Post on 25-Dec-2021
PLT 132 Plant Propagation
Seeds – part 2: Plant Breeding Principles D. W. Still
dwstill@csupomona.edu
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
Examples
Plant breeding can be facilitated by using marker-assisted selection (MAS)
1. Identify polymorphism between parents
2. Obtain genotype from parents and progeny
3. Obtain phenotype from parents and progeny
4. Establish association between genotype and phenotype
5. Future selections can be based on DNA-based markers
Marker assisted selection
Confirmation of hybrids using polymorphic DNA markers
P2
F2
F2
P1
Polymorphic
1. Adaptation to environment has a genetic basis.
2. Revegetation / reclamation work may require local sourcing of seeds for this reason.
3. Example: Echinacea angustifolia collected along a 1300 mile N-S climatic gradient.
4. Methods: Collect samples, extract DNA, compare DNA among populations, correlate to environmental variables (heat, cold, ppt)
Ecotypes, clines, and provenances
Photo by D.W. Still
Geographic & Climatic Cline
Collection of Echinacea species along a 1500 km cline
Still et al., 2006 Annals Bot
Geographic & Climatic Cline
Still et al., 2006 Annals Bot
CDD – cooling degree days HDD – heating degree days FFD – freeze-free days
1. ND 2. ND 3. SD 4. NE 5. NE 6. NE 7. KS 8. KS 9. OK 10. OK 11. LA
Still et al., 2006 Annals Bot
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