1. Plant Breeding – an Overview

2. Objective 1: know basic plant genetics and breeding terminology

3. 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

4. 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

5. 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)

6. 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

7. What is Plant Breeding?
The genetic adjustment of plants to the service of humankind
---Sir Otto Frankel
Source:

8. Objective 2: know why plant breeding is important and useful
Several examples in soybean

9. Why Plant Breeding
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
Adapted from

10. Plant Breeding Targets
1. Yield
Source: USB photo disc 0976

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

12. Plant Breeding Targets
Improved product quality
Source:

13. H H C C Hydrogenation: flavor and oxidative stability
Trans fats: health issues
FDA label mandate
cis form
saturated
trans form
H H
C C H
C C
H H
C C
Hydrogenation ;
(Source: Wilson, 2004)

14. Plant Breeding Targets
3. Pest and Disease Resistance
Soybean sudden death syndrome

15. Joint Germplasm Release (Drs. Arelli, Pantalone, Allen, Mengistu)
USDA-ARS and
Tennessee Agricultural Exp. Stn.
Release of JTN-5303 Soybean
Resistant to multiple diseases:
Soybean cyst nematode
Sudden death syndrome
Stem canker
Frogeye leaf spot
Charcoal rot

16. Plant Breeding Targets
4. Environmental Stress Tolerance

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

18. Plant Breeding Targets 6. Adaptation to Mechanization
Source:

19. Plant Breeding Targets
7. Environmental sustainability
Conservation Tillage
Source:

20. Objective 3: know the basic principles of plant breeding
Importance of genetic variation and selection

21. What are the causes of biological variation observed in plants?
1. Genetic causes (mode of inheritance)
single genes
multiple genes
2. Environmental
3. GxE: the interaction between the genotype of the plant and the environment in which it grows

22. A plant breeder needs to:
be observant of phenotypic differences among plants
understand the genetics
have the imagination to visualize final product
foresight to predict demand for future plant products

23. In plants, examples include:
Plant selections to improve plant traits are made by assessing plant phenotypes
In plants, examples include:
plant height
plant and leaf morphology
biomass yield
seed yield
chemical composition of plant tissues and seeds

24. Genetic variation: the basis for improvement

25. 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)

26. 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.
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.

27. Cultivar Breeding: A Recurrent procedure
Utilization of
Germplasm Resources
Release of New
Improved Variety
Development of
Genetically Diverse Populations
Vigorous Yield Testing

28. Controlled Cross Pollination
Parent 1 × Parent 2
Stigma

29. Objective 4: know some basic plant breeding methods and strategies

30. How do we breed improved crop cultivars?
1.Inheritance of trait

31. How complex is selection?
Qualitative traits, simple inheritance, controlled by major genes
Quantitative traits, complex inheritance controlled be several gene loci

32. Qualitative traits Classified into discrete classes
Individuals in each class counted
Some environmental influence on phenotype
Controlled by a few (<3) major genes

33. Mendel’s seven traits showing simple inheritance
Figure 2.4
Source: Halfhill and Warwick, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.),
Available:
Often single gene traits are easy to see or measure, since environment typically has limited control over their expression
Tawny (TT or Tt) versus gray (tt) single gene locus on soybean chromosome 6

34. F1 Hybrid Plants: 100% yellow
Figure 2.5.
A. Monohybrid Cross
B. F1 Self Fertilization =
Parent 1
Parent 2
Parent 1
Parent 2 X X YY yy Yy Yy
Gametes: Y Y y y
Gametes: Y y Y y
F1 Fertilization:
F2 Fertilization: YY Yy yy Y y
Parent 1
Parent 2 Yy y Y
Parent 1
Parent 2
YY & Yy Yy
F1 Hybrid Plants: 100% yellow
F2 Plants: 75% yellow
25% green yy
Source: Halfhill and Warwick, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.),
Available:

35. Gene and Genotype Frequencies Example: Self pollinated diploid species
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
0.25
0.50
0.25
Produce all CC plants
Segregate into 0.25(CC ) 0.50% (Cc) and 0.25 (cc)
Produce all cc plants
Resulting F3 population will have
½ (0.25) = CC plants
½ (0.50) = 0.25 Cc plants
½ (0.25) + (0.25) = cc plants

36. Heterozygosity reduced by half in each selfing generationYY Yy yy F2 F3 F4
25% F5 F6 F7
50%
43.75%
46.88%
12.5%
48.44%
6.25%
49.22%
3.135
49.61%
1.56 F8
37.5%
0.78%
When should we select?

