Seeds – Part 2

1. Virtually all agronomic and horticultural crops are produced by plant breeding.

2. Plant breeding defined: “the application of techniques for exploiting the genetic potential of plants”.

3. Domestication of plants and animals began about 13,000 ybp

4. Most plants and animals were domesticated thousands of years ago; very few have been domesticated today.

Malus sieversii

Improving disease resistance of American domestic apples

Analysis of the apple genome suggests that a whole-genome duplication event in an ancestral genome, followed by loss of a single chromosome, led to the 17-chromosome karyotype of the cultivated apple. Expansion of particular gene families may have served as a reservoir for new gene functions, underlying the genetic basis of apple-specific traits.

Whole genome duplication

Domesticated apple (Malus x domestica) originated in Central Asia

Seeds – Part 2

What traits can we breed for?

- almost anything

- qualitative traits

pp PP, Pp

Seeds – Part 2

What traits can we breed for?

- quantitative traits Yield

Skin color

Seeds – Part 2

Terms: 1. Heterogeneous 2. Homogeneous 3. Homozygous 4. Heterozygous

Homogeneous – identical phenotypes / genotypes

Homozygous – Fixed alleles / genotypes

Heterozygous – mixed alleles / genotypes

Heterogeneous – mixed phenotypes / genotypes

Seeds – Part 2

What traits can we breed for?

However, it is not always clear how many genes control a trait

What were the targets of selection?

1. Assemble genetic materials

2. Obtain phenotype

3. Obtain genotype

4. Determine associations b/t 2 and 3

5. Identify quantitative trait loci (QTL)

Step 2: Obtain phenotype

Step 5: Determine associations between phenotype and genotype

Association of SNP haplotype to skeletal size (chromosome 15)

Sutter et al. 2007, Science

IGF1 SNP controls growth (insulin-like growth factor 1) common to all small breeds and nearly absent from giant breeds

Step 5: Determine associations between phenotype and genotype

Association of SNP haplotype to skeletal size (chromosome 15)

Sutter et al. 2007, Science

Few genes, large effects

Genetic consequences of domestication / breeding

1. Genetic bottlenecks 2. Founder effects 3. Genetic drift 4. Inbreeding depression 5. Loss of allelic diversity

6. Improved performance!

Seeds – Part 2

1. Rice is a staple food for much of the world. 2. Two recent major changes: a) Increased harvest index b) heterosis by plant breeding 3. Challenges: a) Insect and disease pressure (~$1.5 billion loss) b) Fertilizer applications (~30% of N – P use; ~10% arable land) c) Water shortage (Ag = 70% total water; rice = 70% of that) d) Quality e) Sustainability

Copyright ©2007 by the National Academy of Sciences

Zhang, Qifa (2007) Proc. Natl. Acad. Sci. USA 104, 16402-16409

Fig. 1. Schematic representation of combinations of genes and approaches for the development of GSR

Seeds – Part 2

Modern breeding = Traditional breeding methods aided by molecular biology

Copyright ©2007 by the National Academy of Sciences

Zhang, Qifa (2007) Proc. Natl. Acad. Sci. USA 104, 16402-16409

Fig. 2. Pest resistance of Minghui 63 individually harboring five different Bt genes

Seeds – Part 2

Control

Control

Control Control

Control

Control

Seeds – Part 2

Breeding Systems

A.) Self pollination

Lettuce

Tomato

Seeds – Part 2

Breeding Systems

B.) Cross pollination (outcrossing species)

Male – whitish yellow; Female (male sterile – red) photo – Gary Odvody TAMU

Sorghum Cactus

Seeds – Part 2

Terms: 6. Fixing of alleles 7. True-breeding 8. Effect of self pollination (Table 5-1) 9. Hybrid vigor = heterosis 10. Perfect flower

Within a population, the amount of heterozygous loci decreases by 50% each generation. Generation Self gen % homozygosity % heterozygosity F1 S0 0 100 F2 S1 50 50 F3 S2 75 25 F4 S3 87.5 12.5 F5 S4 93.75 6.25 F6 S5 96.88 3.12 F7 S6 98.44 1.56 F8 S7 99.22 0.78 F9 S8 99.66 0.34

Effect of self-pollination (inbreeding)

Alleles become “fixed”

Seeds – Part 2

Terms: 11. Perfect Flower 12. Monoecious (maize, cucurbits) 13. Dioecious (asparagus, pistacio) 14. Self incompatibility a) Sporophytic incompatibility b) Gametophytic incompatibility

Monoecious flower - Plant possessing both male and female flowers on the same plant

Dioecious – unisex flowers on different plants

Perfect flower - Flower possessing both stamens and pistils

Seeds – Part 2

Terms: 11. Perfect Flower 12. Monoecious (maize, cucurbits) 13. Dioecious (asparagus, pistacio) 14. Self incompatibility a) Sporophytic incompatibility b) Gametophytic incompatibility

Electron micrographs of pollen

Seeds – Part 2

Pollen is distinct

- the shape of each species is unique and chemically distinct

Mature pollen grains

Seeds – Part 2

Determinants of compatibility are located on the outside layer, called exine

Mature pollen grain – germination

Scanning electron micrograph of a pollinated stigma showing two interacting cell types, papillar cells (P) and pollen grains (Po).

Nasrallah and Nasrallah, 1993. Plant Cell 5:1325-1335

The incompatibility of pollen is determined by the

haploid (n) pollen genotype at the S locus.

(rejection sites are on stigma and style) (Solonaceae, Rosacea, Fabaceae, Poaceae, Onagracea)

Gametophytic Self Incompatibility (GSI)

Pollen is S1S3 or S3S4

Stigma/style is S1S2

Sporophytic Self Incompatibility (SSI)

The incompatibility of pollen is determined by the dipoloid (2n) S genotype of the parent plant.

(rejection sites are on papillar surface) (Brassicaceae, Asteraceae, Convolvulacea, Betulaceae, etc.)

Pollen is S1S3 or S3S4

Stigma/style is S1S2

S1 & S3 or S3 & S4 exine on pollen grains

Seeds – Part 2

Terms: 15. Breeding line 16. Inbred line 17. Hybrid 18. Transgenic line 19. Landrace 20. Variety, cultivar 21. Specific epithet 22. Ecotype 23. Cline 24. Clone 25. Provenance

16.Inbred line – created by repeated selfing

17.Hybrid – offspring from genetically distinct parents

18. Transgenic line – developed from plants with recombinant DNA

19. Landrace – primitive varieties (before breeding)

20. Variety – lowest recognized taxonomic level (similar phenotypes)

25. Provenance – climatic / geographic area from which seed originated

24. Clone – genetically identical; vegetative, apomitic

15. Breeding line – maintained for use in a breeding program

21. Specific epithet – Genus + species; e.g., Lactuca sativa

22. Ecotype – population adapted to a geographic area

23. Cline – continuous variation across geographic area Woody plant propagation

A. P1 B. P2 C. F1 (1) D. F1 (2)

Confirmation of hybrids using polymorphic DNA markers

P2

F1

F1

P1

Polymorphic

Geographic & Climatic Cline

Collection of Echinacea species along a 1500 km cline

Geographic & Climatic Cline

Geographic & Climatic Cline results in genetic / phenotype cline

ND/SD

OK

Still et al., 2006 Annals Bot

Seeds – Part 2

Terms: Maintenance of genetic lines / seed trade 1. Genetic drift 2. Roguing 3. Selection by genotype or phenotype 4. Heritability 5. Genotype x environment interaction 6. Qualitative trait 7. Quantitative trait

Seeds – Part 2