Plant Breeding – an Overview

Plant Breeding –an Overview

Objective 1: know basic plant genetics and breeding terminology

Gamete A mature reproductive cell that is specialized for sexual fusion

Haploid (n) Containing only one set of chromosomes (n). Each gamete is haploid

Cross A mating between two individuals, leading to the fusion of gametes

Diploid (2n) Two copies of each type of chromosome in the nuclei, formed by the fusion of two gametes

Zygote The cell produced by the fusion of the male and female gametes

Gene The inherited segment of DNA that determines a specific characteristic in an organism

Locus The specific place on the chromosome where a gene is located

Alleles Alternative forms of a gene

Genotype The genetic constitution of an organism

Homozygous An individual whose genetic constitution has both alleles the same for a given gene locus (eg, AA)

Heterozygous An individual whose genetic constitution has different alleles for a given gene locus (eg, Aa)

Homogeneous A population of individuals having the same genetic constitution (eg, a field of pure-line soybean; a field of hybrid corn)

Heterogeneous A population of individuals having different genetic constitutions

Phenotype The physical manifestation of a genetic trait that results from a specific genotype and its interaction with the environment

What is Plant Breeding?What is Plant Breeding?

The genetic adjustment of plants to the The genetic adjustment of plants to the service of humankind service of humankind

---Sir Otto Frankel---Sir Otto Frankel

Source: http://www.ars.usda.gov/is/graphics/photos/

Objective 2: know why plant breeding is important and useful

Several examples in soybean

Increased global human population (shown here in billions of people) will lead to increased demand for food, fiber and energy: improving

plant genetics is one tool

0123456789

10

1950 1970 1990 2010 2030 2050

Adapted from http://www.census.gov/population/popclockworld.html

Why Plant Breeding

1. Yield

Source: USB photo disc 0976

Plant Breeding Targets

Plant breeding has contributed to more than 50% of increased USA crop productivity during the last 30 years

Source: http://www.ars.usda.gov/is/graphics/photos/

Improved product quality

Source: http://www.ars.usda.gov/is/graphics/photos/

Plant Breeding Targets

H H

C C

HydrogenationH H

C C

H H

cis form

H

C C

H

saturated trans form

;

• Hydrogenation: flavor and oxidative stability

• Trans fats: health issues

• FDA label mandate

(Source: Wilson, 2004)

Soybean sudden death syndromeSoybean sudden death syndrome

Plant Breeding Targets3. Pest and Disease Resistance3. Pest and Disease Resistance

Joint Germplasm Release(Drs. Arelli, Pantalone, Allen, Mengistu)

USDA-ARS and USDA-ARS and Tennessee Agricultural Exp. Stn.Tennessee Agricultural Exp. Stn.

Release of Release of JTN-5303JTN-5303 Soybean Soybean

Resistant to multiple diseases:Resistant to multiple diseases:Soybean cyst nematode Soybean cyst nematode Sudden death syndromeSudden death syndrome

Stem cankerStem cankerFrogeye leaf spotFrogeye leaf spot

Charcoal rotCharcoal rot

4. Environmental Stress Tolerance 4. Environmental Stress Tolerance

Plant Breeding Targets

5. Ease of Management Deployment of transgenic traits (e.g., transfer of herbicide resistant genes in commercial varieties)

Plant Breeding Targets

6. Adaptation to Mechanization6. Adaptation to Mechanization

Source: http://www.ars.usda.gov/is/graphics/photos/

Plant Breeding Targets

Conservation Tillage

Source: http://www.ars.usda.gov/is/graphics/photos/

7. Environmental sustainability

Plant Breeding Targets

Objective 3: know the basic principles of plant breeding

Importance of genetic variation and selection

1. Genetic causes (mode of inheritance)1. Genetic causes (mode of inheritance) single genessingle genes multiple genesmultiple genes

2. Environmental2. Environmental

3. GxE: the interaction between the genotype 3. GxE: the interaction between the genotype of the plant and the environment in which it of the plant and the environment in which it growsgrows

