Heterosis breeding-Classical and molecular concepts

WELCOME
DivisionofVegetableScience
IndianAgriculturalResearchInstitute

Rahul Kumar
Roll no.-10477
Division of Vegetable Science
Indian Agricultural Research Institute
New Delhi
IndianAgriculturalResearchInstitute,NewDelhi
Heterosis breeding-Classical and
Molecular concepts

Phenotypic manifestation of heterosis.
IndianAgriculturalResearchInstitute,NewDelhiDivisionofVegetableScience
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)

History
 Heterosis was first described by Charles Darwin (Darwin
1876) and independently rediscovered by Shull (1908) and
East(1908).
 Term coined by “SHULL” in (1952) as “ stimulation of
heterozygosity”.
 After maize hybrid was first utilized in field on a large
scale in USA in 1930s.
 1st Hayes and Jones (1916) reported hybrid vigor for
cucumber mainly contributed to notable increasing of fruit
size and number.
 F1 hybrid of brinjal was utilized before 1925 in Japan
(Kakizaki , 1931)

QUANTITATIVE DEFINITION
a
1/2
P1 F1 P2
b
P1 Additive Partiallydominant* Dominant* P2 Overdominant*
www.annualreviews.org • Heterosis in Crop Plants 75
Trait
value
1/2
1/2
Midparent heterosis
Better-parent (or high-parent) heterosis
1/2

Heterosis and additive and non-additive
gene expression
Genomic and epigenetic insights into the molecular bases of heterosis
•Z. Jeffrey Chen
Nature Reviews Genetics- 14, 471–482 (2013)
This explains high-parent or low-parent heterosis

GENETIC MODELS FOR HETEROSIS
Complementing action of
superior dominant alleles from
both parental inbred lines at
multiple loci over the
corresponding unfavorable
alleles, leading to improved
vigor of hybrid plants
Allelic interactions
at one or multiple
loci in hybrids
that result in
superior traits
Tomato rin mutant
A simple case of dominance
complementation, in which
the two recessive
mutations (‘a’ from P1 and
‘b’ from P2) are linked in
trans, or ‘in repulsion’.

Epistatic model for heterosis
The epistasis hypothesis considers
epistatic interactions between nonallelic
genes at two or more loci as the main
factor for the superior phenotypic
expression of a trait in hybrids
(Powers 1945).

Discussion on dominance model
AA CC EEbb aadd cc ddee BB
*
Aa Cc EeBb dd
P1 P2
F1
 Cancelling of deleterious
or inferior alleles
 Heterosis depend on
number of dominant
genes.
 Both parents should
differ in dominant genes.
 Complementation across
loci must be cumulative.
(Coors and Panday,1999), to
produce a superior
phenotype.
– Dominance is considered
more popular one (Charles
worth and Willis, 2009).

Dominance may be insufficient
Rapid rate of inbreed—ing
depression in tetraploids
(Dudley, 1974)
The progressive
heterosis in tetraploids
(Groose, et al.1989)
Is the simple complementation
responsible for heterosis
Several evidences suggest
that mechanisms beyond
simple complementation may
be important in heterosis.
The absence of a decline
in the magnitude of
heterosis from improved
inbred parents
(Duvick 2001)

Is over-Dominance sufficient to explain
heterosis
EVIDENCES LIMITATIONS
 Heterozygous individual
may have an advantage due
to the combination of both
allozymes (Falconer and Mackay,
1996)
 Role of single genes in the
manifestation of heterosis
for various traits in
Arabidopsis and Tomato
(Redei, 1962; Semel et. al., 2006;
Krieger, 2010)
 EXAMPLES OF ODO GENES
SFT Gene in Tomato
Erecta mutant inArabidopsis
 For ODO to produce superior
phenotypes, single gene or
small genomic regions are
needed which seem contradict
to the hybrid performance of
many agronomic important
traits controlled by multiple
genes (Lippman and Zamir, 2007)
Though evident as examples of
overdominance, it is possible
that they involve dosage
effects on regulatory networks
(Birchler , 2010)

IndianAgriculturalResearchInstitute Hemizygous
complementation
Complementation of present–
absent genes
Hemizygous complementation of
many such genes with minor
quantitative effects in hybrids
might thus lead to a significantly
increased performance of hybrid
plants.

Progressive heterosis
Progressive heterosis
refers to the fact that
double cross hybrid
autotetraploids (ABCD)
typically show greater
vigor than single cross
hybrids (AABB; CCDD and
so on).
Increased allelic diversity
creates a more robust
heterotic response.
Quadruplex hybrid, which
contains potentially four
different alleles per locus,
exceeds even that of the
hybrids A–B and C–D.
0
1
2
3
4
5
6
7
There is a genomic dosage effect
operating on heterosis

Relative gene expression levels in hybrids and
regulation of allele-specific gene expression in hybrids
.cis-regulation reflect the
relative expression levels of
the parental inbred lines in
the allelic ratio of gene
expression in the hybrid.
• trans-acting factors show
equal expression of the two
alleles in the hybrid.

