Genetics of Qualitative Phenotypes .....

Genetics of Qualitative Phenotypes explanation with examples

1. GENETICS OF QUALITATIVE PHENOTYPES D.D.T.T.D. Senarathna School of Environmental Resources and Management Asian Institute of Technology

2. OUTLINE Phenotype Gene interactions Epistatic gene interactions Multiple alleles Pleiotropy Penetrance & expressivity Sex-inherited phenotypes Sex-linked traits & genes Sex-linked traits in fish Sex-limited phenotypes References

3. PHENOTYPE Phenotypic variation Genetic polymorphism Qualitative variation Quantitative variation 1 Perceptible Comprise classical genetics Ex . Color and tail type of fish Measurable Ex . Weight and length Least common allele frequency ≥ 1% Single nucleotide polymorphisms (SNPs) Sequence repeats (satellite DNA) Insertions Deletions Recombination A

4. GENE INTERACTIONS Single autosomal genes Additive gene action Non-additive gene action DOMINANT GENE ACTION Allele allele Same gene loci Complete dominance Incomplete dominance Co-dominance 2 Three genotypes: Two phenotypes Three genotypes: Three phenotypes Three genotypes: Three phenotypes 4

5. Examples 3 Albinism in Channel catfish ++ aa +a +a Possible gametes Normally pigmented Albino Normally pigmented P F1 F2 G gene of tilapia: number of melanophores and xanthophores/ body color F1 P F1 GG Gg gg Gg Gg Possible gametes P Gg Gg

6. ADDITIVE GENE ACTION DIHYBRID INHERITANCE 4 Neither allele is dominant Both contribute equally ‘G’ gene in Rainbow trout: golden, palomino, and normally pigmented body color F1 Possible gametes P GG’ GG’ GG GG’ G’G’ FFEE Normal tail: Normal eye ffee Fancy tail: Big eye 9 : 3 : 3 : 1 Golden Palomino Normal

7. EPISTATIC GENE INTERACTIONS 5 Dominant epistasis Recessive epistasis 9 black eyes: 3 brown eyes: 4 pink eyes 12 dark: 3 light: 1 albino M SS, Ss, ss m SS, Ss, ss

8. MULTIPLE ALLELES 6 Many genes have three or more alleles Qualitative phenotypes can range from 1 to more than 12 Three alleles: B gene in Medaka - melanin formation - B, B’ and b alleles More than three alleles: D gene in Angel fish P gene in Platy fish 4 alleles D, D m , d + , d ng 9 phenotypes 9 alleles P + , P C , P M , P MC , P Cc , P O , P Co , P D , P T 27 visible phenotypes

9. PLEIOTROPY 7 Trait A Trait B Trait C Trait D Single gene Do not always produce a given phenotype Advantageous Disadvantageous R ainbow trout - b allele - iridescent metallic blue body color + Improved growth rate. C hannel catfish - a allele - albinism in homozygous state (aa) + Spawn later; produce smaller egg masses; poor quality eggs; poor hatch percentage; less viable progeny b BC GR a BC

10. PENETRANCE & EXPRESSIVITY 8 Genotype does not produce the expected phenotype Dominant allele may affect differently on individuals Specific genotype may exhibit phenotypic variability or a range of different phenotypes Penetrance Expressivity Percentage - exhibit the expected phenotype The physical manifestation of a phenotype Temperature : an agent causing variable penetrance and expressivity in fish Confusing phenotypic ratios and erroneous phenotypic categories : cause problems during genetic analysis and selective breeding programs B Lakna (2017)

11. SEX-INHERITED PHENOTYPES 9 Qualitative phenotype Autosomal genes Sex-linked genes At least two alleles Dominant interaction in both males and females Reciprocal crosses: same results Alleles passed equally Males carry only one allele (hemizygous) Dominance interaction only in females Reciprocal crosses: different results Criss-cross inheritance pattern Traits carried on sex chromosomes Sex-influenced traits Sex-linked traits Sex-limited traits Autosomal traits influenced by sex . Ex. Pattern Boldness Expressed only in one sex Ex . Milk production More males express it. Ex . Color - blindness

