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Building New Hybrids: Opportunities & Challenges

Monday, January 2, 2012
filed under: Research and Development

The Fargo, N.D.-based USDA-ARS Sunflower Research Unit (now reorganized as the Sunflower and Plant Biology Research Unit) has a long history of basic research generating important contributions to the nation’s sunflower industry. For decades, this research group — encompassing the disciplines of botany, entomology, plant pathology, plant breeding, cytogenetics, molecular genetics and biochemistry — has striven to aid the industry through the development and release of elite sunflower germplasm, which then can be accessed by commercial breeders as they work to develop ever-better hybrids for planting by farmers.

The Sunflower has carried numerous articles over the years describing the objectives and accomplishments of USDA-ARS sunflower scientists. In the January 2011 issue, for example, we carried “Update on SNP,” a discussion on the high-tech system (single-nucleotide polymorphism) that facilitates detailed analysis of breeding population traits early on in the breeding process. That, in turn, speeds up the parental selection and breeding line development schedule, thus contributing to faster production of new hybrids.

That January article followed an introduction to the SNP topic in the August/ September 2010 issue of The Sunflower. Both articles featured explanations and commentary from Brent Hulke, USDA-ARS sunflower research geneticist. Hulke has been a central figure in the exploration of SNP’s potential benefits for sunflower breeding and in the construction of the program for its use in his lab and by commercial breeders.

Other articles in recent years have looked at ARS advances in screening and selection for improved tolerance/resistance to such key diseases as Sclerotinia head and stalk rot, Phomopsis, Verticillium wilt, rust and downy mildew. We’ve also highlighted ARS entomologists’ efforts, in concert with university specialists, to locate and incorporate tolerance to important sunflower insects like the seed weevil and stem weevil. Most recently, in our December 2011 issue, we reported on the use of wild sunflower species in the search for improved resistance to Sclerotinia.

The contributions of USDA-ARS sunflower scientists, past and present, have played a critical role in the development of new hybrids required to keep this crop profitable for growers and competitive with other crops. This month, we thought, why not ask those “closest to the action” — commercial sunflower breeders — for their perspective on the value of the ARS program and for their thoughts on other topics related to the hybrids, present and future, planted by the nation’s sunflower growers.

Presented below are summaries of answers received from five prominent sunflower breeders. Because some of them preferred not to identify their company in this article, we are referring to them here simply as Breeder A, Breeder B, etc. We thank them for their candid insights.

— Don Lilleboe

Much of the material that USDA has recently released — or will be releasing in the near future — revolves around improved disease resistance or tolerance. Is this material easily integrated into your program? Are there more disease resistance resources that you can utilize beyond USDA releases?

Breeder A — It depends upon inheritance of the trait. Releases with Sclerotinia tolerance are nearly impossible to use in breeding programs due to the fact that the tolerance is conferred by many genes, and accurate screening is difficult. In addition, the releases have not been “elite” in terms of yield potential and other agronomic traits. Mapping of multi-genic traits is difficult and has not, to date, been successful in a practical breeding program.

Some traits, such as downy mildew resistance, are almost a “must have” due to less-than-perfect control by currently registered fungicides. Any disease that can limit yield or quality needs to be addressed by breeders.

There is material available from other public institutes globally, and the USDA germplasm collection can be used. In addition, wild species in production areas can be sources of resistance genes.

Breeder B — Disease resistance is one of our primary breeding goals. The USDA disease-resistant material has been very useful for this. We have also obtained resistant material from companies in other countries through cooperative agreements.

Breeder C — We have used USDA-released lines, recent and past — especially for downy mildew resistance. It is easily integrated into our oilseed program; but since it is always oilseed-based, not so easily integrated into the confectionery program. Recovering an acceptable confectionery line from a cross that integrates disease resistance from an oil line takes more time and more backcrossing to recover the confection type. It would be great to also have USDA-released confectionery germplasm with improved disease resistant traits.

USDA-released lines have been helpful for Sclerotinia head and stalk rot and, more recently, Phomopsis.

Breeder D — Confection breeders have the challenge of taking the new lines/ traits of interest that typically have been very small [oil-type] black seed into something large and long for the confection market. This takes several generations of backcrossing, screening and selecting. With quantitatively inherited traits, by the time the seed is in a useable form for the confection market, the trait of interest often is either diluted or nonexistent.

This is where the SNP program becomes critical. It is very difficult to combine a disease package to include all the other confection market traits that are needed, i.e., high yield, long seed, large seed (most over 22/64), good color, good kernel size, good flavor, a seed coat that does not scruff, and good plantability. To be able to define, locate and consistently bring traits of interest into new populations, without the need to screen at each generation, will greatly accelerate the breeding process.

Currently, USDA-ARS has been working on incorporating confection-type seed into its future germplasm releases. This will be a big benefit, to not have to start the breeding process from scratch with each new release.

USDA-ARS has done an excellent job of “defining the enemy.” With new races of downy mildew, Phomopsis, etc., they have been very proactive at defining the races we are up against and looking for better sources of resistance that can be incorporated. Once we have defined SNP markers that will enable us to stack multiple known sources of resistance for a particular disease and confidently bring them forward into new populations, hopefully our tolerance will not only be better but also last over a longer period of time.

Breeder E — We have actively bred with disease-tolerant materials released by the USDA for many years. Integration would be facilitated if novel disease resistance genes were presented in more elite and competitive inbreds along with a molecular marker to track the trait in our breeding programs. As it stands, lack of good phenotypic screening to track resistance in breeding populations makes it difficult to extract value, and robust molecular markers would help alleviate this issue.

