The hidden consequences of epigenetics behind the phenomena of heterosis

1. Role of Epigenetics In Heterosis
L-2018-A-110-M
MOHD KYUM
L-2018-A-110-M
Department of Plant Breeding and Genetics
PAU,LUDHIANA

2. Contents…
Introduction of heterosis
Genetic basis of heterosis
Relation of epigenetics with genetics
Introduction of Epigenetics
Mechanism of epigenetics
Role of epigenetics in heterosis
Few case studies showing epigenetics relation
with heterosis
Future knowledge
conclusion

3. HETEROSIS
• Superior performance of heterozygous F1
hybrid plants over their homozygous parental
inbred lines
• Term- G.H.SHULL(1914)

4. HETEROSIS-HYBRID VIGOUR
• Heterosis is most evident for adult traits but is already manifested during
embryo and early seedling development

5. HETEROSIS-HYBRID VIGOUR
Figure. Growth vigour in plant hybrids.

6. HETEROSIS-AN INTRESTING MYSTERY
• Sum total of all genetic interactions in F1 hybrid cant
explain every aspects of heterosis
• Emphasis to non genetic interactions
• Epigenetic effects: regulate gene expression cell fate
and non mendelian inheritance

7.  Heterosis arise from Complementation of defective parental alleles
 Heterosis arise from interaction between parental alleles
 Hybrids rise from interaction between different parental genes
Classical Explanations of Heterosis
1.Dominance Hypothesis
2.Over Dominance Hypothesis
3.Epistasis Hypothesis

8. INTERPRETATION OF CLASSICAL
EXPLANATION
 Hybrids are showing significant differences even within genetic co-linearity in individual
at different levels
 No uniform global expression patterns were observed in different gene expression
studies
 Similar no. of gene showing both Additive and non Additive expression
 Indications from studies that there is no key gene that might directly correlate directly
with heterosis
 Significant expression differences found between parental inbred lines than
between reciprocal hybrids
 There is no directly link between the classical genetic hypothesis and these
gene expression profiles

9. Heterosis Fixation and Differential Gene
Expression
Fig. Fixation of Heterosis
Fig. Additive & non Additive expression

10. A modern concept of heterosis
Epigenetics (The
molecular basis of
heterosis)
How????

11. Epigenetic = Differential expression of genome
Waddington CH, 1942
http://bioinformatics.hgen.slu.se/SLUBIO2018/SLUBIO2018/
Lectures_files/Epigenetics_an%20introduction_1.pdf
Epigenetics (Epi = “above” or “upon”)
Epigenetic effect

12. Cell types
http://www.saburchill.com/chapters/chap0106.html
meristem cell

13. How Epigenetics Works

14. Features of Epigenetics
EPIGENETICS
Epigenetics marks
deviated from
mendelian inheritance
Spatio-temporally
change
Inheritance of
Acquired
Characteristics
DNA and
Chromatin level
Epialleles-identical DNA
different epigenetic
states
Heritable changes
Same genotype
different
phenotypes
No DNA sequence
change

15. Genetics vs Epigenetics
Genetics Epigenetics
DNA sequence Epigenetic marks attached to DNA
sequence/ amino acid sequence
Tells the putative potential of of a
DNA/gene sequence to form protein
Actually tells whether it will express
or not
Tells which particular protein will be
formed from a particular gene
Tells where and when gene product
will be formed
Environment has little effect on
genomic sequence
Environment has considerable effect
on the epigenome
Mutations and transpositions
regulate the gene expression
Epigenetic modifications regulate
gene expression
There is no reprograming There is reprograming
Mostly constant Dynamic

16. MECHANISMS
1. DNA methylation
2. Histone modifications
• Acetylation
• Methylation
• Phosphorylation,
3. RNA mediated
interference

17. 1. DNA Methylation
Methylation types = CG, CNG, CNN (N= A, T and C)
Enzymes = MeT1 (CG), CMT3 (CNG) and DRM (CNN)

18. De novo DNA Methylation in plants
Bond D M and Baulcombe D C (2014) Trends in Cell Biology. 24 (2): 100-7

19. 2. Histone modification
Strahl B D and Allis C D (2000) Nature 403: 41-5

20. Histone modifications and their functions
https://www.quora.com/Why-are-histone-modifications-H3-K4-H3-K36-H3-K79-
active-and-H3-K9-H3-K27-and-H4-K20-modifications-repressive

21. Techniques for determination of
epigenetic markers
MSAP
(Methylation-sensitive
amplified
polymorphism)
Bisulfite
Sequencing
McrBC Digestion
Microarray
Technique
ChIP Technique
(Chromatin
immunopactine
precipitation tech.)

22. Molecular basis of heterosis
Fig. 1. Model for epigenetic inheritances in F1 and the effect
on transcription activities.

