1. STT2073 Plant Breeding and Improvement

2. Quality vs Quantity Quality: Appearance of fruit/plant/seed – size, colour – flavour, taste, texture – shelflife (transport) Composition – fiber, starch, oil & protein as food/ industrial ingredients – recovery and processing – valorization of by-products

3. Quality vs Quantity

4. Breeding for Quality: a moving field (1) Consumer/societyTechnology What are the driving forces?  Flavour (taste, odour)  Convenience  Product appearance  Personal health  Food safety  Awareness environment  breeding strategies èinsight plant processes  new processing techni-ques (e.g. high pressure) èbetter understanding structure- function re-lationships biomolecules èimproved analytics

5. Quality vs Quantity Quantity: Yield  Biotic (disease) resistance  Abiotic resistance Drought resistance Lodging Salt/Salinity Bad soil etc

6. Qualitative vs Quantitative Inheritance Qualitative inheritance Traits (characters) controlled by few genes The few genes express major phenotypic effects Their inheritance = qualitative inheritance. Discontinuous variation  Can be grouped - discrete categories  Classify and count plants  Determine phenotypic ratios

7. Qualitative vs Quantitative Inheritance Quantitative inheritance Traits (characters) controlled polygenically The few genes express minor phenotypic effects Influenced by the environment Their inheritance = quantitative inheritance. Continous variation  Quantitative differences  Measure phenotype – statistical analysis

8. Qualitative vs Quantitative Inheritance Quantitative inheritance The inheritance of multiple genes at each locus = Mendelian; However, the characteristic difference in number and expression (small effect) Important notes: o Qualitative traits - phenotypically and genetically show Mendelian inheritance. o Quantitative traits – phenotypically is NOT Mendelian inheritance but genotypically it IS Mendelian inheritance.

9. Quantitative Inheritance

10. WHY??? Eg. Assuming 2 genes involved AA and BB Assuming each dominant allele contribute to length additively P1 aabb = 40 cm P2 AABB = 80 cm F 1 AaBb = ?? cm For P1, each allele contribute 10 cm For P2, each allele contribute 20 cm F 1 AaBb = 20 + 10 + 20 + 10 = 60 cm

11. Quantitative Inheritance

12. Quantitative Inheritance Nilson-Ehle’s Dark red seeded x white seeded wheat F1 - medium red seeds Partial/incomplete dominance ?

13. Quantitative Inheritance Nilson-Ehle’s Dark red seeded x white seeded wheat F1 - medium red seeds Partial/incomplete dominance ? NO! WHY? Partial/incomplete dominance – interaction between two alleles of one gene This situation is interaction between alleles of two genes

14. Quantitative Inheritance Nilson-Ehle’s Continuous colour variation Phenotypic ratio 1:4:6:4:1 (5 classes) Two genes segregating independently Each dominant allele adding to the intensity of the red colour.

15. Quantitative Inheritance If the ratio of F 2 individuals resembling either of the two most extreme phenotypes can be determined:  number of gene pairs involved (n) can be calculated using 1/4 n. Calculating the number of gene pairs

16. Quantitative Inheritance Example, 1/4 n =1/41/4 n =1/161/4 n =1/64 4 n = 44 n = 164 n = 64 n = 1n = 2n = 3

17. Quantitative Inheritance Example, 1/4 n =1/41/4 n =1/161/4 n =1/64 4 n = 44 n = 164 n = 64 n = 1n = 2n = 3

18. Quantitative Inheritance No. of Phenotype classes = (2n+1) n = the number of genes When n=1, 2n+1 = 3 When n=2, 2n+1 = 5 When n=3, 2n+1 = 7 Calculating the number of phenotype classes

19. Quantitative Inheritance Transgressive segregation Progenies with more extreme phenotypes than the parents Extreme progenies - better than or worse than either parent Progeny that gains higher vigor and is superior than the parents = progeny show heterosis or hybrid vigor. Note: Only when involved polygenic Worse than P1 Better than P2 P1 P2

20. Quantitative Inheritance Transgressive segregation Progenies with more extreme phenotypes than the parents Extreme progenies - better than or worse than either parent Progeny that gains higher vigor and is superior than the parents = progeny show heterosis or hybrid vigor. Note: Only when involved polygenic Worse than P1 Better than P2 P1 P2

21. Quantitative Inheritance Transgressive segregation Plant breeders rely on transgressive segregation to obtain segregates that are superior to the parents Why extreme progenies exist? Progeny may have inherited new combinations of multiple genes with more +ve or –ve effects. > +ve genes/alleles > better; > -ve genes/alleles > worse Worse than P1 Better than P2 P1 P2

