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
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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
Slide2Inter-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
Slide3Cyanide 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)
Slide4Duplicate 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
Slide5Two 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
Slide6Dominant EpistasisExample: fruit color in summer squash (Cucurbita pepo)
P1White fruit xP2Yellow fruitF1Yellow
fruit
F2
12 white:
3 yellow:
1 green
Slide7Dominant 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
Slide8Dihybrid 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
Slide9Dihybrid 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
Slide10Vernalization 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?
Slide11Vernalization 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
Slide12A 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
Slide13Gene 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
Slide14Gene 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
Slide15By 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.