What are the causes of biological What are the causes of biological variation observed in plants?variation observed in plants?

be observant of phenotypic be observant of phenotypic differences among plantsdifferences among plants

understand the geneticsunderstand the genetics have the imagination to visualize have the imagination to visualize

final productfinal product foresight to predict demand for foresight to predict demand for

future plant productsfuture plant products

A plant breeder needs to:A plant breeder needs to:

In plants, examples include: In plants, examples include: plant heightplant height plant and leaf morphologyplant and leaf morphology biomass yieldbiomass yield seed yieldseed yield chemical composition of plant tissues and chemical composition of plant tissues and

seedsseeds

Plant selections to improve plant traits Plant selections to improve plant traits are made by assessing plant phenotypesare made by assessing plant phenotypes

Genetic variation: the basis for improvement

Phenotype vs. Genotype P = G + E + (GxE)

  P is called the phenotypic value, i.e., the

measurement associated with a particular individual

G is genotypic value, the effect of the genotype (averaged across all environments)

E is the effect of the environment (averaged across all genotypes)

If we could measure P in all possible environments and regard E as a deviation, then the mean of E would be zero and P = G.

P1

E1 P5 P2

E5 G E2

E4 E3 P4 P3

The genotype responds more strongly in some environments.

Sets of environments tend to shift the trait value in one direction, other environments in a different direction.

Utilization of Germplasm Resources

Release of NewImproved Variety

Development ofGenetically Diverse Populations

Vigorous Yield Testing

Cultivar Breeding: A Recurrent procedure

Stigma

Controlled Cross Pollination

Parent 1 × Parent 2

Objective 4: know some basic plant breeding methods and strategies

How do we breed improved crop cultivars?

1.Inheritance of trait

How complex is selection?

• Qualitative traits, simple inheritance, controlled by major genes

• Quantitative traits, complex inheritance controlled be several gene loci

• Qualitative traits, simple inheritance, controlled by major genes

• Quantitative traits, complex inheritance controlled be several gene loci

Qualitative traits

Classified into discrete classes

Individuals in each class counted

Some environmental influence on phenotype

Controlled by a few (<3) major genes

Figure 2.4

Often single gene traits are easy to see or measure, since environment typically has limited control over their expression

Mendel’s seven traits showing simple inheritance

Tawny (TT or Tt) versus gray (tt) single gene locus on soybean chromosome 6

Source: Halfhill and Warwick, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.),Available: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html

Figure 2.5.

Parent 1 Parent 2

YY yy

X

Yy Yy

YyYy

y

y

Y Y

Parent 1

Parent 2

F1 Hybrid Plants: 100% yellow

Parent 1 Parent 2

Yy Yy

X

YY Yy

yyYy

Y

Y

Y y

Parent 1

Parent 2

F2 Plants: 75% yellow 25% green

A. Monohybrid Cross

Gametes: Y Y y y Gametes: Y y Y y

Yy

B. F1 Self Fertilization

YY & Yy

yy

F1 Fertilization: F2 Fertilization:

=

Source: Halfhill and Warwick, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.),Available: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html

Upon selfing F2 population; 25% homozygous ‘YY’ will produce only ‘YY’ genotypes, and 25% homozygous ‘cc’ will produce only ‘yy’ genotypes. So only ‘Yy’ will segregate to produce genotypes in proportion of 0.25 (YY):0.50: (Yy):0.25(yy).

F2 population: 0.25(YY ) 0.50 (Cc) 0.25 (cc )

YY Yy Yy yy

Produce all CC plants

0.25 0.50 0.25

Produce all cc plants

Segregate into 0.25(CC ) 0.50%

(Cc) and 0.25 (cc)

Resulting F3 population will have

0.25 + ½ (0.25) = 0.375 CC plants

½ (0.25) + (0.25) = 0.375 cc plants

½ (0.50) = 0.25 Cc plants

Gene and Genotype FrequenciesExample: Self pollinated diploid species

Heterozygosity reduced by half in each selfing generation

YY Yy yyF2

F3

F4

25%

F5

F6

F7

25%50%

43.75%

25%

46.88%

12.5%

48.44%

6.25%

49.22%

3.135

49.61%

1.56

43.75%

46.88%

48.44%

49.22%

49.61%F8

37.5%

0.78%

37.5%When should we select?

