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 Drought tolerance 1RS Alien Seg. 1RS Rye translocation 1307 TSM0120 1RS:1AL, 1RS:1BL, or Non-1RS 1 SSR ABI Dom
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 Linked Al 4DL 1736 WMC0331 Al 4DL 1 SSR ABI CoDom
Abiotic stress Aluminum tolerance 4DL 0 ALMT1 Promoter 6 ALMT1-UPS4 Al Tolerant 1 STS ABIVLong CoDom
Anatomy and morphology related Height 4BS 0 Rht-B1 9764 Rht-B1a-160-KASP Rht-B1a+160(Slightly reduced height) 1 Indel KASP CoDom
Anatomy and morphology related Height 4BS 0 Rht-B1 9765 Rht-B1a-197-KASP Rht-B1a+197(Slightly reduced height) 1 Indel KASP CoDom
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 3BS Close Rht5 104 BAR0102 Rht5 1 SSR ABI Mixed
Anatomy and morphology related Height 2DS 0.6 Rht8 980 GWM0261 Rht8 1 SSR ABI CoDom
Fungal disease resistance Fusarium head blight resistance 2B FHB 2B 990 GWM0276 FHB 2B-Qfhs.umc SSR ABI
Fungal disease resistance Fusarium head blight resistance 3AS FHB 3AS 361 BAR0359 FHB 3AS SSR ABI
Fungal disease resistance Fusarium head blight resistance 3AS FHB 3AS 889 GWM0005 FHB 3AS SSR ABI
Fungal disease resistance Fusarium head blight resistance 3BS 0 FHB 3BS/Fhb1 9661 Fhb1-TaHRC-KASP FHB 3BS/Fhb1 1 Indel 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 Leaf rust resistance 5DL Close Lr1 9658 Lr1_pTAG621 Lr1 1 STS ABI Dom
Fungal disease resistance Leaf rust resistance 5DL Close Lr1 9659 Lr1-RGA567-5 Lr1 1 STS ABI Dom
Fungal disease resistance Leaf rust resistance 2BS Close Lr16 4400 Lr16-RGA-266585 Lr16 3 STS ABI Dom
Fungal disease resistance Leaf rust resistance 7EL:7DL Alien Seg. Lr19 1226 Lr19-130 Lr19 2 STS ABI Dom
Fungal disease resistance Leaf rust resistance 1DS 0 Lr21 1227 Lr21-214 Lr21 1 STS ABI CoDom
Fungal disease resistance Leaf rust resistance 1DS 0 Lr21 4238 Lr21-GQ504819-1346-KASP Lr21 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 3Ag:3DL Alien Seg. Lr24/Sr24 1270 Sr24#12 Lr24/Sr24 1 STS ABI Dom
Fungal disease resistance Leaf rust resistance 7DS .4 Lr34/Yr18 765 csLV34-LR34 Lr34 1 STS ABI CoDom
Fungal disease resistance Leaf rust resistance 7DS 0 Lr34/Yr18 4241 Lr34Exon11-KASP Lr34(exon11) 1 Indel KASP CoDom
Fungal disease resistance Leaf rust resistance 7DS 0 Lr34/Yr18 4250 Lr34JagExon22-KASP Lr34-JagMut(exon22) 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 2NS:2AS Alien Seg. Lr37/Sr38/Yr17 9715 Lr37-URIC-LN2 Lr37/Sr38/Yr17 1 STS ABI CoDom
Fungal disease resistance Leaf rust resistance 2NS:2AS Alien Seg. Lr37/Sr38/Yr17 1393 Lr37-VENTRIUP-LN2 Lr37/Sr38/Yr17 2 STS ABI Dom
Fungal disease resistance Leaf rust resistance 2NS:2AS Alien Seg. Lr37/Sr38/Yr17 4253 Lr37-Yr17-Sr38_GBG-KASP Lr37 2 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 2DS .9 Lr39/Lr41 807 GDM0035PT Lr39/Lr41 1=specific cross only SSR ABI CoDom
Fungal disease resistance Leaf rust resistance 2DS Linked Lr39/Lr41 967 GWM0210 Lr39/Lr41 1=specific cross only SSR ABI CoDom
Fungal disease resistance Leaf rust resistance 1DS Close Lr42 640 CFD0015 Lr42 1 SSR ABI CoDom