EPISTASIS AS GENETIC MODEL
FOR HETEROSIS
The interaction of favorable alleles at different loci contributed
by the two parents, which themselves may show additive, dominant
and overdominant action (Powers, 1945, Yu et. al., 1997; Monforte
and Tanksley, 2000; Li et. al., 2001; Luo et. al., 2001)
 The genetic background and allelic interactions can have an effect
on the heterotic contributions of individual loci
 Recently demonstrated in tomato introgression lines that heterosis
is manifested even in the absence of epistasis (Semel, et al. 2006)

Central role of the circadian clock in plant growth and
development
Internal time keepers or circadian clock Regulators
CCA1 - CIRCADIAN CLOCK ASSOCIATED 1
LHY- LATE ELONGATED HYPOCOTYL
TOC1 TIMING OF CAB EXPRESSION 1
in a major negative feedback loop
GI – Gigantia CK2- protein kinase
NADPH oxidases (NOX proteins)
PSEUDORESPONSE REGULATOR (PRR) 3 5 7 and 9
ZEITLUPE (ZTL),
Phytochromes (PHYs) and cryptochromes (CRYs)
JMJD5 encodes a histone demethylase and
activates the morning-phased clock genes
CCA1 and LHY
NADPH oxidases (NOX proteins) activate
CCA1, LHY and GI, and PCL1 represses PRR9
Protein kinases affecting CCA1 binding
affinity and function and leading to
temperature compensation for the clock
The central clock regulators CCA1 and LHY
mediate output pathways regulate genes
in various biological pathways, such as
flowering
The circadian clock also regulates hypocotyl
growth, through repression mediated by an
evening protein complex

Growing around the clock: a molecular mechanism for
hybrid vigor
Diagram of CCA1 and LHY (red line)
and TOC1 (green line) expression
rhythms in a 24-h clock with 16 h
of light (open bar) and 8 h of
darkness (filled bar).
Period is the time forcompleting one
cycle of rhythms and is shown from
one peak to another (or form one
trough to another).
The expression amplitude of
rhythm is defined as one-half
the distance between the peak
and trough.

Epigenetics as
A cause of heterosis TYPES
DNA
METHYLATION
HISTONE
MODIFICATION
RNA
INTERFERANCE
siRNAs,
miRNAs etcCHROMATIN REMODLING
DivisionofGenetics
19
“Epigenetics” refers to
heritable (through mitosis or
meiosis) alterations in gene
expression that are
independent of DNA sequence:
different epigenetically
regulated forms of a gene are
known as epialleles.
Chromatin status, mediated
through epigenetic
modification, can potentially
affect gene expression in cis (at
the gene itself) or in trans (by
regulating loci indirectly).

DNA methylation and heterosis
Conversion of cytosine to 5 methyl cytosine.
Could generate epigenetic variation/ Epialleles and creation
of hybrid vigour.
DNA methylation does not change the DNA sequence and its
function, but does change its expression level, referred as
an epigenetic change.
Associated with gene silencing, and genes with abundant 5-
methylcytosine in their promoter region are usually
transcriptionally silent. (Jones and Takai, 2001; Dong et
al,2006)
It can be suggested that inbreeding depression partly or primarily results
from lower levels or fewer genes expressed simply due to homozygosity
of methylated DNA in regulating factors.
 Heterosis is from higher levels or larger number of genes expressed
simply due to heterozygous conditions between methylated and non-
methylated DNA in the F1 hybrid.

Molecular changes at epigenetic, genomic, proteomic and
metabolic levels lead to heterosis traits

Small RNAs
small interfering RNAs (siRNAs)
Mediate post-transcriptional gene silencing,
RNA-directed DNA methylation, and chromatin
remodeling.
These RNAS are negative regulators of target
transcript accumulation (Allen et al.,2005).
miRNAs and siRNAs are differentially
expressed between hybrid and its parental
inbred lines (Mica et al.,2006).

A model for small RNAs in the allelic expression of genes and
transposable elements in hybrids and allopolyploids.
Silenced
Expressed
RNA Directed DNA methylatin
Reduced vigour Increased amount of si RNA
cis and trans acting effect
TE –Transposable element, siRNA-Small interfering RNA ,
Gene activation of parent 1
Gene silencing of parent 2

QTL AND HETEROSIS
Molecular breeding may act one of the promising approach to
unreveal 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.
Provide answer to certain questions.
Which genes are involved and their nature?
Epistatic properties of these genes?
Their interaction with environment?
How best to exploit heterosis fully?
Number of genes or genomic regions involved and their distribution?
(Coors and Panday,1999)

Numerous QTLs with different levels of
dominant, over dominant, and epistatic effects
have been mapped for heterosis in
Tomato (Semel et al., 2006),
A. thaliana (Hua et al. 2003;Kusterer et al., 2007;
Melchinger et al., 2007;Meyer., et al 2010).
Besides the involvement of various gene actions found in
these studies, all the three gene actions may condition
heterosis in crops (Li et al, 2008; Swanson-Wagner, et al
2006).

