a requirement for a new variety release. Flavor will lead the way. Plant adaptation will expand as a trait. Plant architecture will continue to get more and more attention. As we consolidate production in closer spaces, using smaller plants that require less area and less labor to manage, many growing in substrate culture, all will lead to a major change in how many of our high-value crops are grown.

Jim Luby, University of Minnesota. One hundred years from now? I have no idea! Consider this: 100 years ago Mendel’s early pea genetics studies had just been rediscovered, and fruit breeders were debating whether they had any relevance to fruit breeding.

Fifty years from now I think we will be breeding based on more complete information on biological pathways in the plants and on how plants interact with other organisms, pathogens, soil, flora, etc. Genetic and physiological information will be very cheap to obtain thanks to advances in functional human medicine.

We will likely still be making crosses but will be choosing parents and progeny with much more knowledge at the genetic and epigenetic levels. New techniques for non-transgenic gene manipulation or “editing” in plants will enable some creative new approaches to combining parents and altering established cultivars.

Fruit will still have appeal to consumers – appearance, aroma, taste, texture. We will have enhanced technology to identify and test for these traits, but someone will still need to taste the fruit!

Breeding for traits and technology that maximizes return from human labor will continue to be important. We can’t even know which diseases and pests will become important in 50 years. Some of them will need genetic solutions in terms of host plant resistance.

Jim Hancock, Michigan State University. The traits fruit breeders look for will never change: productivity, climate and soil adaptation, disease and pest resistance, fruit size, firmness, storability and taste. There will be a much greater emphasis on breeding cultivars that perform well in the hotter and more variable environments that will be associated with climate change. Probably every variety will need to be mechanically harvested.

We are on the cusp of what fruit breeding will look like in 50 years. Nothing will be planted in the field for selection unless it has diagnostic DNA markers for key traits of interest. It will not be long until we are using dozens of these to select parents and cull undesirable progeny, and in 50 years we will likely have hundreds or thousands. This means we will only plant those hybrids in the field that are likely to carry the traits of interest, allowing us to focus better on the traits we do not have diagnostic markers for.

I suspect through genomics that we will have a better understanding of what genes control our traits of interest, and we will be able to modify those genes specifically and incorporate them into elite types through genetic engineering technologies. We might also be able to more effectively screen wild germplasm for useful variants that would aid in our breeding efforts. Thus, we can take our very best cultivars and make them better in a controlled, step-by-step process, and not have to screen thousands of progeny to identify hybrid plants with small improvements.

It is my guess that 100 years from now, we will be using the same techniques as 50 years in the future, but will have more complete knowledge on which genes do what. Also, systems will be developed to extract and analyze the DNA of progeny in seconds.

Having said all this, I doubt that fruit breeders will ever completely abandon making crosses and growing progeny in the field. It is doubtful that in 100 years we will have complete understanding of every gene’s function and interactions.

Neal Carter, Okanagan Specialty Fruits. Now that we have next-generation whole genome sequencing and it is cheap and quick to do, things are going to start to go faster. Plus, an increasing number of plant genomes are now sequenced and their libraries are becoming fairly well annotated – so more and more we know which sequences do what and how.

In 30 years, I believe we will have the DNA editing tools to routinely insert and/or remove DNA sequences in a plant at will. This means we will be able to crank out new events for proof of concept testing quickly and efficiently. Commercial products will flow in far greater numbers from this work. Traits like salt tolerance, drought tolerance, nitrogen fixation, nutritional enhancement, self-fertility and a host of others are all likely to be targeted. Many of these are in the lab now, but solutions will become more robust and they will be moving into additional crop varieties.

I am sure new technologies will continue to be introduced with the goal of being able to modify traits in plants through the changing of a single nucleotide. This is already being done, but it will become much more routine.

Marker-assisted conventional breeding will continue, but it will morph into other new forms of conventional breeding that use molecular biology tools. There is going to be a convergence of technologies, and their boundaries will be much grayer than today.

Kate Evans, Washington State University. I suspect that breeders will have incorporated rapid cycle (fast track) breeding, and so will be much more willing and likely to introduce diverse germplasm to target specific traits, and that “conventional” breeding and GM technology will be fully integrated. Obviously, a full suite of DNA-based tools for selection will be available, too.

We will need tree fruit that are fully adapted to mechanization in the orchard – in terms of how the fruit is presented on the tree, plus ease of detachment.

Other key traits: more sugar, improved water-use efficiency, full suite of disease and pest resistance, plus improved light harvesting and nutrient partitioning. All for more fruit from less inputs, and achieved using a combination of breeding and GM.

Chad Finn, Agricultural Research Service. On one hand, breeding will be exactly what it is now. While that makes it sound like I am a Luddite, I would argue plant breeding has always involved growing out plants and having someone with a discerning eye look at them – and that person with the discerning eye has used the most cutting-edge, practical tools. In the past, that might have been cytology, in vitro technology, transgenics – and currently the rapidly changing field of genomics. So looking to the future, we still need to have people with discerning eyes looking at plants but using the best technology.

