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 Name | Trait Description | Marker Name(s) | Marker Discovery Platform | Marker Conversion Technology | Validated? | Potential / Known IP? | References | Contact |
---|---|---|---|---|---|---|---|---|
Grain weight | Thousand grain weight | GW2-A | KASP | Yes | None | Simmonds et al 2016 | cristobal.uauy@jic.ac.uk | |
Grain weight | Thousand grain weight | GW2-B | KASP | Yes | None | Wang et al 2018 | cristobal.uauy@jic.ac.uk | |
Grain weight | Thousand grain weight | GW2-D | KASP | Yes | None | Wang et al 2018 | cristobal.uauy@jic.ac.uk | |
5A gene (GL1) | Thousand grain weight | GL-1 | KASP | Yes | Only within CIMMYT | unpublished | cristobal.uauy@jic.ac.uk | |
5A QTL flanking | Thousand grain weight | Flanking markers to GL-1 gene | KASP | Yes | None | Brinton et al 2017 | cristobal.uauy@jic.ac.uk | |
6A QTL flanking | Thousand grain weight | Flanking markers for 6A QTL interval | KASP | Yes | None | Simmonds et al 2014 | cristobal.uauy@jic.ac.uk | |
7D QTL flanking | Flowering time (booting & heading. TaFT1= VRN-D3) | Flanking markers for 7D QTL | 35K Axiom® Array | KASP | Yes | simon.griffiths@jic.ac.uk | ||
Target of Eat1 | Putative flowering repressor A:A Avalon/Spark type earlier flowering C:C Savannah/Cadenza type later flowering | TaToe1-B1-A2 | KASP | KASP | Yes | None | Zikhali et al 2017 CerealsDB | simon.griffiths@jic.ac.uk |
Target of Eat1 | Putative flowering repressor (Avalon allele, earlier). | TaToe-B1-A1 | KASP | KASP | Yes | None | Zikhali et al 2017 CerealsDB | simon.griffiths@jic.ac.uk |
Target of Eat1 | Putative flowering repressor (Cadenza allele, later) | TaToe1-B1-C1 | KASP | KASP | Yes | None | Zikhali et al 2017 CerealsDB | simon.griffiths@jic.ac.uk |
Flowering Locus T3-B1 | Putative flowering promoter A:A Spark/Charger type later flowering G:G Rialto/Cadenza type earlier flowering | TaFT3-B1 CN1 | KASP | KASP | Yes | None | Zikhali et al 2017 | simon.griffiths@jic.ac.uk |
Flowering Locus T3-D1 | Putative flowering promoter A:A Spark type later flowering G:G Rialto type earlier flowering | TaFT3-D1 | KASP | Yes | None | CerealsDB | simon.griffiths@jic.ac.uk | |
Vernalization | Vernalization (spring allele) | Vrn-B1b | KASP | Yes | None | simon.griffiths@jic.ac.uk | ||
Vernalization | Vernalization C:C Jagger/Claire type short vrn T:T Veery, Wichita, 2147 type long vrn | Vrn-A1 | KASP | Yes | None | CerealsDB | simon.griffiths@jic.ac.uk | |
Vernalization | Vernalization G:G Winter C:C Spring | Vrn-D1a | KASP | Yes | None | simon.griffiths@jic.ac.uk | ||
Vernalization | Vernalization A:A-vrn-A1/others winter G:G vrn-A1a spring | Vrn-A1a | KASP | Yes | None | CerealsDB | simon.griffiths@jic.ac.uk | |
Photoperiod | Photoperiod | Ppd-B1 CN6-11 | KASP | Yes | None | CerealsDB | simon.griffiths@jic.ac.uk | |
Photoperiod | Photoperiod | Ppd-B1 CN4/5 | KASP | Yes | None | CerealsDB | simon.griffiths@jic.ac.uk | |
Earliness | Earliness per se | Eps-D1 / Ta-ELF3 | KASP | Yes | None | CerealsDB | simon.griffiths@jic.ac.uk | |
Fruiting efficiency | Fruiting Efficiency (grains g-1) | S7A_694497035 | GBS-SNP | KASP | No | TBD, unlikely | mababar@ufl.edu | |
Grain number | Grains (m2) | S4B_13299920 | GBS-SNP | KASP | No | TBD, unlikely | mababar@ufl.edu | |
Internode length | Internode3 Length | S5B_528544894 | GBS-SNP | KASP | No | TBD, unlikely | mababar@ufl.edu | |
Internode 2 partitioning index | Internode2_partitioning_index | S2D_63397962 | GBS-SNP | KASP | No | TBD, unlikely | mababar@ufl.edu | |
Fruiting efficiency | Fruiting efficiency (grains g-1) | S7D_181642401 | GBS-SNP | KASP | No | TBD, unlikely | mababar@ufl.edu | |
Spike partitioning index | Spike_partitioning_index | S5A_438411966 | GBS-SNP | KASP | No | TBD, unlikely | mababar@ufl.edu | |
Internode 3 partitioning index | Internode3_partitioning_index | S2D_78502096 | GBS-SNP | KASP | No | TBD, unlikely | mababar@ufl.edu | |
Internode 2+3 partitioning index | 2+3_partitioning_index | S2D_78502116 | GBS-SNP | KASP | No | TBD, unlikely | mababar@ufl.edu | |
Fruiting efficiency | Fruiting efficiency (grains g-1) | AX-94980956 | 35K Axiom® Array | KASP | No | TBD, unlikely | mababar@ufl.edu | |
BM_PM | Above-ground (aerial) biomass at physiological maturity (g/m2) | AX-95158872 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
BM_PM | Above-ground (aerial) biomass at physiological maturity (g/m2) | AX-94522599 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
BM_PM | Above-ground (aerial) biomass at physiological maturity (g/m2) | AX-94525122 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
BM_PM | Above-ground (aerial) biomass at physiological maturity (g/m2) | AX-94958668 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
BM_PM | Above-ground (aerial) biomass at physiological maturity (g/m2) | AX-94494622 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
BM_PM | Above-ground (aerial) biomass at physiological maturity (g/m2) | AX-94880213 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
BM_E40 | Above-ground (aerial) biomass at emergence +40 days (g/m2) | AX-94407996 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
