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Linkage Lethality Epistasis Major genes and modifying factors Pleiotropism

When the observed phenotypic ratios are not what we expect, we need to consider other factors that may be influencing the expression of the phenotypes:. Linkage Lethality Epistasis Major genes and modifying factors Pleiotropism Penetrance and Expressivity. Mendelian Norm:.

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Linkage Lethality Epistasis Major genes and modifying factors Pleiotropism

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  1. When the observed phenotypic ratios are not what we expect, we need to consider other factors that may be influencing the expression of the phenotypes: • Linkage • Lethality • Epistasis • Major genes and modifying factors • Pleiotropism • Penetrance and Expressivity

  2. Mendelian Norm: Mendelian genetics assumes that all genes act independently of each other Prediction: segregation of dominant alleles for 2 genes, with dominance should yield 4 classes 9:3:3:1 However, we don’t always have these results because …………..

  3. Lethality: Extreme inviability of either gametes or zygotes where: Some individuals (either gametes or zygotes) have either a specific gene (for gamete) or specific gene combination (for zygote) that prevent life. Observed ratios are usually 2:1, which is really a modification of a 1:2:1 ratio where either of the homozygotes is lethal

  4. Epistasis (Bateson 1909, genes that mask the effects of other genes): • Definition expanded to include all inter-allelic interactions • If dominance is the interaction of alleles, • than epistasis is the interaction of loci. • We don’t often ‘see’ epistasis because our research tends to be very narrow. However, with molecular techniques, we are seeing much more. • In self-pollinated crops, can be more important than dominance (ephemeral) • Makes possible recombinations > simple rearranging old traits -- can create novel forms

  5. Epistasis: • Can occur with or without dominance; with dominance- greater number of phenotypes • Will not effect segregation of alleles at a given locus • -can occur with or without linkage • -can occur with or without pleiotropism • -can occur with or without most other situations Therefore, an independent phenomenon

  6. Epistasis: Often based on the biochemistry of the trait of interest This is common in metabolic pathways J K T 1  2  3 blue flowers J K t 1  2  3 orange flowers - locus T controls blue flower colour

  7. Epistasis: J K T 1  2  3 blue flowers J K t 1  2  3 orange flowers J k T 1  2  [ ] yellow flowers j K T 1  [ ]  [ ] whiteflowers So….

  8. Epistasis: Locus J is epistatic to locus K (= K is ‘hypostatic’ to J) Different segregation patterns in F2 and/or Test cross progeny indicate different underlying mechanisms e.g. dominant, recessive, duplicate gene, lethal factor, etc.

  9. Epistasis: Review: 2 inbred lines are crossed, F1 is uniform. Produce a F2 and test cross populations. Assume dominance relationships are present and no maternal inheritance: Expect for 1,2,3,… genes to segregate independently with observable ratios of 3:1, 9:3:3:1, 27:9:9:3:9:3:3:1, And test crosses of 1:1, 1:1:1:1, 1:1:1:1:1:1:1:1, etc… So that: AaBb selfed Ratio A- B- 9 A-bb 3 aaB- 3 aabb 1 Intra-allelic, No inter-allelic Each gene affecting a separate trait

  10. (Rose) AAbb x aaBB (Pea) F1 AaBb (Walnut) Epistasis: Case 1: 2 genes affecting same trait (inter-allelic interaction between dominant genes) (9:3:3:1 w/ new phenotype) Example: Comb color in poultry A gene Rose (A-) > white (aa) B gene Pea (B-) > white (bb) F2Genotype Phenotype Ratio A-B- Walnut 9 A-bb Rose 3 aaB- Pea 3 aabb White 1 New phenotype

  11. A B Substrate 1 Intermediate Product (green) (red) (purple) F2Genotype Phenotype Ratio A-B- Purple 9 A-bb Red 3 aaB- Green aabb Green 4 Epistasis: Case 2: 2 genes affecting same trait (1st genome masks affects of 2nd genome) (9:3:4) Example: Petal color in Onion (aa is epistatic to B or b) Very common ratio; can confirm with test cross (1:1:2)

