Plant Breeding in the 21st Plant Breeding in the 21st CenturyCentury

P. Stephen Baenziger and Soleman AlP. Stephen Baenziger and Soleman Al--OtaykOtaykUniversity of Nebraska & AlUniversity of Nebraska & Al--QassimQassim UniversityUniversity

P. Stephen BaenzigerP. Stephen Baenziger•• B. A. from Harvard UniversityB. A. from Harvard University•• M.S. and Ph.D. from Purdue UniversityM.S. and Ph.D. from Purdue University•• EmploymentEmployment

–– USDAUSDA--ARS: 1976ARS: 1976--19831983–– Monsanto:Monsanto: 19831983--1986 (continue to own 1986 (continue to own

stock)stock)–– University of Nebraska: 1986 to presentUniversity of Nebraska: 1986 to present

The opinions given in this talk represent my views and The opinions given in this talk represent my views and not those of any institution, organization, or committee not those of any institution, organization, or committee upon which I serveupon which I serve. .

Small Grains Improvement TeamSmall Grains Improvement TeamGenetics:Genetics: Entomology:Entomology:Bob Graybosch, USDABob Graybosch, USDA--ARSARS Gary HeinGary HeinIsmail DweikatIsmail Dweikat Ming Chen, USDAMing Chen, USDA--ARSARSGuihua Bai, USDAGuihua Bai, USDA--ARSARSKulvinder Gill, WSUKulvinder Gill, WSU Cropping Systems:Cropping Systems:

Drew LyonDrew LyonPlant Pathology:Plant Pathology: Bob Klein, Charles ShapiroBob Klein, Charles ShapiroStephen WeguloStephen WeguloRoy French, USDARoy French, USDA--ARSARS EndEnd--use Quality:use Quality:Yue Jin, USDAYue Jin, USDA--ARSARS Lan XuLan Xu

Brad Seabourn, USDABrad Seabourn, USDA--ARSARSVariety Testing:Variety Testing:Len NelsonLen Nelson Biometry:Biometry:

Kent EskridgeKent EskridgeTransformation:Transformation: Walt StroupWalt StroupTom ClementeTom Clemente Ken RussellKen Russell

Small Grains Improvement TeamSmall Grains Improvement Team

Modeling:Modeling:Al WeissAl WeissWally WilhelmWally WilhelmGreg McMaster (USDAGreg McMaster (USDA--ARS)ARS)

Triticale:Triticale:Lance Gibson (ISU)Lance Gibson (ISU)Ken Vogel (USDAKen Vogel (USDA--ARS)ARS)

Barley:Barley:My graduate studentsMy graduate students

Topics:

•• The need for plant breeding and crop The need for plant breeding and crop management.management.

•• The phases of plant breeding.The phases of plant breeding.•• Who will be the 21Who will be the 21stst century plant breeders?century plant breeders?•• Critical needs for future plant breeding and Critical needs for future plant breeding and

understanding how to use your resources understanding how to use your resources (competitive advantages).(competitive advantages).

The need for plant breeding and The need for plant breeding and crop management:crop management:

•• The demands on our food system will The demands on our food system will increase: increase: –– Increasing populationIncreasing population–– Increasing prosperityIncreasing prosperity–– To meet environmental needs To meet environmental needs

Increasing Prosperity:Increasing Prosperity:•• 800,000,000 people undernourished800,000,000 people undernourished----will will

change with income growth. change with income growth. •• For each 1% increase in real income, the For each 1% increase in real income, the

demand for wheat will increase 0.5%.demand for wheat will increase 0.5%.•• Increased wheat utilization is due 2/3 to Increased wheat utilization is due 2/3 to

population and 1/3 to income growth. population and 1/3 to income growth. •• Greater demand for meatGreater demand for meat----Already 35% of Already 35% of

world grain supplies are used for livestock world grain supplies are used for livestock productionproduction

Having the Tools vs. Having the Will:

Meeting Environmental Needs:•• Agriculture is often viewed as an enemy of the Agriculture is often viewed as an enemy of the

environmentenvironment----relies on pesticides, fertilizer, relies on pesticides, fertilizer, irrigation. irrigation. Yet intensive agriculture preserves land Yet intensive agriculture preserves land from being used for farming.from being used for farming.

