Plant developmental patterns and environmental adaptation in barley

1
Plant developmental patterns and environmental
adaptation in barley

• Ildikó Karsai
• Agricultural Research Institute of HAS,
  Martonvásár, Hungary

2
Plant developmental genes and frost tolerance

• Dual roles of decreasing temperature and
  shortening photoperiods
• initiation of the hardening process
• prevention of the transition from vegetative to
  generative phase
• Plant developmental genes
• Vernalization response (VRN-H1, VRN-H2, VRN-H3)
• Photoperiod sensitivity (PPD-H1, PPD-H2)
• others (ligth intensity, temperature sensing,
  etc)

3
Genetic regulation of flowering in barley -
background
Cockram et al. J. of Exp Bot 58(2007) 1231
4

• Studying the genetic determinants of plant
  development in barley
• Role of the major genes of plant development
• gene, allele interactions
• regulating impacts of various envrionmental
  factors
• Molecular genetic methods
• QTL analyses based on marker linkage maps of
  bi-parental populations
• Functional marker maps, characterisation of the
  individual gene effects
• association analyses in multi-varietal
  population of wider genetic background based on
  linkage disequilibrium mapping

5

• Studying the genetic determinants of plant
  development in barley
• role of the major genes of plant development
• gene, allele interactions
• regulating impacts of various envrionmental
  factors
• Detailed phenotypic characterisation
  phenomics
• controlled environmental experiments
• major environmental cues on plant development
  photoperiod, vernalization
• gradient experiments of individual environmental
  factors, factorial treatment combinations
• field experiments (autumn, spring sowing,
  winter survival)