12. SEX-LINKED TRAITS & GENES IN FISH 10 Sex-linked traits Found in a few species of fish: Guppy and platy Guppy sex chromosomes: Source: http://dx.doi.org/10.3390/genes9050233 Sex-linked genes Hemizygous : Individuals carrying one allele of a gene: Mammalian males C

13. SEX-LINKED TRAITS IN FISH Y – Linked Genes 11 Inheritance from father to son Y-linked phenotypes are seen in only one sex (Males) Gene Phenotype Y Ma Maculatus pigmentation Y Ir Iridescens pigmentation Y Ar Armatus pigmentation Y Sa Sanguineus pigmentation Y Pa Pauper pigmentation F1 Possible gametes XY ma XX P XX Grey ♀ XY Grey ♂ XY ma Maculatus ♂ 1 grey ♀ : 1 maculatus ♂ Khoo et al. (1999) D Genetic map of the Y chromosome of the guppy

14. X – Linked Genes 12 Mode of gene action: simple dominance Inheritance follows a criss-cross pattern Gene Phenotype X Cp Caudalis pigmentation X Co Coccineus pigmentation X Rdt Red tail X Blt Blue tail X Grt Golden yellow tail X Vi Vitellinus pigmentation X Ci Cinnamoneus pigmentation 2 caudalis ♀ : 1 caudalis ♂ : 1 transparent-tailed ♂ 1 caudalis ♀ : 1 transparent-tailed ♂ X Cp X Cp – Caudalis ♀, X Cp X ch – Caudalis ♀, X ch X ch - Transparenttailed ♀, X Cp Y – Caudalis ♂, X ch Y – Transparenttailed ♂ 1 caudalis ♀ : 1 caudalis ♂ : 1 transparent-tailed ♀ : 1 transparent-tailed ♂

15. SEX-LIMITED PHENOTYPES 13 Traits which are expressed only in one sex The tigrinus phenotype in guppy is controlled by the X Ti dominant sex-linked allele . Many of the sex-limited traits need testosterone to be expressed Most of the X-linked genes in guppy produce phenotypes that’re sex-limited to the males XX Grey ♀ XX Ti Grey ♀ X Ti X Ti Grey ♀ XY Grey ♂ X Ti Y Tigrinus ♂

16. SUMMARY 14 QUALITATIVE PHENOTYPES GENE INTERACTIONS Single autosomal genes Two or more autosomal genes Sex-linked genes Dominant gene action Complete dominance Incomplete dominance Co-dominance Dihybrid inheritance Epistatic gene interactions Dominant epistasis Recessive epistasis Multiple alleles Pleiotropic effects Penetrance Expressivity Traits on sex chromosomes Sex-linked traits in fish Sex-linked genes Y – Linked Genes X – Linked Genes Sex-Limited Phenotypes

17. REFERENCES Khoo, G., Lim, T.M., Chan, W.K., Phang , V.P.E., 1999. Linkage analysis and mapping of three sex-linked color pattern genes in the guppy, Poecilia reticulata. Zoolog . Sci. 16, 893–903. https://doi.org/10.2108/zsj.16.893 Panawala , L., Between, D., 2017. Difference Between Penetrance and Expressivity Main Difference – Penetrance vs Expressivity. A B C D Penetrance versus Expressivity: https://www.mun.ca/biology/scarr/Penetrance_vs_Expressivity.html Guppy sex chromosomes: http://dx.doi.org/10.3390/genes9050233 Genetic map of the Y-chromosome of the guppy, Poecilia reticulata: http://dx.doi.org/10.1016/j.gendis.2015.02.006 https://genetics.thetech.org/ask-a-geneticist/oca2-and-23andme

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