Hybrid-enabled line profiling (HELP) is a new integrated breeding strategy for self-fertilizing crops that combines existing and recently identified elements, resulting in a strategy that synergistically exceeds existing breeding concepts.

1. Cross the Best with the Best, and Select the Best: HELP in Breeding
Selfing Crops
HELP – Hybrid Enabled Line
Profiling
Maarten van Ginkel and Rodomiro Ortiz
A presentation by
SHREYA MANDAL-11733-BIO
RAMESH -11791-GEN
GOVINDA RAI SARMA-11792-GEN
NITESH KUSHWAHA -11793-GEN
SHIVAPRASAD K M -11794-GEN

2. Hybrid breeding in selfing crops has not been a major, consistent commercial success in many crops
(Longin et al. 2012).
Global commercial crop area planted to hybrid cultivars of selfing crops does not even reach 1%.
Hybrid cultivars, result of heterosis or hybrid vigor, they consistently perform better than their
parents.
Hybrid vigor in some F1 populations, reaching 10 to 15% greater than that of the best parent,
continues to arouse repeated flurries of excitement among breeders to exploit hybrid vigor.
Enthusiasm for hybrids in selfing crops
Demand for hybrids in selfing crops

3. Superiority over parents
Heterosis
Methods for Estimation of Heterosis
If superiority of F1 hybrid over mid parent (mean of parents) Midparent Heterosis
If superiority of F1 hybrid over superior parents Heterobeltiosis or Better
parent Heterosis
If superiority of F1 hybrid estimated as superiority over a
commercial check variety
Standard Heterosis or Useful
Heterosis
Term was 1st used by Shull, 1914
(F1-MP)/100 * MP;
F1-mean of F1, MP- mean of two parents
(F1-BP)/100 * BP;
BP- mean of better parent
(F1-Check)/100 * Check

4. Fisher divided the genotypic variation into
Genotypic Variance
Additive Dominance Epistasis
Additive*Additive Additive*Dominance Additive*Dominance
Fixable Heterosis in selfing crops is often driven by additive
and additive*additive gene action, the molecular basis
unravels this newly introduced breeding strategy
hybrid-enabled line profiling (HELP)- predicting high
progeny performance.

5. HELP strategy enables the performance of F1 hybrids to guide the profiling and
development of F1–derived lines or DHs.
In HELP, the F1 hybrids themselves are not the end product of commercial cultivars.
Rather, hybrids help identify (near) homozygous lines or DHs, which are then released as
commercial cultivars.
This strategy integrates modern high-throughput versions of existing and new concepts and
methodologies into a breeding system strategy that focuses on the most superior crosses,
<10% of all crosses.
Hybrid-enabled line profiling (HELP)

6. HELP – Lets seek the help of F1 itself
Homozygous line
(Fn) with same or
superior characters
than F1

7. Background/ Foundation for HELP
• Plant breeding Numbers game
• HELP strategy Reduction in number of crosses
• CIMMYT’s experiments in the Bread Wheat Program led the development of HELP
• ∼8% of the elite new lines in IBWSN derived from <20 crosses, while 92% came from
5000 to 10,000 crosses
• CIMMYT started working on hybrid wheat in 1962
• Belgin Cukadar produced150 to 400 spring bread wheat hybrids each year

8. F2 seed from the top‐yielding 5% of F1 hybrids
Toluca
(highland environment)
Shuttle Breeding
F3 Seed from best adapted, stripe rust, Septoria, and Barley
yellow dwarf virus
Ciudad Obregon
Selection for adaptation to its high‐yield conditions, leaf and stem rust
DHs from the best adapted F3 plants, or the derived F4 plants
Best DHs entered yield trials along with the best advanced lines through
pedigree selection from the other crosses. Top yielders entered into the IBWSN
• Only up to 20 crosses, which had been identified as superior in their
F1 hybrid yield trials spawned a disproportionate number of
superior entries as DHs.
• This strategy selected the best hybrids among the 150 to 400 initial

9. Hybrid’s heterosis in a derived line in SP
crops !!
Need – Knowledge of
a) Physiology of Heterosis
b) Whether A heterotic line can predict
the performance of derived line??
c) What should be the nature of gene
action then ??
Methodology
a) “Best” parent
b) “Best” crosses – “Best with the best”
c) “Best” hybrids
d) Homozygous lines from best hybrids

