Waking up too early: TaMKK3-A sprouting resistance locus, Phs-A1 …...
Transcript of Waking up too early: TaMKK3-A sprouting resistance locus, Phs-A1 …...
Waking up too early: TaMKK3-A underlies the major 4AL sprouting resistance locus, Phs-A1.
Oluwaseyi Shorinola
Monogram, 2017
@Oluwheat
"How does it happen there's no good bread?" asked Mrs.
Henchard
“Oh, 'tis the corn-factor—he's the man that our millers and bakers all
deal wi', and he has sold 'emgrowed wheat, … so that the
loaves be as flat as toads, and like suet pudden inside. I've been a
wife, and I've been a mother, and I never see such unprincipled bread
in Casterbridge as this before”
Thomas Hardy (1886)
“…Norwich’s growed wheat, …unprincipled bread”
Pre-harvest Sprouting (PHS)
The 4AL Phs-A1 locus confers resistance to sprouting
-Phs-A1 +Phs-A1
• Highly multi-genic trait
• Phs-A1 is major locus identified in numerous diverse global germplasm
• Phs-A1 delays dormancy loss during seed after-ripening.
***
0Days after Harvest Maturity
14
• Near isogenic lines (NILs) and recombinant lines (RILs) were developed for fine-mapping of Phs-A1 from two bi-parental populations.
0 20 40 60 80 100
% sproutingwmc420barc170wmc707wmc760wmc313
Robigus
Alchemy
NIL Group 1
NIL Group 2
NIL Group 3
NIL Group 4
NIL Group 5
NIL Group 6
NIL Group 7
5 cM Centromere
Chromosome 4A
Fine-mapping of Phs-A1 in bi-parental populations
Shorinola et al (2016) JxB 67: 4169-4178
Robigus (Non-dormant)
x Alchemy (Dormant)
Phs-A1 is further delimited to a sub-cM interval
Claire (Non-dormant)
xOption
(Dormant)
Chromosome 4A
barc170 wms894 xhbe03
0.5cM
RIL Group 1 (7)
RIL Group 2 (9)
RIL Group 3 (6)
RIL Group 4 (5)
Claire Control RIL
Option Control RIL
Centromere 0 10 20 30 40 50 60
% Sproutingwmc420
Shorinola et al (2016) JxB 67: 4169-4178
Brachypodium
Wheat
3 kb
5 kb
Synteny reveals gene content of the critical interval
• Good co-linearity between wheat and Brachypodium in the Phs-A1 interval.
• Synteny sometimes gives an incomplete picture.
Shorinola et al (2016) JxB 67: 4169-4178
Physical mapping of Phs-A1 interval
Shorinola et al. Manuscript in preparation
1
scaffold92430-3Chromosome 4A
250,000595,750,000596,750,000 596,500,000 596,250,000 596,000,000 595,500,000Wild-Emmer Physical Map
CS BAC Cluster 285 CS BAC Cluster 16421
Wheat Physical Map
High resolution fine-mapping of the Phs-A1 locus
Shorinola et al (2016) JxB doi: 10.1093/jxb/erw194
Stw17 PM19-A2
wms894
PP1-Like –LRR Kinase 2 ACC Oxidase-1
0.05 cM
xhbe03
Centromere
OTU Cysteine Protease
Robigus
Alchemy
RIL Group 21 (2)
RIL Group 22 (9)
RIL Group 23 (1)
RIL Group 25 (6)
RIL Group 24 (2)
Robigus (Non-dormant)
x Alchemy (Dormant)
0 20 40 60 80 100
% Sprouting
Claire
Option
Option Control RIL
RIL Group 11 (1)
RIL Group 12 (4)
RIL Group 13 (1)
RIL Group 14 (4)
RIL Group 15 (1)
Claire Control RIL
0 20 40 60 80 100
% Sprouting
High resolution fine-mapping of the Phs-A1 locus
Shorinola et al (2016) JxB 67: 4169-4178
Claire (susceptible)
xOption
(Resistant)
Stw17 PM19-A2
wms894
PP1-Like –LRR Kinase 2 ACC Oxidase-1
0.05 cM
xhbe03
Centromere
OTU Cysteine Protease
Robigus
Alchemy
RIL Group 21 (2)
RIL Group 22 (9)
RIL Group 23 (1)
RIL Group 25 (6)
RIL Group 24 (2)
Robigus (Non-dormant)
x Alchemy (Dormant)
0 20 40 60 80 100
% Sprouting
BAC Cluster 285 BAC Cluster 16421
Finding the causal gene for the Phs-A1 locus
Shorinola et al Manuscript in preparation
Phs-A1
Amino acid substitution in the catalytic domain caused by a C>A mutation results is associated with Phs-A1 effect.