Questions based on F5 single plant derived progeny rows from one population formed from crossing two pure line parents:

Selfing a double het (AaBb × AaBb) produces a 9:3:3:1 phenotypic ratio only if trait governed by complete dominance

FreqFreq GenotypeGenotype

1/161/16 AABBAABB

2/162/16 AABbAABb

1/161/16 AAbbAAbb

2/162/16 AaBBAaBB

4/164/16 AaBbAaBb

2/162/16 AabbAabb

1/161/16 aaBBaaBB

2/162/16 aaBbaaBb

1/161/16 aabbaabb

Phenotypic RatioPhenotypic Ratio Underlying Underlying GenotypesGenotypes

99 AABB = AABb =AaBB = AaBb

33 AAbb = Aabb

33 aaBB = aaBb

11 aabb

Note: only 1 out of 16 is homozygous favorable allele for both gene loci

Selfing a double het (AaBb × AaBb) produces 9 genotypic classes

Freq Genotype No. of CAP alleles

1/16 AABB 4

2/16 AABb 3

1/16 AAbb 2

2/16 AaBB 3

4/16 AaBb 2

2/16 Aabb 1

1/16 aaBB 2

2/16 aaBb 1

1/16 aabb 0

1 4 6 4 1

4 kg 5 kg 6 kg 7 kg 8 kg

Figure 3.1

FreqFreq No. of CAP No. of CAP allelesalleles

1 0

44 11

66 22

44 33

11 44

Source: Tinker, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.), Available: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html

Quantitative traits

Express continuous variation (normal distribution)

Individuals measured, not counted

Significant environmental influence on phenotype

Controlled by many minor (or major) genes, each with small (or large) effects

AA, bb (6 kg)

aa, BB (6 kg)

X

Aa, Bb (6 kg)

Self-pollinate

4 kg:aa, bb

5 kg:Aa, bb (x2) aa, Bb (x2)

6 kg:Aa, Bb (x4)AA, bb aa, BB

7 kg:Aa, BB (x2)AA, Bb (x2)

8 kg:AA, BB

1 4 6 4 1

4 kg 5 kg 6 kg 7 kg 8 kg Figure 3.1

Histogram depicts dominant genotype effect with yield: “capital” alleles (0, 1, 2, 3, 4)

Source: Tinker, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.),Available: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html

Note: Consider upper case letter represents the favorable allele for each gene

25

10

28

36

32

40

19

14

1

0

5

10

15

20

25

30

35

40

45

1300 1500 1700 1900 2100 2300 2500 2700 2900 3100

Yield kg ha-1

Fre

qu

ency

Frequency distribution of seed yield for 187 different recombinant inbred lines (RIL) in the soybean population 5601T x Cx1834-1-2 (Scaboo et al., 2009)[no transgressive segregates for this trait in this population]

5601T = 3252Cx1834-1-3

High yielding low-phytate parental lines is the goal

0

0.25

0.5

0.75

1

1.25

0 1 2 3 4 5 6 7 8 9 10 11 12

Pro

po

rtio

n o

f h

omo

zygo

us i

ndiv

idua

ls

Generations of self-fertilization

Proportion of homozygous individuals after various generations of selfing, for 1, 5, 10, 20 independently inherited gene pairs

1-Gene5-Genes10-Genes20-Genes

1/2

3/4

7/815/16

(1/2)20 (3/4)20

(7/8)20

(15/16)20

= [1-(½)G]L

Even if 20 genes is involved, using the power of inbreeding 5 generations, over half the proportion of individuals will be completely homozygous!

Adapted from Allard, 1999Then find the better individuals among the homozygous plants (those accumulating the greatest number of superior alleles). Can be done with DNA technologies and progeny row testing.

How do we breed improved crop cultivars?