23. EPIGENETIC VARIATION & HETEROSIS
Fig: Genetic and epigenetic regulation of gene expression in hybrids
Guangming et al., 2013

24. Molecular basis of heterosis

25. Figure 2. Hemizygous complementation in maize hybrids and showing further
inbreeding depression (Loss of Genetic Colinearity)
Molecular Basis of Heterosis

26. Gene Expression Levels In Hybrids
Figure . Relative gene expression levels in hybrids and regulation of allele-specific
gene expression in hybrids

27. Mechanisms of Epigenetics with relation to
heterosis
Fig. 2.2 A possible model linking epigenetics to the alteration of biological networks

28. TRANSPOSABLE ELEMENTS

29. Role of Transposable Elements in Heterosis
Figure. A model for small RNAs in the allelic expression of genes and
transposable elements in hybrids and allopolyploids.

30. 1. Case study
Fig.-Heterotic phenotypes of 35-d-old
Arabidopsis F1 hybrids (Flc and Fcl)
relative to their parents (Ler and C24).
 Material and methods-
• They compared methylation at single- base-
pair resolution in genome of Arabidopsis
thaliana ecotypes, Landsberg erecta and
C24 parental lines and their reciprocal F1
hybrids.
• Methylation is estimated by using bisulfite
sequencing method.
 Objective-
To investigated whether DNA
methylationplays a role in heterosis in
plants or not.

31. Fig-Bulk methylation levels of Ler and
C24 parental line and their reciprocal
hybrids when 0 mismatch mapping was
allowed.
 Both reciprocal F1 hybrids exhibited
significant growth vigour in many
characters, including fresh weight, leaf
number, root length, and silique number.
 Both hybrids displayed increased DNA
methylation across their entire genomes.
 They found that 77 genes are sensitive to
methylome remodelling.
 These genes are transcriptionally repressed
in both reciprocal hybrids, including genes
involved in flavonoid biosynthesis and late
elongation of hypocotyl.
Result-

32. 2. Case study
Objective –
Toinvestigatechange in genome wide methylation pattern for tolerantand
susceptible cultivars of rice, under drought stress condition.
Material and methods-
• Two varieties of rice DK151 (drought tolerant) and IR64 (drought
susceptible ) were used in the experiment.
• The DNA methylation changes in DK151 and IR64 under drought stress and
subsequent recovery were assessed using methylation-sensitive amplified
polymorphism technique (MASP).

33. Under stress condition- IR64 suffered yield losses of 96.4%.
DK151 yielded 3.1 times as much as IR64, indicating its good
level of drought tolerance.
The better Drought tolerance of DK151 was associated with 7
–8
days of earlier heading and significantly improved fertility and
grain filling under drought.
Under irrigated control conditions- DK151 (DT) suffered
significant yield penalty by 17.3% and its yield was 23.2%
lower than IR64 under the irrigated control conditions.
RESULTS

34.  Drought induced genome-wide changes in DNA
methylation and demethylation patterns.
 Large difference in DNA methylation and
demethylation sites between drought tolerance and
drought sensitive varieties.
 Resistant genotype is highly methylated and also
retain methylation under stress condition.
 Susceptible genotype is less methylated and lesser
retention of methylation under stress condition.
interpretations

35. 3. Case study
Objective-
 To investigate effect of salt stress induced histone acetylation on
expression of cell wall related genes in roots of maize plant.
 Material- Maize variety huayu 5 was used.
 Treatment- Seedlings were grown in hydroponic cultures in
buckets containing 1/2 Hoagland’s nutrient solution in a
controlled environment.
When the seedlings were on two leaves stage, 200 mM NaCl was
added to nutrient solution to initiate the saline treatment.

36. A) Effect of different salt concentrations on root
growth.
B) Growth in control and salt stress at different
intervals.
 Phenotypic results
• After exposure to 200 mM
NaCl seedling growth was
inhibited as well as the
number of secondary roots
were reduced .
• Roots were swollen at the
elongation zone and the
length of the meristematic
zone was decreased.
• After 96 h the primary root
length was decreased by 27%
and the plant height was
reduced by 26% as compared
with the control group.

37.  By using in situ chromatin immune
staining technique they found that the
H3K9 and H4K5 acetylation levels under
normal growth conditions were not
significantly altered at the indicated times
but salt stress induced an increase in
global acetylation of H3K9 and H4K5 as
the duration of exposure was increased
 By using chip (Chromatin immune
precipitation)technique they found that
up-regulation of the ZmEXPB2 and
ZmXET1 genes was directly associated
with the elevated H3K9 acetylation
levels.
• Conclusion-Histone modification as a
mediator may contribute to rapid
regulation of cell wall related gene
expression, which reduces the
damage of excess salinity on plants.
 RESULTS
H3K9 (A) and H4K5 (B).showing increased
acetylation level at the indicated times.

38. Unanswered Questions
1.Direct and strong evidence for
heterosis?
2.How epigenetics variation builds up
in hybrids ?
3.How they interact with genetic
variations ?

39.  The field of epigenetics has rapidly developed into one of the
most influential areas of scientific research.
 Recent advances in analytical methodology have allowed for a
significant expansion of what is known about genome wide
mapping of DNA methylation and histone modifications.
 Good knowledge of epigenetic mechanisms leads to better
understanding of regulation of gene expression at
transcriptional and post-transcriptional levels.
 Epigenetic mechanisms such as DNA methylation and histone
modification play a key role in plant development and stress
response.
 Mechanism of trans-generational epigenetic inheritance is still
not clear.
CONCLUSIONS

40. THANK YOU