•• Agriculture is the largest and most flexible Agriculture is the largest and most flexible managed ecosystem. It will be asked to remediate managed ecosystem. It will be asked to remediate the detrimental effects of human activities.the detrimental effects of human activities.

•• Future agriculture will rely more on genetics and Future agriculture will rely more on genetics and less on chemical inputs. less on chemical inputs.

Revolutions in Agriculture

•• FertilizerFertilizer•• Pesticides (herbicides, insecticides, Pesticides (herbicides, insecticides,

fungicides)fungicides)•• IrrigationIrrigation•• GeneticsGenetics

–– Hybrids (better in diploids than polyploids)Hybrids (better in diploids than polyploids)–– SemiSemi--dwarf cultivars for intensive managementdwarf cultivars for intensive management

Which of these revolutions will be Which of these revolutions will be available in the future?available in the future?

P = P = GG + + EE + + GxEGxEP = G + E + M + P = G + E + M + GxMGxM + GxE + + GxE + GxMxEGxMxE

Environment: Weather, tillage, pesticides, Environment: Weather, tillage, pesticides, irrigation, fertilizer, and prior history. It has both irrigation, fertilizer, and prior history. It has both a fixed and a random component. a fixed and a random component. Genotype: What Plant breeders are modify.Genotype: What Plant breeders are modify.Genotype x environment Interaction: How the Genotype x environment Interaction: How the genotypes respond to different environments.genotypes respond to different environments.

How will the next production gains be obtained? Have How will the next production gains be obtained? Have we reached the upper genetic limit (can genetic we reached the upper genetic limit (can genetic Improvement continue)?Improvement continue)?

Phases of Plant Breeding:Phases of Plant Breeding:

•• Introduction of genetic variationIntroduction of genetic variation•• Genetic segregation and selection ( may or Genetic segregation and selection ( may or

may not be accompanied by inbreeding) may not be accompanied by inbreeding) •• Evaluation and releaseEvaluation and release

Plant breeders will change their programs to do something which Plant breeders will change their programs to do something which they could not previously do or to do something they could they could not previously do or to do something they could previously do in a better way. previously do in a better way. Everything must be tempered by Everything must be tempered by finding your competitive advantage, your nichefinding your competitive advantage, your niche——which will differ.which will differ.

Introduce VariationIntroduce Variation

Segregation and SelectionSegregation and Selection

Evaluation and ReleaseEvaluation and Release

Traditional PlantTraditional PlantBreedingBreeding

Introducing Variation:Introducing Variation:

Introduce VariationIntroduce Variation

Segregation and SelectionSegregation and Selection

Evaluation and ReleaseEvaluation and Release

TransgenesTransgenes

Wide hybridsWide hybrids(embryo rescue)(embryo rescue)

Traditional PlantTraditional PlantBreedingBreedingAllied SciencesAllied Sciences

Mutations

Crop Transformation:Crop Transformation:•• Fundamental question is does a plant breeder have enough Fundamental question is does a plant breeder have enough

genetic diversity (variation) within those species and genetic diversity (variation) within those species and genera that can be hybridized with the crop of interest? genera that can be hybridized with the crop of interest?

•• According to James (2006), 100 million hectares were According to James (2006), 100 million hectares were planted to transgenic crops of which 54.6 million hectares planted to transgenic crops of which 54.6 million hectares were in the US. On a global basis, 57% of soybeans, 25% were in the US. On a global basis, 57% of soybeans, 25% of maize, 13% of cotton, 5% of canola, and 0% of wheat of maize, 13% of cotton, 5% of canola, and 0% of wheat and 0% of rice are transgenic.and 0% of rice are transgenic.

