USDA CENTRAL SMALL GRAIN GENOTYPING LAB, MANHATTAN KS

Commonly Used Markers in The USDA Central Small Grain Genotyping Lab, Manhattan, KS (Sorted by Trait Category, Gene, and Marker)

We have thousands of SSR markers and many more STS markers that we can use in any genotyping job, but these are the most commonly used markers in our lab. Contact us for custom, newer, or specialty markers. Marker ID is an internal ID number. Marker rating indicates which marker is best for a specific gene. Detection types are: ABI = Applied Biosystems Inc. DNA sequencer, Gel = agarose gel electrophoresis, KASP = fluorescence (FRET) based end-point assay, SNapShot = single-base extension assay.


Trait Category Trait Chromosome cM To Allele Gene Marker ID Marker Alleles Marker Rating Marker Type Detection Type Marker Dominance
Abiotic stress Aluminum tolerance 2A Al 2A 975 GWM0249 Al-2A, Non-Al-2A 1? SSR ABI CoDom
Abiotic stress Aluminum tolerance 3BL Al 3BL 346 BAR0344 Al-3BL, Non-Al 3BL 1 SSR ABI CoDom
Abiotic stress Aluminum tolerance 4DL 4.8 Al 4DL 841 GDM0125 Al-4DL, Non-Al-4DL 2 SSR ABI CoDom
Abiotic stress Aluminum tolerance 4DL Al 4DL 1736 WMC0331 Al-4DL, Non-Al-4DL 1 SSR ABI CoDom
Abiotic stress Aluminum tolerance 4DL 0 ALMT1 Promoter 6 ALMT1-UPS4 Al Tolerant, Non-Al Tolerant 1 STS Gel CoDom
Abiotic stress Drought tolerance 1RS Alien Seg. 1RS Rye translocation 1307 TSM0120 1RS:1AL, 1RS:1BL, Non-1RS 1 SSR ABI Dom
Anatomy and morphology related Height 4BS 0 Rht1-B1 4262 RhtB1_cim-KASP Rht1-B1a-Tall, Rht1-B1b-Short 1 SNP KASP CoDom
Anatomy and morphology related Height 4DS 0 Rht2-D1 4265 RhtD1-KASP Rht2-D1a-Tall, Rht2-D1b-Short 1 SNP KASP CoDom
Anatomy and morphology related Height 2DS .6 Rht8 980 GWM0261 Rht8, Non-Rht8 1 SSR ABI CoDom
Fungal disease resistance Fusarium head blight resistance 3BS FHB 3BS/Fhb1 4295 Fhb1_SNP319-KASP FHB 3BS/Fhb1, Non-FHB 3BS/Fhb1 1 SNP KASP CoDom
Fungal disease resistance Fusarium head blight resistance 3BS Close FHB 3BS/Fhb1 4232 FHB3BS-SNP8-KASP FHB 3BS/Fhb1, Non-FHB 3BS/Fhb1 2 SNP KASP Mixed
Fungal disease resistance Fusarium head blight resistance 3BS FHB 3BS/Fhb1 1076 GWM0533 FHB 3BS/Fhb1, Non-FHB 3BS/Fhb1 1=Fhb1, Don't use for Sr2 SSR ABI CoDom
Fungal disease resistance Fusarium head blight resistance 3BS <4 FHB 3BS/Fhb1 1387 UMN10 FHB 3BS/Fhb1, Non-FHB 3BS/Fhb1 1 STS ABI CoDom
Fungal disease resistance Fusarium head blight resistance T7AL·7Lr#1S FHB 7AL/Fhb3 3950 FHB3-BE585744 FHB 7AL/Fhb3, Non-FHB 7AL/Fhb3 1 STS ABIVLong Dom