6
Analyses in bi-parental maping populations
7
Allele types of the parental lines
Type and site of functional polymorphism
Gene / locus
Kompolti
Morex
Kompolti
Morex
Dicktoo
winter
spring
facultative
Intron1
In
/Del
Intron1
In
/Del
HvBM5A
o
t
w
s
winter
spring
winter
VRN-H1
(5H)
Presence/ absence of the gene
ZCCT-H
spring
spring
t
o
s
w
winter
VRN-H2
(4H)
SNP in intron1
HvFT1
HvFT1
spring
winter
winter
VRN-H3
(7H)
(7H)
SNP in CCT domain
Sensitive to long days
HvPRR7
Sensitive to long days
Insensitive to long days
S
I
S
I
PPD-H1
(2H)
Presence/ absence of the gene
HvFT3
HvFT3
Sensitive to short days
Insensitive to short days
Sensitive to short days
PPD-H2
I
I
S
S
(1H)
(1H)
8
Allele types of the parental lines
Type and site of functional polymorphism
Gene / locus
Kompolti
Morex
Kompolti
Morex
Dicktoo
winter
spring
facultative
Intron1
In
/Del
Intron1
In
/Del
HvBM5A
o
t
w
s
winter
spring
winter
VRN-H1
(5H)
Presence/ absence of the gene
ZCCT-H
spring
spring
t
o
s
w
winter
VRN-H2
(4H)
SNP in intron1
HvFT1
HvFT1
spring
winter
winter
VRN-H3
(7H)
(7H)
SNP in CCT domain
Sensitive to long days
HvPRR7
Sensitive to long days
Insensitive to long days
S
I
S
I
PPD-H1
(2H)
Presence/ absence of the gene
HvFT3
HvFT3
Sensitive to short days
Insensitive to short days
Sensitive to short days
PPD-H2
I
I
S
S
(1H)
(1H)
9
Dicktoo Morex marker linkage map (169 locus)
10
Allele types of the parental lines
Type and site of functional polymorphism
Gene / locus
Kompolti
Morex
Kompolti
Morex
Dicktoo
winter
spring
facultative
Intron1
In
/Del
Intron1
In
/Del
HvBM5A
o
t
w
s
winter
spring
winter
VRN-H1
(5H)
Presence/ absence of the gene
ZCCT-H
spring
spring
t
o
s
w
winter
VRN-H2
(4H)
SNP in intron1
HvFT1
HvFT1
spring
winter
winter
VRN-H3
(7H)
(7H)
SNP in CCT domain
Sensitive to long days
HvPRR7
Sensitive to long days
Insensitive to long days
S
I
S
I
PPD-H1
(2H)
Presence/ absence of the gene
HvFT3
HvFT3
Sensitive to short days
Insensitive to short days
Sensitive to short days
PPD-H2
I
I
S
S
(1H)
(1H)
11
Allele types of the parental lines
Type and site of functional polymorphism
Gene / locus
Kompolti
Morex
Kompolti
Morex
Dicktoo
winter
spring
facultative
SNP in promoter
HvBM5A
winter
spring
winter
VRN-H1
(5H)
Presence/ absence of the gene
ZCCT-H
spring
spring
t
o
s
w
winter
VRN-H2
(4H)
HvFT1
HvFT1
silent SNP in coding region
spring
winter
winter
VRN-H3
(7H)
(7H)
SNP in CCT domain
Sensitive to long days
HvPRR7
Sensitive to long days
Insensitive to long days
S
I
S
I
PPD-H1
(2H)
Presence/ absence of the gene
HvFT3
HvFT3
Sensitive to short days
Insensitive to short days
Sensitive to short days
PPD-H2
I
I
S
S
(1H)
(1H)
12
Dicktoo Kompolti korai linkage map (246 locus)
Karsai et al. (2007) Cereal Res Commun 351551-
13
Effect of photoperiod duration and vernalization
treatment on PPD-H1, PPD-H2 and VRN-H1 in the
absence of VRN-H2
Dicktoo (facultative) ? Morex (spring) population
14
Photoperiod gradient and vernalization on VRN-H1
and PPD-H1 loci in the Dicktoo ? Morex population
Unvernalized
Vernalized
Karsai et al. (1997) Theor. Appl Genet.
94612-618
15
Photoperiod gradient and vernalization on VRN-H1
and PPD-H1 loci in the Dicktoo ? Morex population
Interaction between the PPD-H1 and VRN-H1 loci
under long photoperiods
a
Days to flowering
b
c
d
Two-loci allele classes
Karsai et al. (1999) Plant Breeding 118399-403.
16
Photoperiod dependent effect of the PPD-H2 locus
on plant development
17
Effect of photoperiod duration and vernalization
treatment on VRN-H2 in the presence of the winter
allele at VRN-H1
Dicktoo (facultative) ? Kompolti korai (winter)
population
18
Effect of VRN-H2 locus in the Dicktoo ? Kompolti
korai population under long photoperiod (16 h)
Without vernalization
In vernalized treatment
Karsai et al. (2005) Theor Appl Genet
1101458-1466.
19
Effect of VRN-H2 locus in the Dicktoo ? Kompolti
korai population in photoperiod gradient after
vernalization
Karsai et al. (2006) Plant Breeding 125468-472.
20
Interactions between VRN-H2 and VRN-H1 loci in
the Dicktoo ? Kompolti korai population
21
Role of additional environmental factors on
VRN-H1 and on its interactions
22
Role of additional environmental factors on
VRN-H1 and on its interactions
23
Dicktoo ? Morex population
24
Dicktoo ? Morex population
Karsai et al. (2008) J. of Experimental Botany
25
Dicktoo ? Morex population
of changes from 18 ?C constant to 10 ?C
constant temperature
Variation within the PPD-H1 / VRN-H1 haplotype
groups
26
Gene allele interactions as functions of specific
environmental conditions in Dicktoo ? Morex
population

• Role of PPD-H2 under long photoperiod

27
Gene allele interactions as functions of specific
environmental conditions in Dicktoo ? Morex
population

• Role of PPD-H2 under long photoperiod

28
Role of additional environmental factors on
VRN-H1 and on its interactions
29
Dicktoo ? Kompolti korai population
30
Dicktoo ? Kompolti korai population
31
Dicktoo ? Kompolti korai population
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Summary

• The systematic phenotypic characterizations
  combined with functional QTL analyses proved to
  be efficient in identifying environmental factor
  dependent gene functions and allele interactions.
  