22. Quantitative Inheritance Transgressive segregation How to identify the superior transgressive segregates? Do an experiment (in same environment) !!! Grow the selected progenies and parents Obtain the mean performance of progenies and parents Compare the mean performance of progenies and parents. Worse than P1 Better than P2 P1 P2

23. Quantitative Inheritance Remember: Quantitative inheritance involves multiple genes The multiple genes are expressed through different types of gene action: Dominance Overdominance Additive and other Epistasis Each gene may have different alleles Eg. for diploid plants 2 alleles – three diploid combinations 3 alleles – six diploid combinations 4 alleles – 10 diploid combinations Possible allele combination = n(n+1)/2; n = no. of allele Polyploid???? – makes thing more complicated

24. Gene interactions dictate the type of variety to develop Types of varietyGenetic components exploited Pure lines or inbred varieties Additive Additive x additive Hybrids Dominance Dominance x dominance Overdominance Open pollinated varieties All types of gene action: Additive Dominance Additive x additive Additive x dominance Dominance x dominance

25. Gene interactions dictate the type of variety to develop

26. Quantitative Inheritance Components of phenotype variability V P = V G + V E + V GE V P = V A + V D + V I + V E + V GE Only V A is more important in predicting the phenotypes of offspring from the phenotypes of their parents VG = VA + VD + VIVG = VA + VD + VI

27. Quantitative Inheritance Components of phenotype variability V A = Additive genetic variance  The proportion of genetic variance that is due to additive effects of alleles at loci controlling the quantitative traits. V D = Dominance genetic variance  The proportion of genetic variance due to transient interactions between alleles at loci controlling the quantitative traits. V I = Epistasis genetic variance  The proportion of genetic variance due to interactions among alleles at different loci controlling the quantitative traits.

28. Quantitative Inheritance Heritability Heritability is a measure of the genetic contribution to phenotypic variability Examine the contribution of genetic vs environment factors to the phenotype Heritabilty can be expressed as a fraction or percentage.

29. Quantitative Inheritance Broad-sense HeritabilityNarrow-sense Heritability

30. Quantitative Inheritance Broad-sense and Narrow-sense Heritability A “0” = no V P is due to genetic differences. A “1” = all V P is due to genetic differences The closer is to “1”, the greater is the proportion of the total phenotypic variance that is additive genotypic variance and the greater our ability to predict the phenotypes of the offspring.

31. Quantitative Inheritance The principal uses of heritability To determine the relative importance of genetic effects which could be transferred from parent to offspring To determine which selection method would be most useful to improve the character To predict gain from selection (genetic advance)

32. In cross-pollinated crops Gene frequency - The proportions of the different alleles or genes in the gene pool of a breeding population. Genotype frequency - The proportions of various genotypes in a population. Gene pool - The total variety and number of alleles within a population or species

33. Gene equilibrium In cross-pollinated plants, the gene pool is shared by plants in the population. The gene frequency and genotype frequency may remain constant from generation to generation if the population is in the state of genetic equilibrium. In other words, “Genotypes that maintain the same gene frequency in successive generations are in genetic equilibrium.”

34. Gene equilibrium To reach the genetic equilibrium the following conditions must be met. (1) infinitely large size of the population (2) no mutation of the alleles (3) no selection that may favour a particular allele (4) no migration of alleles in and out the population (5) random mating

35. Hardy-Weinberg Law The principle of genetic equilibrium and the mathematical relationship that the probability of two alleles mating = product of frequency of the alleles in the population. If the gene frequencies of the dominant allele is p, the gene frequency of the recessive allele is and q, and p+q =1, then the genotype frequency in the progeny can be expressed by expansion of the binomial (p+q) 2 (p + q) 2 = p 2 +2pq + q 2 = 1 where genotype frequencies of the genotype AA, Aa and aa are expressed as the product of p 2, 2pq and q 2 respectively.

36. Gene frequency and gene equilibrium Selection for or against a particular allele or group of alleles contributing to a quantitative character will change the frequency of the allele or alleles in the population and consequently its genotype frequency. Selection for a dominant allele in a limited number of generations will not completely eliminate the recessive alleles from the populations because the homozygous dominant and heterozygous phenotypes cannot be distinguished from each other. Selection for homozygous recessive alleles will eliminate the dominant alleles from the population in one generation.