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Gene Regulation – Part 2: Gene Regulation – Part 2:

Gene Regulation – Part 2: - PowerPoint Presentation

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Gene Regulation – Part 2: - PPT Presentation

Interlocus Interactions PBG 430 Locus A Allele A Allele a Locus B Allele B Allele b Phenotype Interlocus interactions Epistasis Interactions between alleles at different loci ie interaction between genes ID: 816123

dominant locus allele gene locus dominant gene allele recessive aabb duplicate wwyy epistasis cyanide vernalization interaction fruit needed sensitivity

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Slide1

Gene Regulation – Part 2: Inter-locus Interactions

PBG 430

Locus

A

Allele A

Allele a

Locus

B

Allele B

Allele b

Phenotype

Slide2

Inter-locus interactions (Epistasis)Interaction(s) between alleles at different loci (i.e. interaction between genes)Gene interactions are the rules rather than the exceptionsMany types of epistasis Example of duplicate recessive epistasis = cyanide production in white clover

Slide3

Cyanide concentration in clover: A case studyExample parental, F1, and F2 phenotypes:

Parent 1Low cyanideXParent 2Low cyanideF1

High cyanide

F2 (9 High cyanide :

7 Low cyanide)

Slide4

Duplicate recessive epistasisCyanide concentration is determined by two genes under duplicate recessive epistasisOne dominant allele at each locus will lead to high cyanide concentrationThe effects of dominant alleles are “masked” if either locus is homozygous recessiveWhat would be the doubled haploid ratio?AAbb

Low CyanidexaaBBLow CyanideF1AaBbHigh Cyanide

F2

AB

Ab

aBab

AB

AABBAABb

AaBB

AaBbAb

AABb

AAbb

AaBb

Aabb

aB

AaBB

AaBb

aaBB

aaBb

ab

AaBb

Aabb

aaBb

aabb

9 High

:

7 Low Cyanide

Slide5

Two models explaining Duplicate Recessive EpistasisRegulatory gene modelStructural gene vs. regulatory gene

Metabolic pathway modelEach gene encodes a different enzymeCyanide production in cloverPrecursor enzyme 1 (AA; Aa)Glucoside

Enzyme 2 (BB; Bb)

Cyanide

Slide6

Dominant EpistasisExample: fruit color in summer squash (Cucurbita pepo)

P1White fruit xP2Yellow fruitF1Yellow

fruit

F2

12 white:

3 yellow:

1 green

Slide7

Dominant Epistasis: Example squash fruit colorTwo genes determine fruit color in Cucurbita pepoThe expression of any allele at the Y locus is masked by a dominant allele at the W locuswwyy will produce green fruitWWyy