BM_E40 | Above-ground (aerial) biomass at emergence +40 days (g/m2) | AX-94416856 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
BM_InB | Above-ground (aerial) biomass at initiation of booting (g/m2) | AX-95080277 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
BM_InB | Above-ground (aerial) biomass at initiation of booting (g/m2) | AX-94884567 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
BM_InB | Above-ground (aerial) biomass at initiation of booting (g/m2) | AX-94779538 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUE_E40InB | Radiation Use Efficiency from emergence +40 days to initiation of booting (g/MJ) | AX-94861179 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUE_E40InB | Radiation Use Efficiency from emergence +40 days to initiation of booting (g/MJ) | AX-94796636 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUE_E40InB | Radiation Use Efficiency from emergence +40 days to initiation of booting (g/MJ) | AX-95093243 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUE_E40InB | Radiation Use Efficiency from emergence +40 days to initiation of booting (g/MJ) | AX-94874193 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUEGF | Radiation Use Efficiency during grain filling (from flowering +7 days to physiological maturity, g/MJ) | AX-95158872 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUEGF | Radiation Use Efficiency during grain filling (from flowering +7 days to physiological maturity, g/MJ) | AX-94556635 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUEGF | Radiation Use Efficiency during grain filling (from flowering +7 days to physiological maturity, g/MJ) | AX-94425642 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUEGF | Radiation Use Efficiency during grain filling (from flowering +7 days to physiological maturity, g/MJ) | AX-95628663 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUEGF | Radiation Use Efficiency during grain filling (from flowering +7 days to physiological maturity, g/MJ) | AX-94740180 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUET | Radiation Use Efficiency Total (from emergence +40 days to physiological maturity, g/MJ | AX-95158872 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUET | Radiation Use Efficiency Total (from emergence +40 days to physiological maturity, g/MJ | AX-94765421 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUET | Radiation Use Efficiency Total (from emergence +40 days to physiological maturity, g/MJ | AX-94781486 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUET | Radiation Use Efficiency Total (from emergence +40 days to physiological maturity, g/MJ | AX-94525122 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
RUET | Radiation Use Efficiency Total (from emergence +40 days to physiological maturity, g/MJ | AX-94440814 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
LI_E40 | Light interception at emergence +40 days (% of incident light intercepted by the canopy) | AX-94796636 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
LI_E40 | Light interception at emergence +40 days (% of incident light intercepted by the canopy) | AX-94491417 | 35K Axiom® Array | No | None | Molero et al 2018 | Anthony.Hall@earlham.ac.uk | |
Am25(2) | Maximum photosynthetic capacity in the secondary leaf | 77382_7A | 90K iSelect Illumina Infinium SNP array | No | None | andrew.merchant@sydney.edu.au | ||
Am25(2) | Maximum photosynthetic capacity in the secondary leaf | 66495_7B | 90K iSelect Illumina Infinium SNP array | No | None | andrew.merchant@sydney.edu.au | ||
Am25(2) | Maximum photosynthetic capacity in the secondary leaf | 25756_1B | 90K iSelect Illumina Infinium SNP array | No | None | andrew.merchant@sydney.edu.au | ||
Am25(2) | Maximum photosynthetic capacity in the secondary leaf | 48422_1B | 90K iSelect Illumina Infinium SNP array | No | None | andrew.merchant@sydney.edu.au | ||
Am25(2) | Maximum photosynthetic capacity in the secondary leaf | 7806_1B | 90K iSelect Illumina Infinium SNP array | No | None | andrew.merchant@sydney.edu.au | ||
Am25(2) | Maximum photosynthetic capacity in the secondary leaf | 47867_4A | 90K iSelect Illumina Infinium SNP array | No | None | andrew.merchant@sydney.edu.au | ||
Am25(2) | Maximum photosynthetic capacity in the secondary leaf | 65626_5A | 90K iSelect Illumina Infinium SNP array | No | None | andrew.merchant@sydney.edu.au | ||
Am25(2) | Maximum photosynthetic capacity in the secondary leaf | 76596_6B | 90K iSelect Illumina Infinium SNP array | No | None | andrew.merchant@sydney.edu.au | ||
Am25(2) | Maximum photosynthetic capacity in the secondary leaf | 77256_7A | 90K iSelect Illumina Infinium SNP array | No | None | andrew.merchant@sydney.edu.au | ||
Am25(2) | Maximum photosynthetic capacity in the secondary leaf | 2420_7A | 90K iSelect Illumina Infinium SNP array | No | None | andrew.merchant@sydney.edu.au | ||
Days to Anthesis | Phenology | chr5B-27404243 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
Days to Anthesis | Phenology | chr6B-189683325 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