10. a. Physiology of Heterosis
Additive nature
• Additive > Dominant or epistatic
• Additive x Additive interaction which do not contribute to inbreeding depression
appear to be a major component of Midparent heterosis
• Heterosis - allele-specific expression - most energy-saving - stable alleles.
• Allele-specific expression has multiple opportunities to express the more stable gene
product.
• If these are alleles are dominant we can fix them in the homozygous condition
• So here in HELP the physiology of Heterosis should be such that it must be regulated
by additive gene action – and if dominance is the cause of heterosis it can also be
utilized
(Melchinger et al., 2007)
(Goff, 2011)

11. Epistasis
heterosis is due to different alleles at different loci
• De novo non allelic interactions – elevated epistasis. (Rasmusson
and Philips 1997).
• AAbb x aaBB and AAbb x aaB’B’
AAbb x aaBB
AaBb
AABB
AAbb x aaB’B’
AaB’b
AAB’B’
DNA marker-aided selection
for increasing exotic
subgenomic components in
further generations.

12. Can overdominance be exploited?
• Yes in some Disomic Polypoid
• Or in Amphidiploids
• Because of the Amphidipoid nature (A1A1 and A’A’) genes in the
homoeologous chromosomes gives a nature heterozygosity always.
• So i.e. disomic polyploids as wheat does not allow intergenomic
recombination, thus keeping the same heterozygosity level across
generations (Comai, 2005).

13. b. (i) Prediction of Heterosis
1. Genomic Genetic Diversity – not always leads to heterosis
2. Past parental performance and perse performance – Genomic analysis
Genotyping of A/* and B/* are known - A/B can be predicted. r =
0.749
It is relevant if it is heterosis is due to Additive gene action.
• Martin et al., 1995; Barbosa-Neto et al., 1996; Corbellini et al.,
2002 in wheat;
• Geleta et al., 2004 in pepper (Capsicum annuum L.);
• Teklewold and Becker, 2006 in mustard (Brassica carinata A.
Braun); and
• Luo et al., 2016; Tian et al. 2016 in rapeseed [Brassica napus L.]).
• (RFLP in maize by Bernardo, 1994 and Bernardo, 1996).
• (Jacobson et al., 2014)

14. 3. Genomic Selection – GEBV is the prediction of Parental value or
parental Performance - lines with high GEBV were good combiners
Genomic selection in Maize – Grain yield and quality traits>MAS
It have high Accuracy (r=0.72-0.74 for testcross yields)
When r (Marker prediction/Phenotype) >0.50 GS was effective.
GS is effective in identifying parental hybrid combinations
Prediction of end-use quality traits using GS was also powerful
(Massman et al., 2013)
(Albrecht et al., 2011)
(Krchov and Bernardo, 2015)
in maize hybrids under drought (Beyene et al., 2015)
in wheat hybrids (Liu et al., 2016)

15. b. (ii) Prediction of Derived Line
Performance
1. Based on Performance of F1 –
• Cross prediction in selfing crops was first given By Jinks and Co workers
• F6 lines with superior yield and stripe rust resistance (Hill et al., 2000)
• GCA and specific heterosis in lines indicates that grain yield is
determined by both additive and non additive effects (in CIMMYT
germplasm for Africa) (Ortiz et al., 2008)
• Wheat Lines performing superior or equivalent to F1 were derived –
(Matzinger and Busch et al., 1963; Cregan and Busch, 1977)
(Jinks and Perkins, 1972; Jinks and Pooni, 1976)

16. 2. Based on early generation bulk
Highest yielding Line selections < top yielding cross bulks
Low yielding bulks can be discarded
(Harlan et al., 1940)
Similar results in selfing crops –
Wheat (Harrington, 1940)
Chickpea (Byth et al., 1980)
Soybean (Burton and Brownie, 2006; Friedrichs et al., 2016)

17. c. Gene Action to be captured - Additive
Dominance is a more important form of gene action than
overdominance;
Additive gene expression exceeds nonadditive gene action
The more the D and i gene actions in hybrids dominate, the more
effectively the F1 performance predicts subsequent derived line
performance
Capturing of additive gene action of heterosis yiels superios line?? !!
(Kaeppler, 2012; Huang et al., 2015)
(van Ginkel and Ortiz, 2018)