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

38. Selfing a double het (AaBb × AaBb) produces a 9:3:3:1 phenotypic ratio only if trait governed by complete dominance
Freq
Genotype
1/16
AABB
2/16
AABb
AAbb
AaBB
4/16
AaBb
Aabb
aaBB
aaBb
aabb
Phenotypic Ratio
Underlying Genotypes 9
AABB = AABb =
AaBB = AaBb 3
AAbb = Aabb
aaBB = aaBb 1
aabb
Note: only 1 out of 16 is homozygous favorable allele for both gene loci

39. Selfing a double het (AaBb × AaBb) produces 9 genotypic classes
Freq
Genotype
No. of CAP alleles
1/16
AABB 4
2/16
AABb 3
AAbb 2
AaBB
4/16
AaBb
Aabb 1
aaBB
aaBb
aabb
Figure 3.1
Source: Tinker, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.), Available:
Freq
No. of CAP alleles 1 4 6 2 3

40. 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

41. X aa, BB (6 kg) AA, bb (6 kg) Aa, Bb (6 kg)
Note: Consider upper case letter represents the favorable allele for each gene
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
Histogram depicts dominant genotype effect with yield: “capital” alleles (0, 1, 2, 3, 4)
Figure 3.1
Source: Tinker, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.),
Available:

42. High yielding low-phytate parental lines is the goal
Frequency distribution of seed yield for 187 different recombinant inbred lines (RIL) in the soybean population 5601T x Cx (Scaboo et al., 2009) [no transgressive segregates for this trait in this population]
5601T = 3252 Cx
High yielding low-phytate parental lines is the goal

43. 15/16 7/8 3/4 1/2 (15/16)20 (7/8)20 (3/4)20 (1/2)20 = [1-(½)G]L
Adapted from Allard, 1999
Then 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.
15/16
7/8
3/4
1/2
(15/16)20
(7/8)20
(3/4)20
(1/2)20
Even if 20 genes is involved, using the power of inbreeding 5 generations, over half the proportion of individuals will be completely homozygous!

44. How do we breed improved crop cultivars?
2. Understand the effect of reproductive behavior

45. 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

46. Cultivar development for self-pollinated species: pedigree method
Cultivar, local or exotic landraces, wild relatives
Germplasm
Hybridization
Parents are usually inbred
F1 Nursery, all plants heterozygous
Homogeneous population if parents were inbred
F2 Nursery, all plants heterozygous
Every single plant is a different genotype
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

47. Cultivar development for self-pollinated species: bulk method
Cultivar, local or exotic landraces, wild relatives
Germplasm
Hybridization
Parents are usually inbred
F1 Nursery, all plants heterozygous
Homogeneous population if parents were inbred
F2 population, all plants heterozygous
Collect equal amount of seed from each plant
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.

48. Cultivar development for cross-pollinated species: recurrent phenotypic selection
Starting population cycle 0 (C0)
Select best plants (phenotypes)
Produce cycle-1 (C1) seeds
Polycross selected plants
Repeat cycle
Space-plant C1 population, select the best plant (with respect to target trait)
Eliminate unselected, intercross selected & harvest seed & bulk
Harvest seeds from selected plants & bulk
Field testing of seed in each cycle

49. Field testing of new synthetics: evaluation
Cultivar development for cross-pollinated species: recurrent phenotypic selection, continued
Phenotypic selection
Progeny evaluation
- Genotypic selection among families
- Selection among-and-within families
Repeat cycle
Select superior genotypes of superior families
Select parents producing superior families
Intermate selected genotypes
Synthetic seed production
Field testing of new synthetics: evaluation
Multilocation yield test