•• Are wheat and rice destined to become Are wheat and rice destined to become ““orphanedorphaned”” crops crops due to limited technology?due to limited technology?

http://www.isaaa.org/resources/publications/briefs/35/executiveshttp://www.isaaa.org/resources/publications/briefs/35/executivesummary/default.htmlummary/default.html

Variation Through Mutations:

S R S R1A.1R 1A.1R Translocation inTranslocation in‘‘CenturyCentury’’ WheatWheatXX--ray chromosomeray chromosomeBreakage.Breakage.Wenzel and Rayburn (2000)Wenzel and Rayburn (2000)

Imidazolinone-tolerance and wild typesusceptibility in wheat. Sodium azidemutagenesis.

Introduce VariationIntroduce Variation

Segregation and SelectionSegregation and Selection

Evaluation and ReleaseEvaluation and Release

Better assaysBetter assaysMarker assistedMarker assistedSelectionSelectionDoubled haploidyDoubled haploidy

Traditional PlantTraditional PlantBreedingBreedingAllied SciencesAllied Sciences

Segregation and Selection:Segregation and Selection:

•• Nothing is more efficient than visual selection Nothing is more efficient than visual selection when it can be used.when it can be used.

•• With the size of modern breeding programs, With the size of modern breeding programs, nothing is more necessary than visual selection.nothing is more necessary than visual selection.

•• There is a hierarchy of assays where you use the There is a hierarchy of assays where you use the easier, less expensive assays first, so fewer lines easier, less expensive assays first, so fewer lines have to be evaluated with expensive assays.have to be evaluated with expensive assays.

Marker Assisted Selection:Marker Assisted Selection:

•• Best use of technology: onBest use of technology: on--site or cooperativesite or cooperative•• Recommendation:Recommendation:

–– Small local effort for specific projects, especially for Small local effort for specific projects, especially for training.training.

–– Centralized labs for the large jobs. Needed for skilled Centralized labs for the large jobs. Needed for skilled personnel, and for higher quality and modern personnel, and for higher quality and modern equipment. Also, the equipment is becoming so fast equipment. Also, the equipment is becoming so fast that a few machines have enormous capacity. Also, it that a few machines have enormous capacity. Also, it is difficult for many individual programs to have the is difficult for many individual programs to have the latest equipment.latest equipment.

Fusarium head blight:Fusarium head blight:•• The disease assay is The disease assay is

difficult and time difficult and time consuming, usually consuming, usually done on flowering done on flowering wheat plants.wheat plants.

•• There are major There are major resistance genes, but resistance genes, but they often have to be they often have to be pyramided to give pyramided to give useful levels of useful levels of resistance. resistance.

•• Natural infections are Natural infections are not uniformnot uniform——maturity dependent maturity dependent

•• The major genes are The major genes are tagged with tagged with molecular markers.molecular markers.

Fusarium head blight: Breeding StrategyFusarium head blight: Breeding Strategy

•• Cross HRS/SRW//HRWCross HRS/SRW//HRW•• Two doses of hard textureTwo doses of hard texture•• Two doses of winter growth habitTwo doses of winter growth habit•• Can fix the FHB QTL or at least allow it to Can fix the FHB QTL or at least allow it to

more frequent in the 3 way cross.more frequent in the 3 way cross.•• Need to remove the spring growth habit lines Need to remove the spring growth habit lines

that are soft or low protein. Can be done in that are soft or low protein. Can be done in the Fthe F2 2 or For F33 generation using selection.generation using selection.

Stem Rust: Stem Rust: •• The disease assay is simple and quick, The disease assay is simple and quick,

usually done on seedlings.usually done on seedlings.•• There are major resistance genes, and are There are major resistance genes, and are

effective when used singly. Races change effective when used singly. Races change slowly or quickly (e.g. Ug99).slowly or quickly (e.g. Ug99).

•• Natural and artificial infections can be Natural and artificial infections can be induced in the field. induced in the field.

•• Many major genes are tagged with Many major genes are tagged with molecular markers.molecular markers.