Fungal disease resistance Leaf rust resistance 7EL:7DL Alien Seg. Lr19 1226 Lr19-130 Lr19, Non-Lr19 1 STS ABI Dom
Fungal disease resistance Leaf rust resistance 1DS 0 Lr21 1227 Lr21-214 Lr21, Non-Lr21 1 STS ABI CoDom
Fungal disease resistance Leaf rust resistance 1DS 0 Lr21 4238 Lr21-GQ504819-1346-KASP Lr21, Non-Lr21 2 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 3Ag:3DL Alien Seg. Lr24/Sr24 1270 Sr24#12 Lr24/Sr24, Non-Lr24/Sr24 1 STS ABI Dom
Fungal disease resistance Leaf rust resistance 7DS 0 Lr34/Yr18 4241 Lr34Exon11-KASP Lr34(exon11), Non-Lr34(exon11) 1 Indel KASP CoDom
Fungal disease resistance Leaf rust resistance 7DS 0 Lr34/Yr18 4244 Lr34Exon12_A-KASP Lr34(exon12), Non-Lr34(exon12) 2 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 7DS 0 Lr34/Yr18 4247 Lr34Inron4_A-KASP Lr34(intron4), Non-Lr34(intron4) 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 7DS 0 Lr34/Yr18 4250 Lr34JagExon22-KASP Lr34-JagMut(exon22), Non-Lr34-JagMuT(exon22) 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 2NS:2AS Alien Seg. Lr37/Sr38/Yr17 1393 VENTRIUP-LN2 Lr37, Non-Lr37 1 STS ABI Dom
Fungal disease resistance Leaf rust resistance 2DS Lr39/Lr41 126 BAR0124 Lr39, Lr39(Fuller), Lr39(Overley), Non-Lr39 2 SSR ABI CoDom
Fungal disease resistance Leaf rust resistance 2DS .9 Lr39/Lr41 807 GDM0035PT Lr39, Lr39(Fuller), Lr39(Overley), Non-Lr39 1=specific cross only SSR ABI CoDom
Fungal disease resistance Leaf rust resistance 2DS Lr39/Lr41 967 GWM0210 Lr39, Lr39(Fuller), Lr39(Overley), Non-Lr39 1=specific cross only SSR ABI CoDom
Fungal disease resistance Leaf rust resistance 1DS Lr42 640 CFD0015 Lr42, Non-Lr42 1 SSR ABI CoDom
Fungal disease resistance Leaf rust resistance 1DS 0.6 proximal Lr42 4288 Lr42-113325_01-KASP Lr42, Non-Lr42 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 1DS 0.6 proximal Lr42 1837 WMC0432 Lr42, Non-Lr42 1 SSR ABI Dom
Fungal disease resistance Leaf rust resistance 1BL Close Lr46 4256 Lr46-Yr29_JF2-2-KASP Lr46, Non-Lr46 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 7S:7A Alien Seg. Lr47 1236 Lr47-Codominant Lr47, Non-Lr47 1 STS ABI CoDom
Fungal disease resistance Leaf rust resistance T5DL·5DS-5MgS(0.95) Alien Seg. Lr57/Yr40 2258 Lr57-Yr40-CAPS16 Lr57/Yr40, Non-Lr57/Yr40 1 CAP ABI Dom
Fungal disease resistance Leaf rust resistance 7BL Lr68 4175 Lr68-csGS Lr68, Non-Lr68 New STS ABI Dom
Fungal disease resistance Leaf rust resistance 6BL Lr9 4259 Lr9a-KASP Lr9, Non-Lr9 1 SNP KASP CoDom
Fungal disease resistance Stem rust resistance 3BS 0 Sr2 3859 csSr2-CAP Sr2, Non-Sr2 1 CAP ABI Mixed
