mechanisms creating heterosis in the genotypes at molecular level i.e., in the areas of transcriptomics, proteomics and metabolomics by DNA methylation, small RNAs, histone modifications and parent-of-origin effect

1. Molecular basis
of Heterosis
Presented by:
RAD/18-20;
K. Divya
PROFESSORJAYASHANKARTELANGANASTATEAGRICULTURALUNIVERSITY
Collegeof Agriculture,Rajendranagar-500030

2. Heterosis:
• Superior performance of heterozygous F1 hybrid plants in
terms of increased biomass, size, yield, speed of
development, fertility, resistance to disease and insect
pest, or to climatic rigors of any kind compared to the
average of their homozygous parental inbred lines (Shull,
1952 & Falconer, 1996).
• Term coined by “SHULL”
• In 1914 as “stimulation of heterozygosis ”

4. Introduction
 Molecular breeding may act one of the promising approach to un
reveal genetic basis of heterosis.
 Mainly used to identify genes or genomic regions that contribute
heterosis for trait of interest, that may be used in MAS to increase
performance of hybrids but still challenging.
• The degree of heterosis may shift during different stages of growth
and development
Eg: If growth vigor shown at seedling stage may show at reproductive
stage also, but in some plants it is not.
• Because they are controlled by different sets of genes and
regulatory pathways.
 Sequencing methods can also detect allelic interactions, including
the silencing of one allele that is compensated by the
upregulation of another.

6. Heterosisand gene expression
Genome wide changes in geneexpression
• Intraspecific
hybrids
A. thaliana, rice,
maize, wheat
• allopolyploid
Arabidopsis, cotton
wheat, Senecio
Tragopogan
• Results:
Some changes are
additive and
others are non-
additive

7. • Hybridization between two parental lines can cause changes in
the expression of a variety of proteins, and it can be concluded
that the altered pattern of gene expression at translational level
in the hybrid may be responsible for the observed heterosis.
• The maternal contribution of nutrients and metabolites to
growth vigour is consistent with the parent-of-origin effect on
biomass vigour in reciprocal hybrids.
• Limited numbers of particular metabolites provide useful
‘biomarkers’ for the prediction of heterosis (Korn et al, 2010)

8. Molecular mechanisms of reprogramming interacting genes
HISTONE
MODIFICATION
CHROMATIN REMODLING
Small RNAs
siRNAs, miRNAs etc

9. small RNAs
• Small RNAs, including small interfering RNAs (siRNAs), microRNAs
(miRNAs) and trans-acting siRNAs (ta-siRNAs), mediate gene
expression and/or epigenetic regulation
• Most siRNAs are derived from TEs & repeats, thus have diverged
between sp. can target homologous genomic DNA sequences for
cytosine methylation
• Differences in siRNA levels between hybrids or allopolyploids and
their parents could alter allelic patterns of expression, RNA directed
DNA methylation (RdDM) and overall genomic stability
• These siRNAs are predicted to serve as a genetic buffer for balancing
‘genome shock’ (also known as genetic chaos) in newly formed
allopolyploids

10. • 24-nucleotide siRNAs guide the de novo methyltransferase DRM2
to homologous loci to establish DNA methylation, which leads to
transcriptional silencing (Law and Jacobsen, 2009, 2010)

11. DNAMethylation
• Addition of methyl group to cytosine
residue (CG, CHG & CHH) (H= A,C or
G )
• In plants, CG and CHG methylation is
maintained by DNA
METHYLTRANSFERASE1 (MET1) and
CHROMOMETHYLASE3 (CMT3)
• CHH methylation by DOMAINS
REARRANGED
METHYLTRANSFERASE (DRM2)
• Greatest increase at CG site is 18-26%
in parents to 36-37% in hybrids
• Degree of methylation changes in
hybrids depends on parental
divergence (higher in diverse parents)
(Law and Jacobsen, 2010)

12. • Silencing mechanism predominant in transposons and repetitive
DNA elements
• >96% of methylation increase in hybrids corresponds to siRNA
generating regions that are divergent between parents (RdDM)
• In maize, pericentromeric regions with recombination suppression are
under strong selection in inbred lines, and the genetic divergence
between these regions is predicted to affect heterosis (this region
probably contain divergent TEs & genes affected by siRNA & RdDM)
---(Gore et al, 2009)
• Clock genes including CCA1 & LHY are unregulated in DNA
methylation mutants (CCA1 & LHY repressed normally)

13. Histone modifications
• In Arabidopsis allotetraploids, expression peaks of CCA1 and LHY and
of their regulators TOC1 and GI are altered relative to the progenitors
and are positively associated with levels of histone H3 lysine 9
acetylation (H3K9ac) and H3K4 dimethylation (H3K4me2)
siRNA (RdDM)

14. Epigenetic effects:
Parent-of-Origin and Transgenerational effects:
• These effects could be associated with a major group of Pol IV-
dependent siRNAs (p4-siRNAs), as these siRNAs are maternally
transmitted.
• The expression of maternal p4-siRNAs correlates negatively with the
expression of a group of AGAMOUS-LIKE (AGL) genes that encode
type I MADS-box transcription factors which are expressed in
endosperm and are involved in regulating seed size