Fungal disease resistance Leaf rust resistance 1DS 0.6 proximal Lr42 4288 Lr42-113325_01-KASP Lr42 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 1DS Lr42 9649 Lr42-pB12-KASP Lr42 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 1DS 0.6 proximal Lr42 4289 Lr42-TC425250_08-KASP Lr42 3 SNP KASP
Fungal disease resistance Leaf rust resistance 1BL Close Lr46 4256 Lr46-Yr29_JF2-2-KASP Lr46/Yr29 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 7S:7A Alien Seg. Lr47 9749 Lr47-1-KASP Lr47 New SNP KASP CoDom
Fungal disease resistance Leaf rust resistance T5DL·5DS-5MgS(0.95) Alien Seg. Lr57/Yr40 2258 Lr57-Yr40-CAPS16 Lr57/Yr40 1 CAP ABI Mixed
Fungal disease resistance Leaf rust resistance 4DL Lr67 9650 Lr67-SNP1-TM4-KASP Lr67 2 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 4DL Lr67 9651 Lr67-SNP2-TM10-KASP Lr67 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 7BL Linked Lr68 9750 Lr68-2-KASP Lr68 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 7BL 1.2 Lr68 4175 Lr68-csGS Lr68 New STS ABI Dom
Fungal disease resistance Leaf rust resistance 3B Lr77 9725 Lr77-3B-12260-KASP Lr77 1 SNP KASP CoDom
Fungal disease resistance Leaf rust resistance 6BL Lr9 4259 Lr9a-KASP Lr9 1 SNP KASP CoDom
Fungal disease resistance Stem rust resistance 3BS 0 Sr2 3859 csSr2-CAP Sr2 1 CAP ABI Mixed
Fungal disease resistance Stem rust resistance 7AL Alien Seg. Sr22 4415 Sr22_A-KASP Sr22 1 SNP KASP CoDom
Fungal disease resistance Stem rust resistance 7AL Alien Seg. Sr22 2328 Sr22-cssu22 Sr22 1 STS ABI CoDom
Fungal disease resistance Stem rust resistance 6AL Sr26 4413 Sr26_A-KASP Sr26 1 STS KASP CoDom
Fungal disease resistance Leaf rust resistance 1RS:1BL Sr31/Lr26/Yr9 9652 Sr31/Lr26/Yr9-iag95 Sr31/Lr26/Yr9 ? STS ABILong Mixed
Fungal disease resistance Stem rust resistance 2S.2BS Alien Seg. Sr32,Sr39,Sr40 3963 Sr39-Sr40Res Sr32, Sr39, Sr40 1-best for Sr40 STS ABI CoDom
Fungal disease resistance Stem rust resistance 3Am:3AL Alien Seg. Sr35 9669 Sr35-856-KASP Sr35 1 SNP KASP Dom
Fungal disease resistance Stem rust resistance 2BS Alien Seg. Sr36/Pm6 4274 Sr36-Pm6_8085-KASP Sr36, Non-Sr36 1? SNP KASP CoDom
Fungal disease resistance Stem rust resistance 2BS Alien Seg. Sr36/Pm6 9768 Sr36-Pm6-8068-KASP Sr36/Pm6 1 SNP KASP CoDom
Fungal disease resistance Stem rust resistance 2S.2BS Alien Seg. Sr39/Lr35 3856 Sr39-rwgs27 Sr39 1 STS ABILong CoDom
Fungal disease resistance Stem rust resistance 2S.2BS Alien Seg. Sr39/Lr35 4279 Sr39-Seg3-SNP3-KASP Sr39, Non-Sr39 1 SNP KASP Mixed
Fungal disease resistance Stem rust resistance 2S.2BS Alien Seg. Sr40 2289 Sr39#22Dom Sr39, Sr40 1=Sr40?, 3=Sr39 STS ABILong Dom
Fungal disease resistance Stem rust resistance 2S.2BS Alien Seg. Sr40 4281 Sr40-Seg2-SNP1-KASP Sr40, Non-Sr40 1 SNP KASP Mixed
Fungal disease resistance Stem rust resistance 2DS Mod. Sr46 967 GWM0210 Sr46 1=specific cross only SSR ABI CoDom
Fungal disease resistance Tan spot 5BL 0 Tsn1 9779 Tsn1-KASP tsn1(InsenResRes) 1 SNP KASP Dom
Fungal disease resistance Tan spot 5B .2 Tsn1 1382 Tsn1-Xfcp394 Tsn1-DomSusceptible, tsn1(RecessiveResistant) 1 STS ABI CoDom
Fungal disease resistance Tan spot 5B Close Tsn1 9738 Tsn1-Xfcp620 Tsn1-DomSusceptible 1 STS ABI CoDom
Fungal disease resistance Tan spot 5B Close Tsn1 9739 Tsn1-Xfcp623(Tsn1) tsn1(RecessiveResistant) 1 STS ABI Dom