A mutation in TaMKK3-A is associated with Phs-A1 effect
Shorinola et al Manuscript in preparation
Torada et al (2016) Curr Biol 26 (6):782-787
TaMKK3-A C>A mutation
PM19-A1 promoter InDel
Robigus A Deletion
Alchemy C Insertion
Claire A Deletion
Option C Insertion
Baxter A Deletion
Chara A Deletion
Westonia A Deletion
Yitpi C Insertion
SW95-50213 A Deletion
Cunningham C Deletion
Münstertaler A Insertion
Kitamoe C Insertion
Haruyokoi A Insertion
OS21-5 C Insertion
A mutation in TaMKK3-A is associated with Phs-A1 effect
UK
Au
stra
liaJa
pan
Non-dormant
Dormant
TaMKK3-A allele distribution in global germplasm
Germplasm Description
Triticumurartu
Diploid progenitor of bread wheat
T. diccocoides
Tetraploid progenitor of bread wheat
Watkins Global landraces before 1930
Gediflux European germplasm 1945-2000
Shorinola et al. Manuscript in preparation
H_ 1 C C T C G G C C G C A T T T T G G A G A C G G C C T A C C G A T G C G A A T T
H_ 2 C C T C G G C C G C A T T T T G G A G A C G G C C T A C C G A T G G G A A T T
H_ 3 C C T C G G C C G C A T T T T G G A G A C G G T C T A C C G A T G G G A A T T
H_ 4 C C T C G G C C G C A T T T T G G C G A C G G C C T A C C G A T G G G A A T T
H_ 5 C C T C G G C C G C A T T T T G G C G A C G G C c T A C T T G C A G G G C C G
H_ 6 C C T C G G C C G C A T t T T G G C G A C G G C c T A C C G G C A G G A A T T
H_ 7 C C T C G G C C G C A T T T T G G C G A C G G C C T A C C G G C A G G G C C G
H_ 8 C C T C G G C C G C A T T T T G G A G A C G G T C T A A T T G C A G G G C C G
H_ 9 C C T C G G C C G C A T T T T G G C G A C G G C C T A C C G A T G G G A C C G
H_ 10 C T C C G T C T G C C C C T C G A C A G C A A C C A G C C G G C A G G G C C G
H_ 11 C T C C G T C T G C C C C T C G A c A G C A A C C A G C C G G C A G G A A T T
H_ 12 C T C C G T C T G C C C C T C G A C A G C A A C C A G C C G G C A G T G C C G
H_ 13 C T C C G T C T G C C C C T c G A C A G C A A C C A G C C G G C A G T G C T T
H_ 14 T C C G A T T T A T C C C C C A A C A G G A G C T A G A T T G C A G G G C C G
ERF-C
Fourteen haplotypes around the Phs-A1 locus in global germplasm
BAC Cluster 285 BAC Cluster 16421
PP1-Like TaMKK3-A ASC1-Like LRR1-Kinase 1
LRR1-Kinase 2 PM19-A2 PM19-A1
Shorinola et al. Manuscript in preparation
• Using newly available wheat haplotype resource: “A haplotype map of allohexaploid wheat ..”Jordan et al. (2015). Genome Biol 16:48.
Implication for PHS breeding
Non-Dormant
37%Dormant
63%H3H8
H1/H2
EU Unique
H12
H10
H14Others
Non-Dormant
56%
Dormant44%
H1/H2
H3 H8 Aus Unique
H5/H7H10
H11
H6
Others
UK (176 varieties)
Australia (200 varieties)
Helium:Shaw et al. (2014) BMC Bioinf 15: 259
TaMKK3-A and “unprincipled bread”
NABIM Group End-use
Group 1 Bread-making
Group 2 Bread-making potential
Group 3 Biscuits, cakes etc
Group 4 Animal feed
Summary
- Phs-A1 + Phs-A1
1
ZavitanScaffold92430-3
250,000
ZavitanChromosome 4A
595,750,000596,750,000 596,500,000 596,250,000 596,000,000 595,500,000
TaMKK3-A is the major causal gene underlying Phs-A1 in UK germplasm.
Phs-A1 confers major resistance to sprouting in diverse population.
TaMKK3-A mutation present in progenitors and increased in elite modern germplasm
TaMKK3-A marker is associated to grain end-use in the UK
John Flintham
Nicholas Bird
Cristobal Uauy
Jose Sanchez Barrero (CSIRO, Aus)Atshushi Torada (HIRA, Japan)Peter Jack (RAGT, UK)Simon Berry (Limagrain, UK)Tina Henriksson (Lantmannen)Peter Werner (KWS, UK)
Acknowledgements
Tanja Gergets (UoN, UK)Duncan Scholefield (UoN, UK)Michael Holdsworth (UoNt, UK)Miroslav Valarik (IEB, Czech Rep)Bara Klocova (IEB, Czech Rep)Assaf Distelfeld (TAU, Israel)
Uauy lab members