Plant Breeding – an Overview

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

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

9. 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 Why Plant Breeding Adapted from http://www.census.gov/population/popclockworld.html

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

12. Plant Breeding Targets Improved product quality Source: http://www.ars.usda.gov/is/graphics/photos/

13. H H C C H H H C C H H H CC • Hydrogenation: flavor and oxidative stability • Trans fats: health issues • FDA label mandate cis form saturated trans form 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: http://www.ars.usda.gov/is/graphics/photos/

19. Plant Breeding Targets 7. Environmental sustainability Conservation Tillage Source: http://www.ars.usda.gov/is/graphics/photos/

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. 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. 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. • 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.

27. Cultivar Breeding: A Recurrent procedure Release of New Improved Variety Utilization of Germplasm Resources 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. Qualitative traits, simple inheritance, controlled by major genes • Quantitative traits, complex inheritance controlled be several gene loci How complex is selection?

32. Qualitative traits • Classified into discrete classes • Individuals in each class counted • Someenvironmental 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: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html 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. Parent 1 Parent 1 Y y Y Y YY Yy Yy Yy Y y Parent 2 Parent 2 Yy yy Y Yy Yy y Figure 2.5. A. Monohybrid Cross B. F1 Self Fertilization = Parent 1 Parent 2 Parent 2 Parent 1 X X Yy YY yy Yy Gametes: Y Y y y Gametes: Y y Y y F1 Fertilization: F2 Fertilization: YY & Yy Yy F2 Plants: 75% yellow 25% green F1 Hybrid Plants: 100% yellow yy Source: Halfhill and Warwick, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.), Available: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html

35. Gene and Genotype FrequenciesExample: 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 0.25 0.50 Produce all CCplants Segregate into 0.25(CC ) 0.50% (Cc) and 0.25 (cc) Produce all ccplants Resulting F3 population will have ½ (0.50) = 0.25 Ccplants ½ (0.25) + (0.25) = 0.375 ccplants 0.25 + ½ (0.25) = 0.375 CCplants

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

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 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 Figure 3.1 Source: Tinker, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.), Available: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html

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: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html

42. 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 = 3252 Cx1834-1-3 High yielding low-phytate parental lines is the goal

43. = [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. Self pollinated Cross pollinated Vegetative reproduction Reproductive Behavior Perfect flower Monoecy Self-incompatible Dioecy No flowering/limited flowering - Synthetic variety – heterogeneous population (not a pure line) - Hybrid variety, if inbred development is possible • Pure line variety • Hybrid variety • Clonal variety • Hybrid

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 Every single plant is a different genotype F2 Nursery, all plants heterozygous 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 Collect equal amount of seed from each plant F2 population, all plants heterozygous 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. 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 parents producing superior families Select superior genotypes of superior families Synthetic seed production Intermate selected genotypes Field testing of new synthetics: evaluation Multilocation yield test

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