Stem Rust: Breeding StrategyStem Rust: Breeding Strategy

•• Resistance is a critical trait. Excellent Resistance is a critical trait. Excellent germplasm is available.germplasm is available.

•• Cross Resistant by Resistant or R/S//R and Cross Resistant by Resistant or R/S//R and select in the Fselect in the F55 and thereafter seedling and thereafter seedling stage.stage.

•• Use race differentials or molecular markers Use race differentials or molecular markers to identify pyramided gene combinations.to identify pyramided gene combinations.

Understanding Grain YieldUnderstanding Grain Yield

•• Complex trait controlled by many genes.Complex trait controlled by many genes.•• Can be difficult to identify differences, Can be difficult to identify differences,

especially in relatively low yielding especially in relatively low yielding environments. Average grain yield for environments. Average grain yield for wheat in Nebraska is 2.5 t/ha.wheat in Nebraska is 2.5 t/ha.

•• Very large environmental effects.Very large environmental effects.•• Need very effective tools.Need very effective tools.

Effect of Wichita Chromosome s on Yield in Cheyenne Background

Wichita Chromosomes

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1A 2A 3A 4A 5A 6A 7A 1B 2B 3B 4B 5B 6B 7B 1D 2D 3D 4D 5D 6D 7D

Effect of Cheyenne Chromosome s on Yield in Wichita Background

-0.8

-0.6

-0.4

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1A 2A 3A 4A 5A 6A 7A 1B 2B 3B 4B 5B 6B 7B 1D 2D 3D 4D 5D 6D 7D

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Cheyenne Chromosomes

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Segregation of RFLP probe BCD907, in the RICLs-3A population of Wheat

= Polymorphic band

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Grain YieldGrain Yield

Chromosome 3AChromosome 3A

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0.0 8.8 22.8 36.6 48.7 58.5 70.7 83.7 97.7 106.4 120.0

CombinedLincoln 1999Lincoln 2000Lincoln 2001Mead 2000Mead 2001Sidney 2001Average Significance Threshold

RR22 = 28.1% A.E. = + 66 kg ha= 28.1% A.E. = + 66 kg ha--11

WI genotype adds 132 kg haWI genotype adds 132 kg ha--11

Region 1Region 1 Region 2Region 2

Region 3Region 3

Region 4Region 4

QTL RegionsQTL RegionsXb

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Region 5Region 5

GYLD GYLD KPSMKPSM

Change in MagnitudeChange in MagnitudeXBARC67 -GYLD

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

-2.00 -1.50 -1.00 -0.50 0.00 0.50 1.00 1.50Environmental Index

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CNN alleleWI alleleLinear (WI allele)Linear (CNN allele)

Crossover InteractionCrossover InteractionXCDO549 -PHT

90

95

100

105

110

115

120

125

130

-15.00 -10.00 -5.00 0.00 5.00 10.00 15.00 20.00 25.00Environmental Index

Plan

t Hei

ght (

cm)

CNN alleleWI alleleLinear (WI allele)Linear (CNN allele)

KPSM vs. GYLD at Xbarc67

y = 0.0002x + 1.095R2 = 0.632R = 0.83**

3.00

3.10

3.20

3.30

3.40

3.50

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9000 9500 10000 10500 11000 11500 12000

KPSM

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WI ALLELE

CNN ALLELE

Coefficient0.20 0.40 0.60 0.80 1.00

Windstar Alliance Scout66 Cheyenne(CNN) WI(CNN3A) CNN(WI6A) CNN(WI6A) WI(CNN3A) Wesley Eagle Cougar Scout66 Bennett Colt Agate Brule Homestead Heyne Arapahoe Culver Harry Wichita(WI) CNN(WI3A) CNN(WI3A) WI(CNN6A) WI(CNN6A) Turkey Sentinel Nuplains Jagalene Trego Vista Millennium Arlin Buckskin Hondo Centurk78 Centurk Centurk HiplainsAlsen Pronghorn Goodstreak Nekota Sage Wahoo Rawhide Warrior Baca Siouxland Scoutland Lancota Cody Capitan NE96623 Niobrara Akron Betty NE96628 Jagger

Fig 5

CNN

WI

New Allele

Selection Techniques:Selection Techniques:

•• The importance of selection seems to becoming The importance of selection seems to becoming less researched and less understood. less researched and less understood.

