Trait Linked Markers

Several research projects in the IWYP Science Plan have identified molecular genetic markers linked to target IWYP phenotypic and physiological traits that have the potential to be used in marker assisted selection (MAS) breeding strategies to improve the genetic yield potential of wheat. Below is a compilation of the current set of markers that have been discovered. Where these have been shown to have a demonstrated genetic effect on the trait(s) of interest, this is then indicated in the table below. For more information about a particular marker trait association (MTA) please refer to the publication (if listed) or contact the PI of the project directly.

Disclaimer: Markers listed as validated are considered diagnostic to the best of our knowledge and we would highly recommend that a user contact the originator of the discovery to confirm. In some instances, such as when applied in different genetic backgrounds the effect of selecting the favorable allele may not be apparent. Further, primers may behave differently when used in different laboratory situations and may require optimization.


Trait NameTrait DescriptionMarker Name(s)Marker Discovery PlatformMarker Conversion TechnologyValidated?Potential / Known IP?ReferencesContact
Grain weightThousand
grain weight
GW2-AKASPYesNoneSimmonds et al 2016cristobal.uauy@jic.ac.uk
Grain weightThousand
grain weight
GW2-BKASPYesNoneWang et al 2018cristobal.uauy@jic.ac.uk
Grain weightThousand
grain weight
GW2-DKASPYesNoneWang et al 2018cristobal.uauy@jic.ac.uk
5A gene (GL1)Thousand
grain weight
GL-1KASPYesOnly within CIMMYTunpublishedcristobal.uauy@jic.ac.uk
5A QTL flankingThousand
grain weight
Flanking markers to GL-1 geneKASPYesNoneBrinton et al 2017cristobal.uauy@jic.ac.uk
6A QTL flankingThousand
grain weight
Flanking markers for 6A QTL intervalKASPYesNoneSimmonds et al 2014cristobal.uauy@jic.ac.uk
7D QTL flankingFlowering time
(booting & heading.
TaFT1= VRN-D3)
Flanking markers for 7D QTL35K Axiom® ArrayKASPYessimon.griffiths@jic.ac.uk
Target of Eat1Putative flowering repressor
A:A Avalon/Spark type
earlier flowering
C:C Savannah/Cadenza type later flowering
TaToe1-B1-A2KASPKASPYesNoneZikhali et al 2017
CerealsDB
simon.griffiths@jic.ac.uk
Target of Eat1Putative flowering repressor
(Avalon allele, earlier).
TaToe-B1-A1KASPKASPYesNoneZikhali et al 2017
CerealsDB
simon.griffiths@jic.ac.uk
Target of Eat1Putative flowering repressor
(Cadenza allele, later)
TaToe1-B1-C1KASPKASPYesNoneZikhali et al 2017
CerealsDB
simon.griffiths@jic.ac.uk
Flowering Locus T3-B1Putative flowering promoter
A:A Spark/Charger type later flowering
G:G Rialto/Cadenza type earlier
flowering
TaFT3-B1 CN1KASPKASPYesNoneZikhali et al 2017simon.griffiths@jic.ac.uk
Flowering Locus T3-D1Putative flowering promoter
A:A Spark type later flowering
G:G Rialto type earlier flowering
TaFT3-D1KASPYesNoneCerealsDBsimon.griffiths@jic.ac.uk
VernalizationVernalization (spring allele)Vrn-B1bKASPYesNonesimon.griffiths@jic.ac.uk
VernalizationVernalization
C:C Jagger/Claire type short vrn
T:T Veery, Wichita, 2147 type
long vrn
Vrn-A1KASPYesNoneCerealsDBsimon.griffiths@jic.ac.uk
VernalizationVernalization
G:G Winter
C:C Spring
Vrn-D1aKASPYesNonesimon.griffiths@jic.ac.uk
VernalizationVernalization
A:A-vrn-A1/others winter
G:G vrn-A1a spring
Vrn-A1aKASPYesNoneCerealsDBsimon.griffiths@jic.ac.uk
PhotoperiodPhotoperiodPpd-B1 CN6-11KASPYesNoneCerealsDBsimon.griffiths@jic.ac.uk
PhotoperiodPhotoperiodPpd-B1 CN4/5KASPYesNoneCerealsDBsimon.griffiths@jic.ac.uk
EarlinessEarliness per seEps-D1 / Ta-ELF3KASPYesNoneCerealsDBsimon.griffiths@jic.ac.uk
Fruiting efficiencyFruiting Efficiency (grains g-1)S7A_694497035GBS-SNPKASPYesYesmababar@ufl.edu
Grain numberGrains (m2)S4B_13299920GBS-SNPKASPYesYesmababar@ufl.edu
Internode lengthInternode3 LengthS5B_528544894GBS-SNPKASPYesYesmababar@ufl.edu
Internode 2 partitioning indexInternode2_partitioning_indexS2D_63397962GBS-SNPKASPYesYesmababar@ufl.edu
Fruiting efficiencyFruiting efficiency (grains g-1)S7D_181642401GBS-SNPKASPYesYesmababar@ufl.edu
Spike partitioning indexSpike_partitioning_indexS5A_438411966GBS-SNPKASPYesYesmababar@ufl.edu
Internode 3 partitioning indexInternode3_partitioning_indexS2D_78502096GBS-SNPKASPYesYesmababar@ufl.edu
Internode 2+3 partitioning index2+3_partitioning_indexS2D_78502116GBS-SNPKASPYesYesmababar@ufl.edu
Fruiting efficiencyFruiting efficiency (grains g-1)AX-9498095635K Axiom® ArrayKASPYesYesmababar@ufl.edu
BM_PMAbove-ground (aerial) biomass
at physiological maturity (g/m2)
AX-9515887235K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
BM_PMAbove-ground (aerial) biomass
at physiological maturity (g/m2)
AX-9452259935K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
BM_PMAbove-ground (aerial) biomass
at physiological maturity (g/m2)
AX-9452512235K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
BM_PMAbove-ground (aerial) biomass
at physiological maturity (g/m2)
AX-9495866835K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