50. How cultivar development can be accelerated
One method: backcross breeding

51. BC1F1 75 % TN Line BC2F1 87.5 % TN Line BC3F1 93.5 % TN Line
With Traditional Backcross Breeding:
2000 F1 50 % TN Line
BC1F1 75 % TN Line
BC2F % TN Line
BC3F % TN Line
BC4F % TN Line
BC5F % TN Line
BC6F % TN Line
With traditional backcrossing you increase the amount of your recurrent parent each generation and it takes 6 generations to recover 99% of your chosen parent.
With the use of molecular markers we have already been able to speed up this process. Notice that these calculated values show that the BC1F1 should contain on average 75% of the desired line. A BC1F1 is produced by using the Recurrent line 5601T as the female and using the F1 as the donor or pollen source. A BC2F1 is produced by using the Recurrent line 5601T as the female and using the BC1F1 as the donor or pollen source.
2006 – just a few pods produced

52. Molecular markers allow visualization of genotypesRR RR RR rr rr rr rr Rr
Gel electrophoresis of DNA markers: we can now ‘see’ genotypes

53. 2003 winter plant-row increase 2004 TN yield tests & re-selections:
Molecular genetic markers can accelerate breeding with fewer generations needed
F1 50 % TN Line
BC1F % TN Line
BC2F % TN Line
BC3F % TN Line
2003 winter plant-row increase
2004 TN yield tests & re-selections:
2005 harvest 100+ bushels 5601T-RR
With traditional backcrossing you increase the amount of your recurrent parent each generation and it takes 6 generations to recover 99% of your chosen parent.
With the use of molecular markers we have already been able to speed up this process. Notice that these calculated values show that the BC1F1 should contain on average 75% of the desired line. A BC1F1 is produced by using the Recurrent line 5601T as the female and using the F1 as the donor or pollen source. A BC2F1 is produced by using the Recurrent line 5601T as the female and using the BC1F1 as the donor or pollen source.
2002

54. 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
LG L
LG N
Maximum
LOD: 6.4 R 2
: 13%
LOD :
25.5
: 40%
Pha-002
Pha-001

55. 2008 phytate yield trial 33 new BC lines
Less agronomic
QTL for HT
QTL for MAT a
BU/A a b 55

56. Biotechnology can be used to improve crop cultivars?
3. Transgenic varieties

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

58. TN soybean producers of
IMPACT
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

59. USG Allen #1 and better than average in every county
Yields of 18 Maturity Group V Roundup Ready soybean varieties in 9 County Standard Tests in TN and KY during 2007. MS
Brand/Variety
AvgYld
Moist
Carl
Dyer
Gibs 1
Gibs 2
Hayw
Laud
MREC
Obio
Weak
bu/a %
planted 5/26
5/21
6/18
5/14
5/17
5/22
5/15
6/7
5/23 A
*USG Allen
41.3
16.0
63.1
53.0
37.0
41.1
32.2
29.7
33.5
35.6
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
***Delta King DK5567
39.9
67.4
50.5
34.1
37.8
34.5
33.6
27.4
34.2
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
Ag 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
Dyna-Gro 33X55
38.0
15.6
56.7
51.6
33.2
26.4
31.5
26.5
37.6
44.8
BCD
**Dyna-Gro 33B52
13.3
46.0
36.5
22.8
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
53.3
Schillinger 557RC
35.3
15.2
56.9
54.1
17.3
21.5
30.0
23.9
31.9 DE
Stine RR/STS
33.3
15.4
47.8
39.1
22.3
20.4
28.7
24.4
31.3 EF
Vigoro V51N7RS
30.3
14.3
45.3
42.7
16.9
20.8
29.5
24.6
32.4
EFG
FFR 5116
30.2
14.1
46.5
18.2
29.2
20.6
34.3
27.3
Armor 52-U2
29.9
14.0
50.9
44.2
18.8
16.4
29.4
18.4
Dairyland 8512
14.6
44.5
19.0
19.3
19.5
38.5 FG
Progeny 5115
13.5
50.6
14.5
22.6
15.7
28.3
Deltapine DP5115 RR/S
26.8
48.2
27.5
15.0
17.9
25.9
18.3
Delta King DK5066
53.6
10.1
12.1
33.4 G
Dairyland 8509
25.8
13.6
54.0
21.8
16.1
14.9
26.0
Average (bu/a)
54.5
42.8
34.0
23.7
23.8
32.1
38.6
+7.8
+8.6
+10.2
+17.4
+8.4
+10.7
+7.5

60. For the plant breeder patience is a virtue
…when working with new genetics

61. 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