•• Natural Selection and selection nurseriesNatural Selection and selection nurseries•• Cropping systems and optical sorting.Cropping systems and optical sorting.

•• The question is one of opportunity costsThe question is one of opportunity costs-- What What technologies are we giving up for those we are technologies are we giving up for those we are accepting? Also, one technology is not right for accepting? Also, one technology is not right for everyone.everyone.

Sorting bins

NIR spectrum collected here

Vacuum wheel for picking up single kernels

4-way kernel sorter

Bin for unsorted kernels

Optical Kernel Sorting:Optical Kernel Sorting:

Segregation and Selection:Segregation and Selection:

Evaluation and Release:Evaluation and Release:

•• Cropping systems: Crops have to evaluated Cropping systems: Crops have to evaluated in the manner to which they are to be in the manner to which they are to be grown.grown.

•• Biometry: Statistical approaches to identify Biometry: Statistical approaches to identify differences. More efficient designs allow differences. More efficient designs allow better evaluation (nearest neighbors, alpha better evaluation (nearest neighbors, alpha lattices, etc.)lattices, etc.)

•• Modeling: Will allow the trial data from a Modeling: Will allow the trial data from a limited number of tests to be extrapolated to limited number of tests to be extrapolated to other environments.other environments.

The effect of drought: Field VariationThe effect of drought: Field Variation

The effect of snow cover: Field VariationThe effect of snow cover: Field Variation

Hybrid Crops: WheatHybrid Crops: WheatHybrid wheat is grown in India, SouthHybrid wheat is grown in India, SouthAfrica, and Australia.Africa, and Australia.

Seed costs and the lower levels of heterosisSeed costs and the lower levels of heterosisare major limitations to hybrid wheatare major limitations to hybrid wheatadoption.adoption.

Though considerable effort has been made onThough considerable effort has been made onCHA, CMS systems appear to be the most CHA, CMS systems appear to be the most efficacious and reliable. Restoration has beenefficacious and reliable. Restoration has beena problem.a problem.

All testing is done at All testing is done at ½½ the pureline seeding rate. This cuts the the pureline seeding rate. This cuts the seed costs in half.seed costs in half.

Hybrid Crops: WheatHybrid Crops: Wheat

CMS FemaleCMS Female

Multiple OvaryMultiple Ovary

Experimental hybridsExperimental hybrids

Hybrid production fieldHybrid production field

Critical Needs for 21st Century Plant Breeding: FearlessPredictions

Critical Needs for 21st Century Plant Breeding

•• Have we reached our upper genetic limit? Have we Have we reached our upper genetic limit? Have we reliable cropping systems to allow breeders to select for reliable cropping systems to allow breeders to select for higher yield?higher yield?

•• Can we better identify the worldCan we better identify the world’’s agroecological zones to s agroecological zones to foster germplasm exchange among similar zones?foster germplasm exchange among similar zones?

•• Need a global consensus on the appropriate use of Need a global consensus on the appropriate use of technology.technology.

•• Need publicNeed public--private partnerships to benefit all in plant private partnerships to benefit all in plant breeding. The public sector need to rebreeding. The public sector need to re--evaluate how it evaluate how it deploys its resources so as not to duplicate the private deploys its resources so as not to duplicate the private sector research and to address the great problems affecting sector research and to address the great problems affecting our crop productivity (e.g hybrid wheat or nonour crop productivity (e.g hybrid wheat or non--hybrid hybrid maize).maize).

... a good past is positively dangerous ... a good past is positively dangerous if it makes us content with the present if it makes us content with the present and unprepared for the future.and unprepared for the future.

Charles EliotCharles Eliot

Thank YouThank You