SPAD: chlorophyll content per unit flag leaf area | Nitrogen content | chr2B-106930486 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
SPAD: chlorophyll content per unit flag leaf area | Nitrogen content | chr2D-16845994 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
SPAD: chlorophyll content per unit flag leaf area | Nitrogen content | chr5A-3550988 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
SPAD: chlorophyll content per unit flag leaf area | Nitrogen content | chr6D-456495062 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
NDVI: Normalized Difference Vegetation Index | Vegetation Index | chr7D-608810464 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
GNDVI: Green Normalized difference vegetation index | Vegetation Index | chr2B-153275048 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
GNDVI: Green Normalized difference vegetation index | Vegetation Index | chr3B-723108033 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RDNVI: Red Normalized difference vegetation index | Vegetation Index | chr7A-711982572 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RDNVI: Red Normalized difference vegetation | Vegetation Index | chr7D-608810464 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
NDII: Normalized difference infrared index | Vegetation Index | chr6A-497983531 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
NDMI: Normalized difference matter index | Vegetation Index | chr2B-669669845 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
EVI: Enhanced vegetation index | Vegetation Index | chr6B-174740483 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
EVI: Enhanced vegetation index | Vegetation Index | chr3D-523811772 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSa: chlorophyll a | Pigmentation composition | chr2A-16347452 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSa: chlorophyll a | Pigmentation composition | chr2B-20043565 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSa: chlorophyll a | Pigmentation composition | chr2B-149018684 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSa: chlorophyll a | Pigmentation composition | chr7B-135775607 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
PSSa: chlorophyll a | Pigmentation composition | chr2A-17001351 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSb: chlorophyll b | Pigmentation composition | chr2B-153898371 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSb: chlorophyll b | Pigmentation composition | chr3B-20186940 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSb: chlorophyll b | Pigmentation composition | chr3B-715184359 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSc: carotenoids | Pigmentation composition | chr3B-20358957 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSc: carotenoids | Pigmentation composition | chr7A-676592398 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSc: carotenoids | Pigmentation composition | chr7B-722589303 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
RARSc: carotenoids | Pigmentation composition | chr7D-608810464 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
SIPI: Structural independent pigment index | Pigmentation composition | chr3B-711119921 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
SIPI: Structural independent pigment index | Pigmentation composition | chr7D-610551080 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
R750/550 - Total Chlorophyll Content | Pigmentation composition | chr2B-2619111 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
R750/550 - Total Chlorophyll Content | Pigmentation composition | chr2B-153275048 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
R750/550 - Total Chlorophyll Content | Pigmentation composition | chr2B-153275048 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
R750/550 - Total Chlorophyll Content | Pigmentation composition | chr3B-736709296 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
NPQI: Normalized Pheophytinization Index | Senescence/degradation indices | chr7A-539405222 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
PSRI: Plant senescence reflectance index | Senescence/degradation indices | chr3B-718670251 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
Water Index: WI2 | Water indices | chr3A-616891767 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
Water Index: WI3 | Water indices | chr1B-572799923 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
Water Index: WI3 | Water indices | chr7A-34727282 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
Water Index: WI4 | Water indices | chr3A-616891767 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
Water Index: WI4 | Water indices | chr3D-611549913 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
Leaf Mass Area (LMA) | Physiology predictor | chr3D-336170196 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
Leaf Mass Area (LMA) | Physiology predictor | chr1B-65889406 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk | |
Respiration rate per Dry Matter (R_DM) | Physiology predictor | chr1D-397474458 | 12Mb capture probe set | No | None | Joynson et al 2021 | Anthony.Hall@earlham.ac.uk |