What traits will breeders be looking for?
 Anything related to reducing costs, reducing labor inputs, increasing efficiency of inputs and increasing yield and increasing quality.

What techniques will they use to find them? They will continue to fine-tune -omics (genomics, proteomics, metabolomics), in concert with a better understanding of what these -omics are identifying in the plants.

Amy Iezzoni, Michigan State University. Fruit breeders will continue to prioritize fruit quality but will be able to develop cultivars that also have high-priority traits such as disease resistance and resistance to temperature stress. Breeding will be more efficient, as breeders will be able to rely more on the use of DNA tests to predict progeny performance. This should translate into a faster rate of superior cultivar release.

Breeders will take advantage of technological innovations to make phenotyping more efficient and accurate. This will include hand-held or robotic data recording and imaging devices. New cultivar releases will be accompanied by management recommendations that will be based on the cultivar’s gene expression profiles.

Phil Stewart, Driscoll’s. One hundred years is a long way out, but I think we’ll see an increase in the role played by molecular techniques. In the past, it was like trying to perfect something you’re cooking but you couldn’t look at the recipe. You could only look at the outcome. You stumble around because you can’t see what’s going on at the genetic level. As sequencing gets better, marker technology will be as much a part of what we do as walking the field and tasting fruit. We will always do that, but will be more split between lab and field.

In the near term, gene mapping and markers will take on more importance. In 50 years it will be a given. You will know the sequence of every selection in your program, will be designing cultivars – which set of genes in which combination.

One hundred years from now, we could be blurring boundaries between species – questioning what we think is a strawberry, completely outside our range of current assumptions.

Gene-editing techniques will be important. Instead of making crosses, it will be a more directed process: conscious choices about which specific allele we want, or to change one part of one variety.

One hundred years from now, we will see less emphasis on timing traits. It will be a given that you can have more or less whatever supply of fruit you want whenever you want it. Fruit crops historically have been rare seasonal things, enjoyed for a few weeks in a specific region. Now they’re nationwide things, and we’re still grappling with that transformation. We worry less about getting enough fruit in a particular week and more about competing for market share within the vast space of crops available to people. Because of that, breeders like me must make strawberries (for example) good enough to make people want them.

We will never get away from disease-resistance breeding. We’re locked in an endless battle, and if anything the chemical options are getting worse.

I predict the continuing rise of private breeding programs, but I hope public programs continue to play a role. Those are important to the industry. They lower the barriers to entry and keep the industry dynamic, creative and competitive. But there’s good work going on in the private side. There are a lot of reasons why private programs have thrived. They’ve done some cool things.

Marion Wood, The New Zealand Institute for Plant & Food Research. As plants grow and develop, constantly adjusting and responding to a diverse range of stimuli, information via specific signals is passed from cell to cell, tissue to tissue. Understanding and tapping into this information superhighway is the challenge of future breeders. With the advent of miniaturization of experimental setups down to the nano- and pico-range, automated minuscule non-destructive sampling techniques and the wealth of genomic and proteomic knowledge identifying “-omic fingerprints” of elite breeding lines based upon these profiles, under a range of growth conditions, will become feasible. This “-omic fingerprint” will not only allow the breeders to determine the profile of the future fruit long before the parental plant has reached maturity, but can be used as a handheld screening tool by growers to maximize the plant’s fruit potential by modifying growth regimes in response to ever-changing growth conditions.

Bart Janssen, The New Zealand Institute for Plant & Food Research. There are two ways of looking at fruit breeding in 50 years. The first and easiest to digest is to think conservatively, imagine progressive improvements in classical breeding methods, breeders making crosses in the field, using modern methods to assess those crosses for genes and traits and then planting out a group of progeny and selecting the best ones. That’s how breeding has worked for 10,000 years. The assessment methods get a bit better with each generation, but the fundamentals remain the same. Under that model, an apple will still be an apple and taste fundamentally applish. It’s likely the breeder will use handheld sequencers to select parents and progeny, trees will be constantly monitored during growth, fruit will be measured instantly for desirable traits using non-invasive techniques. Everything will happen faster, but a breeder now will still probably understand what is going on.

But there’s another way of looking at it. In 50 years, we will understand genetic regulation of any pathway we care to examine, we will know exactly how a tree controls every aspect of fruit development and we will use genetic techniques to maximize every step required, with precision. We will use analytical tools to confirm that changes made are exactly the changes intended. Those tools exist today in primitive forms, but in 50 years they will be ordinary. In that environment, a fruit breeder is nothing like the breeder of 10,000 years ago. They will be guided by consumer desires and needs and will select developmental and biosynthetic modules from multiple organisms to create exactly what is needed. They may choose to make something that looks like an apple, but is exactly spherical, ripens on a specific date, contains a perfect balance of nutrients for a 7-year-old child and lasts exactly 12 days on the market shelf. They will assemble the elements they need and engineer the plants directly in the lab growth chamber. Analytical tools will confirm the changes made are exactly as planned, and the plants will be shifted to a greenhouse, where they will be checked by the regulatory authorities to confirm safety. By the time the plants are producing fruit in the field, breeders will be filling the next custom-designed fruit order.

– Matt Milkovich