BM_PMAbove-ground (aerial) biomass
at physiological maturity (g/m2)
AX-9449462235K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
BM_PMAbove-ground (aerial) biomass
at physiological maturity (g/m2)
AX-9488021335K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
BM_E40Above-ground (aerial) biomass
at emergence +40 days (g/m2)
AX-9440799635K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
BM_E40Above-ground (aerial) biomass
at emergence +40 days (g/m2)
AX-9441685635K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
BM_InBAbove-ground (aerial) biomass
at initiation of booting (g/m2)
AX-9508027735K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
BM_InBAbove-ground (aerial) biomass
at initiation of booting (g/m2)
AX-9488456735K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
BM_InBAbove-ground (aerial) biomass
at initiation of booting (g/m2)
AX-9477953835K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUE_E40InBRadiation Use Efficiency
from emergence +40 days
to initiation of booting (g/MJ)
AX-9486117935K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUE_E40InBRadiation Use Efficiency
from emergence +40 days
to initiation of booting (g/MJ)
AX-9479663635K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUE_E40InBRadiation Use Efficiency
from emergence +40 days
to initiation of booting (g/MJ)
AX-9509324335K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUE_E40InBRadiation Use Efficiency
from emergence +40 days
to initiation of booting (g/MJ)
AX-9487419335K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUEGFRadiation Use Efficiency
during grain filling (from flowering +7 days
to physiological maturity, g/MJ)
AX-9515887235K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUEGFRadiation Use Efficiency
during grain filling (from flowering +7 days
to physiological maturity, g/MJ)
AX-9455663535K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUEGFRadiation Use Efficiency
during grain filling (from flowering +7 days
to physiological maturity, g/MJ)
AX-9442564235K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUEGFRadiation Use Efficiency
during grain filling (from flowering +7 days
to physiological maturity, g/MJ)
AX-9562866335K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUEGFRadiation Use Efficiency
during grain filling (from flowering +7 days
to physiological maturity, g/MJ)
AX-9474018035K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUETRadiation Use Efficiency
Total (from emergence +40 days
to physiological maturity, g/MJ
AX-9515887235K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUETRadiation Use Efficiency
Total (from emergence +40 days
to physiological maturity, g/MJ
AX-9476542135K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUETRadiation Use Efficiency
Total (from emergence +40 days
to physiological maturity, g/MJ
AX-9478148635K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUETRadiation Use Efficiency
Total (from emergence +40 days
to physiological maturity, g/MJ
AX-9452512235K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
RUETRadiation Use Efficiency
Total (from emergence +40 days
to physiological maturity, g/MJ
AX-9444081435K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
LI_E40Light interception
at emergence +40 days
(% of incident light intercepted by the canopy)
AX-9479663635K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
LI_E40Light interception
at emergence +40 days
(% of incident light intercepted by the canopy)
AX-9449141735K Axiom® ArrayKASPNoNoneMolero et al 2018Anthony.Hall@earlham.ac.uk
Am25(2)Maximum photosynthetic capacity in the secondary leaf77382_7A90K iSelect Illumina Infinium SNP arrayNoNoneandrew.merchant@sydney.edu.au
Am25(2)Maximum photosynthetic capacity in the secondary leaf66495_7B90K iSelect Illumina Infinium SNP arrayNoNoneandrew.merchant@sydney.edu.au
Am25(2)Maximum photosynthetic capacity in the secondary leaf25756_1B90K iSelect Illumina Infinium SNP arrayNoNoneandrew.merchant@sydney.edu.au
Am25(2)Maximum photosynthetic capacity in the secondary leaf48422_1B90K iSelect Illumina Infinium SNP arrayNoNoneandrew.merchant@sydney.edu.au
Am25(2)Maximum photosynthetic capacity in the secondary leaf7806_1B90K iSelect Illumina Infinium SNP arrayNoNoneandrew.merchant@sydney.edu.au
Am25(2)Maximum photosynthetic capacity in the secondary leaf47867_4A90K iSelect Illumina Infinium SNP arrayNoNoneandrew.merchant@sydney.edu.au
Am25(2)Maximum photosynthetic capacity in the secondary leaf65626_5A90K iSelect Illumina Infinium SNP arrayNoNoneandrew.merchant@sydney.edu.au
Am25(2)Maximum photosynthetic capacity in the secondary leaf76596_6B90K iSelect Illumina Infinium SNP arrayNoNoneandrew.merchant@sydney.edu.au
Am25(2)Maximum photosynthetic capacity in the secondary leaf77256_7A90K iSelect Illumina Infinium SNP arrayNoNoneandrew.merchant@sydney.edu.au
Am25(2)Maximum photosynthetic capacity in the secondary leaf2420_7A90K iSelect Illumina Infinium SNP arrayNoNoneandrew.merchant@sydney.edu.au