Fungal disease resistance Stem rust resistance 3BS 0 Sr2 4271 Sr2_ger9_3p-KASP Sr2, Non-Sr2 3 SNP KASP Mixed
Fungal disease resistance Stem rust resistance 7AL Sr22 2328 Sr22-cssu22 Sr22, Non-Sr22 1 STS ABI CoDom
Fungal disease resistance Stem rust resistance 6AL Tight Sr26 1272 Sr26#43 Sr26, Non-Sr26 1 STS ABI Dom
Fungal disease resistance Stem rust resistance 2S.2BS Alien Seg. Sr32,Sr39,Sr40 3963 Sr39-Sr40Res Sr32,Sr39,Sr40, Sr32,Sr39,Non-Sr40, Non-Sr32,Non-Sr39,Sr40, Non-Sr32,Non-Sr39,Non-Sr40 1-best for Sr40 STS ABI CoDom
Fungal disease resistance Stem rust resistance 3Am:3AL Alien Seg. Sr35 3953 Sr35-Cyrille-64A22-1 Sr35, Non-Sr35 1 SSR ABI CoDom
Fungal disease resistance Stem rust resistance 2BS 0-Alien Seg? Sr36 4274 Sr36-Pm6_8085-KASP Sr36, Non-Sr36 1? SNP KASP CoDom
Fungal disease resistance Stem rust resistance 2BS 0-Alien Seg? Sr36 1274 Sr36-STM773-2 Sr36, Non-Sr36 1 STS ABI CoDom
Fungal disease resistance Stem rust resistance 2S.2BS Alien Seg. Sr39/Lr35 3856 Sr39-rwgs27 Sr39, Non-Sr39 1-best for Sr39 STS ABILong CoDom
Fungal disease resistance Stem rust resistance 2S.2BS Close Sr39/Lr35 4279 Sr39-Seg3-SNP3-KASP Sr39, Non-Sr39 1 SNP KASP Mixed
Fungal disease resistance Stem rust resistance 2S.2BS Close Sr40 4281 Sr40-Seg2-SNP1-KASP Sr40, Non-Sr40 1 SNP KASP Mixed
Fungal disease resistance Stem rust resistance 2D-2S#1 SrAes1t 4298 csSrAes1t csSrAes1t ? STS ABI Dom
Fungal disease resistance Stripe rust resistance 1BS 5.7 Yr15 987 GWM0273 Yr15, Non-Yr15 1 SSR ABI CoDom
Fungal disease resistance Stripe rust resistance 1BS 4.4 Yr15 1044 GWM0413 Yr15, Non-Yr15 1 SSR ABI CoDom
Fungal disease resistance Stripe rust resistance 2BL Yr5 2244 Yr5-CAPS Yr5, Non-Yr5 1 CAP ABI CoDom
Growth and development Pre-harvest sprouting 3AS 0 PHS 3AS 4278 PHS1-SL-SNP1-KASP PHS 3AS, Non-PHS 3AS 1 SNP KASP CoDom
Growth and development Vernalization 5AL Close Vrn-A1 570 CDO708 Vrn-A1a-weak winter type, Vrn-A1b-intermediate winter type 1 STS ABI CoDom
Growth and development Vernalization 5AL 0 Vrn-A1 1396 VRN-A1-SNP Vrn-A1a-Early, Vrn-A1b-Late 1 STS SNapShot CoDom
Growth and development Vernalization 7D Close Vrn-D3 1397 VRN-D3 Vrn-D3a-Early, Vrn-D3b-Late 1 STS ABI CoDom
Growth and development Vernalization/Photoperiod 2DS Close Ppd-D1 1240 PPD-D1 PPD-D1a-Long-day insensitive, PPD-D1b-Long-day sensitive 1 STS ABI CoDom
Insect damage resistance Greenbug resistance 7DL Gb3 113 BAR0111 Gb3, Non-Gb3 2 SSR ABI CoDom
Insect damage resistance Greenbug resistance 7DL Tight Gb3 796 GB3_EST39_STS Gb3, Non-Gb3 1 CAP ABI CoDom
Insect damage resistance Greenbug resistance 7DL Tight Gb3 2039 WMC0634 Gb3, Non-Gb3 2 SSR ABI CoDom