18. Exploited D & i gene action from superior F1
Rice
Markers indicated D & i fuels
heterosis for grain yield in rice up
to 20% > best parent.
Derived F8 lines yielded ≈ the
original hybrid (Xiao et al., 1995).
D & i determines heterosis for
grain yield and spikelets per
panicle, respectively (Garcia et
al., 2008; He et al., 2010)
Down- and upregulation of
specific genes in hybrids relative
to their parents Liu et al. (2015),
with most having additive effects
(Gu et al., 2016).
The down regulating of genes
allowed hybrid vigor to increase.
Wheat
Heterosis for grain yield was
observed early on and in many
programs of wheat (Chwang et al.,
1963).
r GCA prediction and grain yield =
medium to high in winter wheat for
grain yield in France - primarily
additive gene action (Gowda et al.,
2012).
Heterosis for grain yield in Brazil
was due to i effects (Beche et al.,
2013).
Heterosis for grain yield under
drought was also due to high levels
of additive gene action. (Farshadfar
et al., 2013)
Barley
Heterosis due to additive and
“homozygous–homozygous” gene
effects. F8 lines were selected
from a heterotic F1 barley hybrid,
and some lines did outyield the
original F1 hybrid. (Aastveit,
1964).
The ratios GCA/SCA in the F2 and
F3 pplnof two sets of barley
crosses, a 5:1 advantage for GCA
over SCA was found for grain
yield (Smith and Lambert, 1968).
Additive genetic systems - seed
yield in barley, lines >> hybrids
could be derived.

19. If we have
• high GCA for parents – Additive gene action
• Any prediction method for both Heterosis and Derived line
• Any rapid advancement method for attaining homozygosity
Then
97% of crosses can be dropped in F1 itself or before the cross
Very superior F1 cross can be produced –
Cost of breeding can be reduced

20. Steps involved in
Hybrid-Enabled Line
Profiling (HELP)

21. 1. Characterization of “Best” Parents
for Hybrid-Derived Lines
• Desired Traits in derived lines
• Genotyping of potential parents for desired traits based on genetic
aspects of traits
1. Per se Performance of Parents
GCA for grain yield should strongly correlated with per se
performance of the parents
2. Parental Performance in Earlier Crosses
Parental record in good-performing hybrids (GCA/Genomic
selection/DNA marker)through additive gene action, has a higher
probability to produce outstanding hybrids.

22. 2. Cross the “Best with the Best”
Parents Most Effectively
• “Pure” cross-fertilization requires the complete absence of self-
fertilization by the female parent.
• stray selfing by the female will skew the results - and may lead to wrong
conclusions. Hence, male sterility in the female must be 100% reliable.
1. chemical hybridizing agents
2. Environmental manipulation
3. Modify the genetic makeup of the plant (Male sterility system –
GM).

23. 3. Select the Best F1 Hybrids
• MET testing of the hybrids for 1 or 2 yr
in major representative and predictive target production
ecologies
• F1 should a. exceed the best parent,
b. but this superiority must be shown to be due mostly to
additive and additive x additive gene effects
• 3 to 5% of the F1 hybrids to be selected as the best and promoted for
derivation of lines or DHs
• 95 to 97% of the crosses made and evaluated as F1s in METs need to be discarded at the end of each
hybrid evaluation cycle as they will not met all science- and data-based “line profiling” requisites,
outlined above

24. 4. Move Quickly from the “Best”
Hybrids to Derive Superior
Homozygous Lines
1. Single-Seed Descent (Rapid breeding can be adopted)
2. Shuttle Breeding
full-fledged selection takes place during two or more cycles per year,
implemented in complementary selection environments.
Breeding is not only faster but also identifies more widely adapted
germplasm.
3. Doubled Haploids
Single recombination event -individuals carrying all desired alleles
from both parents will be rare.

26. CONCLUSION
• HELP strategy, show how hybrids can help identify the best
performing homozygous lines with mostly additive and additive x
additive gene action, which are then released as commercial
cultivars.
• HELP strategy’s advantage is, it has parental control, increase
selection intensity, and reduce time per cycle, thus improving
accuracy and saving resources.
Do precise cross – rely on the genetic data - work less – save more –
Generate valuable Lines