White FruitxwwYYYellow FruitF1WwYyWhite Fruit

F2

WY

WywY

wy

WY

WWYYWWYy

WwYY

WwYyWy

WWYy

Wwyy

WwYy

Wwyy

wY

WwYY

WwYy

wwYY

wwYy

wy

WwYy

Wwyy

wwYy

wwyy

Slide8

Dihybrid F2 ratios with epistasis

Gene InteractionControl PatternA-B-A-bbaaB-

aabb

RatioAdditive

No interaction between loci

9

3

3

19:3:3:1

Duplicate Recessive

Dominant allele from each locus required

9

3

3

1

9:7

Duplicate

Dominant allele from each locus needed

9

3

3

1

9:6:1

Recessive

Homozygous recessive at one locus masks second

9

3

3

1

9:3:4

Dominant

Dominant allele at one locus masks other

9

3

3

1

12:3:1

Dominant Suppression

Homozygous recessive

allele at dominant suppressor locus needed

9

3

3

1

13:3

Duplicate Dominant

Dominant allele at either of two

loci needed

9

3

3

1

15:1

No gene interaction

Slide9

Dihybrid doubled haploid ratios with epistasis

Gene InteractionControl PatternAABBAAbb

aaBBaabb

Ratio

AdditiveNo interaction between loci

1

1

1

11:1:1:1

Duplicate Recessive

Dominant allele from each locus required

1

1

1

1

1:3

Duplicate

Dominant allele from each locus needed

1

1

1

1

1:2:1

Recessive

Homozygous recessive at one locus masks second

1

1

1

1

1:1:2

Dominant

Dominant allele at one locus masks other

1

1

1

1

2:1:1

Dominant Suppression

Homozygous recessive

allele at dominant suppressor locus needed

1

1

1

1

3:1

Duplicate Dominant

Dominant allele at either of two

loci needed

1

1

1

1

3:1

No gene interaction

Slide10

Vernalization sensitivity: An important trait showing epistasisIn vernalization-sensitive genotypes, exposure to low temperatures is required for a timely transition from the vegetative to the reproductive growth stage Why is vernalization a trait of interest?Flowering time is related to productivity (yield)Vernalization sensitivity is often correlated with low temperature tolerance, which is required for winter survivalFall-planted, low temperature-tolerant cereal crops  a tool for dealing with climate change and improve water use efficiency from winter precipitation

Is vernalization-sensitivity a pre-requisite for low temperature tolerance?

Slide11

Vernalization sensitivity in barleyTakahashi and Yasuda (1971)Three-locus epistatic interaction: VRN-H1, VRN-H2, VRN-H3

VRN-H_ loci and allelic configurationsVernalization sensitivityV1

V2V3

V

VV

No V

V

vNo

Vv

VNo

V

vv

No

v

V

V

No

v

V

v

Yes

v

v

V

No

v

v

v

No

Slide12

A model for inter-locus repression and expression Domestic barley varieties  vernalization trait explained by interaction of two genesVRN-H2 and VRN-H1Winter barleys are sensitive to vernalization while spring and facultative barleys are not

Slide13

Gene regulation – beyond intra-locus and inter-locus interactionsDNA sequences outside the coding sequence and outside the geneFactors beyond the DNA level

Coding sequence = Exon 1 + Exon 2 + Exon 3 + Exon 4Same genotype, but different phenotypes

Slide14

Gene regulation summary Outside coding sequencePromoters - constitutive, tissue-specific, inducible: CaMV 35S (constitutive), Glutelin GT1 (tissue-specific), Cis-Jasmone (inducible)Outside gene (i.e. another gene)Transcription factors - Facilitate, enhance, repress: Vrs1, Nud, VRN-H2Beyond DNA levelRNAi: miRNA, siRNA, hnRNA, lncRNA, puRNA, shRNA, snoRNA, tiRNA, …. mRNA stability - minutes to months: 5’ cap, 3

’ tail protect mRNA from nucleasesChromatin remodeling: Accessibility of DNA to transcription machineryLevel of condensation/compaction, DNA methylationTranslational and post-translational modification of proteins:Protein synthesis rate, transport, stability, activity Gene coding sequenceInter- and intra-locus interactions

Slide15

By now, you should be able to…Define epistasis. Use cyanide production in clover (a type of Duplicate Recessive Epistasis) and fruit color in summer squash (a type of Dominant Epistasis) as examples for your explanation.Describe the two models proposed to explain Duplicate Recessive Epistasis. For each model, explain why a loss of function in either locus will produce the mutant phenotype.Given a type of epistasis (we will limit ourselves to the two types covered in detail – digenic Duplicate Recessive and Dominant), and the genotype of the parents, predict the phenotypic ratios in an F2 and in a doubled haploid (produced from the F1) generation. Differentiate the three growth habits possible in barley based on vernalization sensitivity, cold

tolerance, and planting time.For each growth habit, explain the genetic cause of vernalization (in)sensitivity based on the 2-locus model (assuming the third locus is homozygous).Describe other ways in which genes are regulated, besides inter- and intra-locus interactions. Remember, genes can be regulated by DNA sequences outside the coding sequence of a gene, outside genes, and even by factors beyond the DNA level. Give examples of gene regulation mechanisms that can affect phenotype without changing the genotype.