Insect damage resistance Hessian fly resistance 1AS .3 H09 265 BAR0263 H09, Non-H09 ? SSR ABI CoDom
Insect damage resistance Hessian fly resistance 1AS .5 H09 597 CFA2153 H09, Non-H09 ? SSR ABI CoDom
Insect damage resistance Hessian fly resistance 1AS 2.8 H09 1123 H9-SOPO05 H09, Non-H09 1 STS ABILong CoDom
Insect damage resistance Hessian fly resistance 1AS .3 H10 265 BAR0263 H10, Non-H10 ? SSR ABI CoDom
Insect damage resistance Hessian fly resistance 1AS .5 H10 597 CFA2153 H10, Non-H10 ? SSR ABI CoDom
Insect damage resistance Hessian fly resistance 1AS 1.7 H11 265 BAR0263 H11, Non-H11 ? SSR ABI CoDom
Insect damage resistance Hessian fly resistance 1AS .3 H11 597 CFA2153 H11, Non-H11 ? SSR ABI CoDom
Insect damage resistance Hessian fly resistance 6DS Tight H13 720 CFD0132 H13, Non-H13 ? SSR ABI CoDom
Insect damage resistance Hessian fly resistance 6DS 2.7 H13 808 GDM0036 H13, Non-H13 ? SSR ABI CoDom
Insect damage resistance Hessian fly resistance 4A from WGRC20, but can be on others H25 1039 GWM0397 H25, Non-H25 1 SSR ABI CoDom
Insect damage resistance Hessian fly resistance 1AS Hdicoccum 597 CFA2153 Hdicoccum, Non-Hdicoccum ? SSR ABI CoDom
Insect damage resistance Russian wheat aphid resistance 7DS 3.82 Dn1 922 GWM0111 Dn1, Non-Dn1 ? SSR ABI CoDom
Insect damage resistance Russian wheat aphid resistance 7DS 3.05 Dn2 922 GWM0111 Dn2, Non-Dn2 ? SSR ABI CoDom
Insect damage resistance Russian wheat aphid resistance 1DS 7.38 Dn4 919 GWM0106 Dn4, Non-Dn4 ? SSR ABI CoDom
Insect damage resistance Russian wheat aphid resistance 1DS Dn4 1016 GWM0337 Dn4, Non-Dn4 ? SSR ABI CoDom
Insect damage resistance Russian wheat aphid resistance 7DS 3.2 Dn5 922 GWM0111 Dn5, Non-Dn5 ? SSR ABI CoDom
Insect damage resistance Russian wheat aphid resistance 7DS 14.63 Dn6 900 GWM0044 Dn6, Non-Dn6 ? SSR ABI CoDom
Insect damage resistance Russian wheat aphid resistance 7DS 3.04 Dn6 922 GWM0111 Dn6, Non-Dn6 ? SSR ABI CoDom
Insect damage resistance Russian wheat aphid resistance 1RS Dn7 1129 IB267 Dn7, Non-Dn7 1 STS ABI Dom
Insect damage resistance Russian wheat aphid resistance 7DS 1.52 Dnx 922 GWM0111 Dnx, Non-Dnx ? SSR ABI CoDom
Insect damage resistance Wheat curl mite 1RS:1AL Alien Seg. Cmc3 1307 TSM0120 Cmc3(1RS:1AL), Non-Cmc3(1RS:1BL), Non-Cmc3(Non-1RS) 1 SSR ABI Dom
Insect damage resistance Wheat curl mite 6DS Cmc4 3884 CMC4 Cmc4, Non-Cmc4 ? STS ABI Dom
Quality Gluten strength 1AL Close Glu-A1 1388 UMN19 Glu-A1a(Ax1)/c(AxNull), Glu-A1b(Ax2*) 1 STS ABI CoDom