2. Understand the effect of reproductive behavior

Reproductive Behavior

Self pollinated

- Pure line variety- Hybrid variety

Monoecy

Cross pollinated

Dioecy Self-incompatible

- Synthetic variety – heterogeneous population (not a pure line)

- Hybrid variety, if inbred development is possible

Perfect flower

• Clonal variety• Hybrid

No flowering/limited flowering

Vegetative reproduction

Cultivar development for self-pollinated species: pedigree method

Germplasm

Hybridization

F1 Nursery, all plants heterozygous

Parents are usually inbred

Homogeneous population if parents were inbred

F2 Nursery, all plants heterozygous

Every single plant is a different genotype

Cultivar, local or exotic landraces, wild relatives

F3: head rows Select the best rows, select best plant within selected rows, proceed to F4 head rows

This is typical pedigree method of selection in self-pollinated crop. Each head row is called line. Most F6 or F7 lines are uniform enough for preliminary yield testing

This is typical pedigree method of selection in self-pollinated crop. Each head row is called line. Most F6 or F7 lines are uniform enough for preliminary yield testing

Cultivar development for self-pollinated species: bulk method

Germplasm

Hybridization

F1 Nursery, all plants heterozygous

Parents are usually inbred

Homogeneous population if parents were inbred

F2 population, all plants heterozygous

Collect equal amount of seed from each plant

Cultivar, local or exotic landraces, wild relatives

F3: bulk population Repeat one or two more generation, then follow head rows

This is bulk method of breeding self-pollinated crop. Most F6 or F7 lines are uniform enough for preliminary yield testing. This is less resource consuming.

This is bulk method of breeding self-pollinated crop. Most F6 or F7 lines are uniform enough for preliminary yield testing. This is less resource consuming.

Cultivar development for cross-pollinated species: recurrent phenotypic selection

- Produce cycle-1 (C1) seeds

Starting population cycle 0 (C0)Select best plants (phenotypes)

Harvest seeds from selected plants & bulk

Field testing of seed in each cycle

Polycross selected plants

Rep

eat

cycl

e

- Space-plant C1 population, select the best plant (with respect to target trait)

Eliminate unselected, intercross selected & harvest seed & bulk

Progeny evaluation- Genotypic selection among families

- Selection among-and-within families

Phenotypic selection

Intermate selected genotypes

Select superior genotypes of

superior families

Select parents producing

superior families

Multilocation yield test

Synthetic seed production

Field testing of new synthetics: evaluation

Rep

eat

cycl

eCultivar development for cross-pollinated species: recurrent phenotypic selection, continued

How cultivar development can be accelerated

One method: backcross breeding

2000 F1 50 % TN Line

BC1F1 75 % TN Line

BC2F1 87.5 % TN Line

BC3F1 93.5 % TN Line

BC4F1 96.9 % TN Line

BC5F1 98.4 % TN Line

BC6F1 99.2 % TN Line

2006 – just a few pods produced

With Traditional Backcross Breeding:

Molecular markers allow visualization of genotypes

rr

RR

Rr rr

RR

Gel electrophoresis of DNA markers: we can now ‘see’ genotypes

rr rr

RR

Molecular genetic markers can accelerate breeding with fewer generations needed

F1 50 % TN Line

BC1F1 80+ % TN Line

BC2F1 98+ % TN Line

BC3F1 99+ % TN Line

2003 winter plant-row increase

2004 TN yield tests & re-selections:

2005 harvest 100+ bushels 5601T-RR

2002

Phytate quantitative trait loci (Walker et al. 2006) now with confirmed quantitative trail locus (QTL) designations (Scaboo et al., 2009)

♦

Satt156

Satt527

Satt561

Satt229

Satt373gs

Satt530

Satt387

Satt339

Satt237

GMABAB

Sat_091

Sat_236

10 cM

10 cM

LG L LG N

Maximum LOD: 6.4

R2: 13%

Maximum LOD: 25.5

R2: 40%

Pha-001Pha-002

42.2

53.6

57.4

40

44

48

52

56

BC1 BC4 5601T

2008 phytate yield trial2008 phytate yield trial33 new BC lines33 new BC lines

BU/A

a

a

b

Less agronomicQTL for HTQTL for MAT

Biotechnology can be used to improve crop cultivars?