Yield and quality are obviously paramount in the development and release of new commercial varieties. What challenges or “baggage” does inserting disease resistance into elite material present to you? Is there an automatic yield drag?

Breeder A — A lot depends on the genetic base of the resistance sources. Wild species donors present significant challenges in introgression. We have had issues with linkage drag for oil content, maturity, seed color and other traits when working with single-gene resistance sources — and even when using markers.

Breeder B — It all depends on the quality of the source material. I have made test hybrids using USDA-released material directly as one of the parents and have seen good yield and quality data. Other releases have not shown similar good results.

Breeder C — No, there is not always an automatic yield drag when inserting disease resistance — especially for more simply inherited traits like downy mildew and rust resistance. We sometimes see yield drag for some disease resistance traits, such as Sclerotinia stalk and head rot and Phomopsis — especially when growing conditions are optimal and the disease is not present.

Breeder D — I think the gap in yield between the oil and confection hybrids is narrowing a bit. Market demand for confection hybrids has put more focus on confection breeding efforts that have contributed to better agronomics as well as size.

Breeder E — Integrating disease resistance alleles into elite germplasm can result in yield drag, particularly if the source material is not elite, is derived from wild species or occupies an unfavorable heterotic pool. Yield drag is not automatic. In fact, good disease tolerance serves to enhance yield performance in environments where disease pressure can negatively impact agronomic performance.

Which diseases are of paramount interest to you in your variety development program for the U.S. market?

Answers from the breeders were quite similar on this question. Sclerotinia head rot, Sclerotinia stalk rot, rust, Phomopsis and downy mildew consistently made the list, with Verticillium also noted by some of the breeders.

Has the evolvement of SNP systems and other molecular genetics systems allowed breeders to “bypass” the yield-drag issue? Will SNP accelerate your ability to add genes in a timely manner?

Breeder A — Markers help, but they do not eliminate the issue. Molecular markers can significantly help introgression of traits by reducing linkage drag and selection for background recovery, resulting in faster conversions. But breeders still must test converted material extensively to determine the extent of yield drag that may be present. We have been using SNP with good success.

Breeder B — Even with SNP technology, there still may be yield drag. Hopefully, SNPs will positively identify that the genes for various resistances exist in given lines; but one still must make the crosses to incorporate the resistance genes into elite parent lines, and other inferior genes may be “dragged” along.

Backcrossing could be used to eliminate these inferior genes. Only some form of single-gene transfer would totally eliminate dragging these inferior genes along with the resistant genes. But this, of course, means GMO sunflower.

SNP technology will definitely be useful, as it will let the breeder know that he has material with a given resistance. Doubled-haploid technology [also] would definitely speed up the breeding in sunflower.

Breeder C — Logic says SNP will allow us to bypass yield-drag issues, but the project isn’t far enough along to know for sure.

Yes, SNP and markers will speed up our ability to incorporate specific genes quickly and more efficiently, with fewer mistakes, during the selection process.

Breeder D — (See answer to first question.)

Breeder E — Molecular marker profiling can help, particularly if the region containing the disease resistance locus is highly saturated with SNPs. In this case, breeders can select for SNPs that are close to or within the disease resistance gene and away from SNPs located outside the resistance locus. Doing this allows the breeder to pull along the favorable genes while minimizing the presence of unfavorable genes in elite breeding populations. SNPs will definitely accelerate trait integration efforts.

Will you be introducing hybrids that are not herbicide resistant?

Breeder A — The goal would be to have herbicide tolerance in nearly all hybrids, assuming the trait being used has no negative impact on the hybrid.

Breeder B — Herbicide resistance is not that important for our primary market (foreign). But herbicide-resistant hybrids remain one of our breeding objectives.

Breeder C — We learn “never to say never.” But at this time we are geared toward all new hybrids having herbicide resistance.

Breeder D — With the ever-changing dynamics of growing sunflower, I think we will need to continue to pursue all areas — whether Clearfield®, Express®, traditional or something new. Providing more options to growers will only benefit the industry in the long term.

Breeder E — Not in the foreseeable future.

Average yields in the U.S. continue to increase annually. In your view, what is the top-end yield potential of today’s sunflower hybrids? In five years?

Breeder A — I would guess 4,000 lbs/ac may be possible today in ideal conditions. I don’t see that changing much in five years, especially if producers demand that breeders continue to focus on incorporating disease and/or herbicide traits. Doing so does take away resources that could have been used to breed for increased yield potential in base genetics.

Breeder B — I could not put a number to yield potential of hybrids, as so much depends upon environmental factors. I do believe sunflower will continue to make progress toward higher yields, but at a slower rate than in the past. I also believe higher yield potential will be the result of developing improved cultural practices as well as through breeding efforts.

Breeder C — In trials, top-end yields are sometimes 3,500 to 4,500 lbs/ac. Top-end farmer-grown yields are usually in the 2,500-3,000-lb range. There’s room for improvement. I think yields can be improved by 300-500 lbs/ac in the next five years.

Breeder D — During a favorable growing season, it is not uncommon for growers to report 3,000-plus lbs/ac. With the incorporation of better disease resistance, etc., we need to strive toward yield stability under high disease pressures rather than increasing peak yield. Most growers would prefer a consistent 2,000 lbs/ac, rather than 3,000 lbs one year and 1,000 the next year with the drop in yield due mainly to disease.

Breeder E — Top end now is roughly 3,000 lbs/ac. In the future, I would expect to see significant improvements to the top end. Many growers currently don’t realize the yield potential of their sunflower acres because they don’t manage the crop for yield. The growers who do manage for yield are achieving very impressive results. But this requires more inputs, scouting and active management.
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