Quality Gluten strength 1AS 0 Glu-A3 864 Glu-A3a Glu-A3a, Non-Glu-A3a 1 STS ABILong Dom
Quality Gluten strength 1AS 0 Glu-A3 867 Glu-A3d Glu-A3d, Non-Glu-A3d 1 STS ABI Dom
Quality Gluten strength 1AS 0 Glu-A3 868 Glu-A3e Glu-A3e, Non-Glu-A3e 1 STS ABILong Dom
Quality Gluten strength 1BL 0 Glu-B1 2281 Bx7oe(LJ) Glu-B1al (Bx7oe), Non-Glu-B1al (Bx7oe) 1 STS ABI Dom
Quality Gluten strength 1BL 0 Glu-B1 568 BxMAR Glu-B1a (Bx7), Glu-B1al (Bx7oe), Glu-B1e (Bx20) 1 STS ABILong CoDom
Quality Gluten strength 1BL 0 Glu-B1 1126 HMWBx Glu-B1-Bx17, Non-Glu-B1-Bx17 1 STS ABILong CoDom
Quality Gluten strength 1BS 0 Glu-B3 873 Glu-B3a Glu-B3a, Non-Glu-B3a 1 STS ABILong Dom
Quality Gluten strength 1BS 0 Glu-B3 875 Glu-B3bef Glu-B3b or Glu-B3e or Glu-B3f 1 STS ABILong Dom
Quality Gluten strength 1BS 0 Glu-B3 876 Glu-B3c Glu-B3c, Non-Glu-B3c 1 STS ABI Dom
Quality Gluten strength 1DL Close Glu-D1 4235 Glu-D1-DX-KASP Glu-D1-Dx2, Glu-D1-Dx5 1 SNP KASP CoDom
Quality Gluten strength 1DL Close Glu-D1 1389 UMN25 Glu-D1-Dx2, Glu-D1-Dx5 1 STS ABI CoDom
Quality Gluten strength 1DL Close Glu-D1 1390 UMN26 Glu-D1-Dy10, Glu-D1-Dy12 1 STS ABI CoDom
Quality Grain protein content 6BS .1 Gpc-B1, HGPC/Yr36 1386 UHW89 HGPC/Yr36, Non-HGPC/Yr36 1 STS ABI CoDom
Quality Grain texture 5DS Tight Pina-D1 1237 PinA-D1 PinA-D1a=Soft, PinA-D1b=Hard 1 STS ABI Dom
Quality Grain texture 5DS Tight Pinb-D1 1238 PinB-D1 PinB-D1a=Soft, PinB-D1b=Hard 1 CAP ABI CoDom
Quality PPO activity 2AL 0 Ppo-A1 1242 PPO18 Ppo-A1-a/c/f/h, Ppo-A1-b, Ppo-A1-d/e 1 STS ABILong CoDom
Quality PPO activity 2DL 0 Ppo-D1 1241 PPO16 PPO-D1a/c 1 STS ABILong Dom
Quality PPO activity 2DL Tight Ppo-D1 1243 PPO29 Non-PPO-D1b 1 STS ABI Dom
Quality Waxy type 7AS & 4AL 0 Wx-A1 & Wx-B1 1399 Waxy-A1 Wx-A1a,Wx-B1a, Wx-A1a,Wx-B1b, Wx-A1b,Wx-B1a, Wx-A1b,Wx-B1b 1 STS ABI Mixed
Quality Waxy type 4AL 0 Wx-B1 1401 Waxy-B1-Dom Wx-B1a-Wild, Wx-B1b-Null 1 STS ABI Dom
Quality Waxy type 7DS 0 Wx-D1 1403 Waxy-D1 Wx-D1a/c, Wx-D1b (null-waxy) 1 STS Gel CoDom
Viral disease resistance BYDV resistance 7DL 0 Bdv2 569 BYAgi Bdv2, Non-Bdv2 1 STS ABI Dom
Viral disease resistance BYDV resistance 7DL:7St Alien Bdv2&3 4294 Bdv2&3 Bdv2&3, Non-Bdv2&3 1 SSR ABI CoDom
Viral disease resistance Soil-Borne Cereal Mosaic resistance 5DL Sbm1 4285 Sbm1-198467-KASP Sbm1, Non-Sbm1 1 SNP KASP CoDom
Viral disease resistance WSMV resistance 4Ai:4DS Alien Seg. Wsm1 2238 WSMV1-BG263898 Wsm1, Non-Wsm1 1 STS ABI Dom
Viral disease resistance WSMV resistance 3BS 1.6 distal Wsm2 104 BAR0102 Wsm2, Non-Wsm2 1 SSR ABI CoDom

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