3. Transgenic varieties

Source: http://en.wikipedia.org/wiki/Gm_crops

For every 1 bushel/acre increase in production, largely through genetic gain,

increased income to TN soybean producers of

15 Million $ annually

5601T UT AgResearch soybean at Obion, TN

IMPACT

Yields of 18 Maturity Group V Roundup Ready soybean varieties in 9 County Standard Tests in TN and KY during 2007.

MS Brand/VarietyAvgYl

dMois

tCarl Dyer Gibs 1

Gibs 2

Hayw

Laud MREC ObioWea

k

    bu/a % planted 5/26 5/21 6/18 5/14 5/17 5/22 5/15 6/7 5/23

A *USG Allen 41.316.0

63.153.0

37.041.1

32.2

29.7

33.535.6

46.1

AB Delta King DK52K6 40.0 15.3 62.4 49.7 40.1 30.1 30.7 35.7 27.2 36.4 47.4

AB ***Delta King DK5567 39.9 16.0 67.4 50.5 34.1 37.8 34.5 33.6 27.4 34.2 39.9

ABC **Armor 54-03 39.2 13.9 61.6 52.5 31.0 25.7 28.1 34.6 27.1 30.8 61.8

ABCAg Genetics South AGS 568

38.2 15.8 56.5 41.0 44.3 34.7 33.9 35.0 28.5 35.2 34.9

ABC Dyna-Gro 33X55 38.0 15.6 56.7 51.6 33.2 34.1 26.4 31.5 26.5 37.6 44.8

BCD **Dyna-Gro 33B52 35.6 13.3 56.7 46.0 36.5 22.8 26.5 33.5 28.4 27.8 42.1

CD Pioneer 95M30 35.4 15.1 51.4 47.2 31.1 23.2 31.7 29.8 19.2 31.7 53.3

CD Schillinger 557RC 35.3 15.2 56.9 54.1 41.0 17.3 21.5 30.0 23.9 31.9 41.3

DE Stine 5482-4 RR/STS 33.3 15.4 54.1 47.8 39.1 22.3 20.4 28.7 24.4 31.7 31.3

EF Vigoro V51N7RS 30.3 14.3 45.3 42.7 30.8 16.9 20.8 29.5 24.6 30.1 32.4

EFG FFR 5116 30.2 14.1 46.5 37.8 30.1 18.2 29.2 27.8 20.6 34.3 27.3

EFG Armor 52-U2 29.9 14.0 50.9 44.2 27.2 18.8 16.4 29.4 18.4 30.2 33.6

EFG Dairyland 8512 29.7 14.6 44.5 37.8 30.8 19.0 19.3 27.1 19.5 31.3 38.5

FG Progeny 5115 28.5 13.5 50.6 37.8 33.6 18.8 14.5 22.6 15.7 28.3 34.2

FG Deltapine DP5115 RR/S 26.8 13.5 48.2 27.5 30.0 15.0 17.9 25.9 18.3 30.3 28.5

FG Delta King DK5066 25.9 14.1 53.6 27.5 27.4 15.1 10.1 19.2 12.1 34.5 33.4

G Dairyland 8509 25.8 13.6 54.0 21.8 34.2 16.1 14.6 25.9 14.9 26.0 24.6

  Average (bu/a) 33.514.6

54.542.8

34.023.7

23.8

29.4

22.832.1

38.6

USG Allen #1USG Allen #1 and better than average in better than average in every every countycounty

+7.8+7.8 +8.6+8.6 +10.2+10.2 +17.4+17.4 +8.4+8.4 +10.7+10.7 +7.5+7.5

For the plant breeder patience is a virtue

…when working with new genetics

Key points

Know basic terminology in transmission genetics and plant breeding

Understand the goals of plant breeding Know plant reproductive syndromes, e.g.,

self-fertilization, and how they effect breeding methods