  12. Example: Flower color in sweet pea A > a B > b AB = new phenotype F2Genotype Phenotype Ratio A-B- Purple 9 A-bb White aaB- White aabb White 7 Epistasis: Case 3: Complementary gene action; 2 genes affecting same trait (9:7) Can get true breeding heterozygote; just need 1 gene homozygous recessive, acts as inhibitor

  13. F2Genotype Phenotype Ratio A-B- White A-bb White aaB- Yellow 3 aabb Green 1 12 Epistasis: Case 4: 2 genes with A epistatic to B (A- masks B) (12:3:1) Example: Fruit color in summer squash Very common ratio; can confirm with test cross (2:1:1)

  14. F2Genotype Phenotype Ratio A-B- Triangle A-bb Triangle aaB- Triangle aabb Round 1 15 Epistasis: Case 5: Duplicate gene action (15:1) Example: Seed capsule shape in Shepard’s Purse A- (triangle) > aa (round) B- (triangle) > bb (round) Very common ratio; polyploids, interspecifics, diploidized plants; can confirm with test cross (3:1)

  15. A- or bb white (color inhibitors) F2Genotype Phenotype Ratio A-B- White A-bb White aaB- Colored 3 aabb White 1 12 Epistasis: Case 6: Gene A is epistatic to gene B and aa is epistatic to bb (13:3) Example: Feather color in foul

  16. F2Genotype Phenotype Ratio A-B- Dark Purple 9 A-bb Purple aaB- Purple aabb White 1 6 Epistasis: Case 7: Dihybrid Epistasis, Cumulative Duplicate Factors (9:6:1) Example: Petal color in geranium; both dominant genes exhibit a cumulative effect when present together but when alone, produce smaller but equal amounts.

  17. F2Genotype Phenotype Ratio 27 W-A-B- 9 W-A-bb Violet 45 9 W-aaB- 3 W-aabb Light Violet 3 9 wwA-B- 3 wwA-bb 3 wwaaB- White 16 1 wwaabb Epistasis: One example of a Trihybrid Epistasis (45:3:16) (must add up to 64) (Violet) (White) WWAABB x wwaabb W = anthocyanin inhibitor A = anthocyanin intensifier B = anthocyanin intensifier Could just as well have been 27:18:3:16 or 27:21:16 or……

  18. Major Genes and Modifying Factors: MF: genes with small effects that either intensify or diminish the expression of major genes Example: Corn, 80 year breeding history • Within 1st 3 years of controlled breeding, all major genes were selected for and fixed in the populations • All remaining improvements associated with the manipulation of modifying factors • Still making progress after 80 years • Analysis 1o by quantitative genetics

  19. Pleiotropism: • The action of one gene affects more than • one trait (phenotype) • Could be the result of very tightly linked loci • Test - can any recombinants be detected in • large progeny populations? • Could the gene product control the activity • of multiple agents within the cell? • (e.g. transcription factor, signal transduction • component, hormone biosynthesis gene, etc.)

  20. Pleiotropy and epistasis can be assumed to be the norm in biological systems, since genes and their products operate within multiple, mutually interdependent networks, both within the cell and between cells.

  21. Carries dominant gene variegated leaf margins However, only 10% normally express variegation said to have 10% penetrance Penetrance and Expressivity: • The ability of a gene to be expressed in the plant that carries a functional copy Example: Lima beans cv ‘Ventura’ Highly influenced by environment- ranges 0% - 100% plus wide range of phenotypes • Incomplete penetrance with variable expressivity • (also related to ‘leaky genes’) • Tends to obscure link between phenotype and genotype

  22. Penetrance and Expressivity: Thresholds- when expression is dependent on some set of environmental conditions Example: Barley cv ‘Atlas’ Seedlings show albinism only when temperature are below 45oF

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