EMERGING MODEL BASED ON
ENERGY USE EFFICIENCY
EnergyBiomass = Energyinput -
Energyconsumed
Mixing of two distant genomes
brings about cis, trans, and
chromatin level changes in the
hybrid.
Differential expression of genes.
Additive or non additive modes of
gene action
May affect major regulatory
pathways
Regulate downstream metabolic
pathways in either a positive or a
negative manner.

Case study 1

Precocious shoot termination in determinate tomatoes
is partially suppressed by sft/+ mutant
heterozygosity.
Indeterminate
leaf production to decrease
(Red: fully ripe fruit; orange: ripening fruit; green: unripe fruit;
yellow: flowers) Arrows represent canonical axillary shoots.
Asterisks

Delay in precocious termination.
Colored bars indicate average leaf numbers within sympodial units with standard deviations. Statistical
significance in B and C was tested by Wilcoxon rank sum test, and significance levels are indicated by
asterisks (*P,0.05, **P,0.01, ***P,0.001). doi:10.1371/journal.pgen.1004043.g001
Continued….

sft/+ heterozygosity induces
weak semi-dominant delays in
both primary and sympodial
flowering transitions.
Note the extremely delayed
flowering of sft sp double
mutants, indicating a weak
semi-dominant effect for
sft/+ heterozygosity.
sft/+ sp plants
show slightly
delayed primary
shoot flowering
time compared to
sp as measured by
leaf production
before formation
of the first
inflorescence.
Statistical differences were tested by Wilcoxon rank sum tests and significance levels
are marked by asterisks (***P,0.001). {sympodial inflorescence meristems (SIM)}
(B–G) Representative images and quantification of
developmental progression (ontogeny) of meristems in
the first inflorescence and sympodial shoot
meristems (SYM) of sp (left images) and sft/+ sp
plants (right images) at 20th DAG.
SYM of sp mutants completed the
flowering transition and differentiated
into the first or second FM and
initiated the next SIM,
Delayed sim

Transcriptome profiling reveals a semi-dominant delay in
meristem maturation from sft/+ heterozygosity.
EVM- Early Vegetative Meristems
MVM -Middle Vegetative Meristems
LVM -Late Vegetative Meristems
TM - Transition Meristem
FM-Flower Meristem
TM - Transition Meristem First sympodial shoot meristem (SYM)
DDI quantification of SYM maturation
scores indicate an intermediate maturation
TM maturation state indicating sft/+
heterozygosity causes a semi-dominant
delay in the primary flowering transition.
Semi dominant delay
Intermediate maturation

Case study 2

Distribution of QTL mode of inheritance for
tomato traits.
QTL
341
QTL
382
QTL
118
QTL classified as dominant means that both the IL (homozygous for the S. pennellii
allele) and the ILH (heterozygous) were very similar to each other
A recessive QTL means that only the IL is significantly different from M82,
whereas the ILH is similar to M82.
Additivity reflects a situation in which the ILH is in between its parents
ODO is inferred where the ILH is significantly higher or lower than both its
parents.

The frequency distribution of the mode-ofinheritanceindex for QTL in
the reproductive and nonreproductive groups.
The ‘‘reproductive’’ curve (QTL for
increasing reproductive traits) has a
peak in the ODO domain,indicating
that many of the QTL fall within this
mode of inheritance
In contrast, most of the QTL for the
nonreproductive group and for the
decreasing reproductive phenotypes
resided in the recessive–additive
domain.
Heterosis is partitioned, in part, into
small genomic regions that convey
advantage in the heterozygous state
(ODO QTL), and, together, they
contribute to the genome-wide effect
Seed no and fruit per plant =Reproductive fitness

CONCLUSION
 Heterosis is result of interacting genomes, resulting in
complex changes at the genetic, epigenetic, biochemical and
regulatory network levels
 Epigenetic regulation of circadian-mediated changes in
chlorophyll biosynthesis and starch metabolism offers one
of the direct links to growth vigor in plant hybrids
 Availability of novel genetic and genomic tools, that allow
for the integrated study of the complex interactions
between genome organization and expression might
contribute to a better understanding of heterosis.

Heterosis breeding-Classical and molecular concepts

Heterosis breeding-Classical and molecular concepts

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