• The various combinations of the additional
  environmental factors (ambient temperature, low
  light intensity, synchronous photo and thermo
  cycles) changed the epistatic interactions
  between PPD-H1 PPD-H2 and VRN-H1, and between
  VRN-H2 and VRN-H1 in allele specific ways.
• Our results suggest that, in addition to their
  role in the vernalization and photoperiod-driven
  regulation of flowering, these loci are also
  involved in the regulation of and/or are
  regulated by other environmental cues.

33
Association analyses in multi-varietal
populations
34

• Collection of a larger set (169) of barley
  varieties
• North and Central America (84)
• West-Europe (30)
• Central-Europe (27)
• East-Europe (8)
• Southern-Europe (10)
• Asia (7)
• Australia (3)

35
Ongoing research (OTKA 2008-2011)

• Extensive genotypic characterisation
• LD mapping using the DArT system
• Detailed characterisation of plant developmental
  genes (functional site primers, ecoTILLING)
• Systematic phenotypic evaluation
• Ambient temperature (13C, 18C, 23C)
• Daily fluctuating factors (continuos vs. 16h
  photoperiod constant vs. daily fluctuating
  temperature)
• Field sown experiments

36
Ongoing research (OTKA 2008-2011)

• Extensive genotypic characterisation
• LD mapping using the DArT system
• Detailed characterisation of plant developmental
  genes (functional site primers, ecoTILLING)
• Systematic phenotypic evaluation
• Ambient temperature (13C, 18C, 23C)
• Daily fluctuating factors (continuos vs. 16h
  photoperiod constant vs. daily fluctuating
  temperature)
• Field sown experiments

37
Allele types of the parental lines
Type and site of functional polymorphism
Gene / locus
Kompolti
Morex
Kompolti
Morex
Dicktoo
winter
spring
facultative
Intron1
In
/Del
Intron1
In
/Del
HvBM5A
o
t
w
s
winter
spring
winter
VRN-H1
(5H)
Presence/ absence of the gene
ZCCT-H
spring
spring
t
o
s
w
winter
VRN-H2
(4H)
SNP in intron1
HvFT1
HvFT1
spring
winter
winter
VRN-H3
(7H)
(7H)
SNP in CCT domain
Sensitive to long days
HvPRR7
Sensitive to long days
Insensitive to long days
S
I
S
I
PPD-H1
(2H)
Presence/ absence of the gene
HvFT3
HvFT3
Sensitive to short days
Insensitive to short days
Sensitive to short days
PPD-H2
I
I
S
S
(1H)
(1H)
38
Functional allele structures of 169 barley
vartieties in the major plant developmental genes
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Characterization of plant development

• Phenological stages
• First node appearance (DEV31)
• Beginning of the extensive stem elongation
  (SE_B)
• Flag leaf appearance (FL)
• Heading (DEV49)
• End of the extensive stem elongation (SE_E)
• Final plant height (PH_final)
• Controlled environmental test with fully
  vernalized plants
• Continuous light regime with constant 18ºC
  ambient temperature

44
Distribution patterns of heading date (DEV49)
under continuous light regime with constant 18ºC
temperature in the group of 169 barleys
45
Grouping of 169 barley vartieties based on their
developmental patterns
Continuous light and constant 18ºC temperature
46
Grouping of 169 barley vartieties based on their
developmental patterns
Dominant recessive for the VRN genes
Insensitive sensitive for the PPD genes
Continuous light and constant 18ºC temperature
47
Grouping of 169 barley vartieties based on their
developmental patterns
Dominant recessive for the VRN genes
Insensitive sensitive for the PPD genes
Continuous light and constant 18ºC temperature
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Martonvásár Research Institute
Hungarian collaboration
Klára Mészáros Vilmos Soós Krisztina Balla Ottó
Veisz Zoltán Bedo Béla Koszegi
Péter Szucs
International collaboration
Patrick M. Hayes, OSU, Ernesto Igartua, Ana
Casas EEAD- Saragoza,
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Thank You for your attention