Fungal disease resistance Stripe rust resistance 1BS Close Yr15 4385 Yr15-R5-KASP Yr15 1 SNP KASP CoDom
Fungal disease resistance Stripe rust resistance 6BS 0 Yr36 9778 Yr36-WKS-KASP HGPC/Yr36 1 Duplication KASP Dom
Fungal disease resistance Stripe rust resistance 2BL Close Yr5 9728 Yr5-2BL-4096-KASP Non-Yr5 1, must also use 6121 SNP KASP Mixed
Fungal disease resistance Stripe rust resistance 2BL Close Yr5 9727 Yr5-2BL-6121-KASP Yr5 1, must also use 4096 SNP KASP CoDom
Growth and development Pre-harvest sprouting 3AS MFT-A1 9751 PHS-MFT-A1-1617R-KASP PHS-res 1 SNP KASP CoDom
Growth and development Pre-harvest sprouting 3AS MFT-A1 9752 PHS-MFT-A1-721J-KASP PHS-res New SNP KASP CoDom
Growth and development Pre-harvest sprouting 3AS 0 PHS 3AS/PHS1 9665 MFT-PHS3A-Promoter_222-KASP PHS3A 1 SNP KASP CoDom
Growth and development Pre-harvest sprouting 3AS 0 PHS 3AS/PHS1 9731 PHS1-3AS-666-KASP PHS1 1 SNP KASP CoDom
Growth and development Pre-harvest sprouting 3AS 0 PHS 3AS/PHS1 4278 PHS1-646-SNP1-KASP PHS 3AS 1 SNP KASP CoDom
Growth and development Pre-harvest sprouting 4A Close PHS 4AL 4301 PHS-4A-34562_92-KASP PHS 4AL 1 SNP KASP CoDom
Growth and development Pre-harvest sprouting 4AL PHS 4AL 9662 PHS-4A-3743-9-KASP PHS 4AL 1 SNP KASP CoDom
Growth and development Vernalization/Photoperiod 2AL Ppd-A1 9757 Ppd-A1-GS100-1027-KASP Ppd-A1a, b New Indel KASP CoDom
Growth and development Vernalization/Photoperiod 2AL Ppd-A1 9758 Ppd-A1-GS105-1117-KASP Ppd-A1a, b ? Indel KASP CoDom
Growth and development Vernalization/Photoperiod 2BS 0 Ppd-B1 9670 Ppd-B1-J1-KASP Ppd-B1-Sensitive, Ppd-B1-Insensitive 1, need j3 also SNP KASP CoDom
Growth and development Vernalization/Photoperiod 2BS 0 Ppd-B1 9672 Ppd-B1-J3-KASP Ppd-B1-Insensitive 3, need J1 also SNP KASP Dom
Growth and development Vernalization/Photoperiod 2DS Close Ppd-D1 1240 PPD-D1 PPD-D1a-insensitive & b-sensitive 1 STS ABI CoDom
Growth and development Vernalization/Photoperiod 2DS Ppd-D1 9760 Ppd-D1-D002-KASP Ppd-D1a, b 1 Indel 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 9771 Vrn-A1-9K1-KASP Vrn-A1(spring) 1 SNP KASP CoDom
Growth and development Vernalization 5AL 0 Vrn-A1 9777 Vrn-A1-E4-vern-KASP vrn-A1a-Early(shortvern), vrn-A1b-Late(longvern) 2 SNP KASP CoDom
Growth and development Vernalization 5AL 0 Vrn-A1 9772 Vrn-A1-E7-FT-KASP vrn-A1a-Early(shortvern), vrn-A1b-Late(longvern) 1 SNP KASP CoDom
Growth and development Vernalization 5AL 0 Vrn-A1 9773 Vrn-A1b-Marq-KASP Vrn-A1b(Marquis-winter), Vrn-A1a(spring) New SNP KASP CoDom
Growth and development Vernalization 5BL 0 Vrn-B1 9774 Vrn-B1_A-KASP Vrn-B1a or b(spring) 1 SNP KASP Dom
Growth and development Vernalization 5BL 0 Vrn-B1 9775 Vrn-B1_B-KASP Vrn-B1b(spring) 1 SNP KASP CoDom
Growth and development Vernalization 5DL 0 Vrn-D1 9776 Vrn-D1a_A-KASP Vrn-D1a(spring) 1 SNP KASP Dom
Growth and development Vernalization 7D 0 Vrn-D3 4387 Vrn-D3-KASP Vrn-D3a-Early, Vrn-D3b-Late 1 SNP KASP CoDom
Insect damage resistance Wheat curl mite 6DS Close Cmc(TAM112) 4428 Cmc(TAM112)-10804-KASP Cmc(TAM112) SNP KASP CoDom
Insect damage resistance Wheat curl mite 6DS Close Cmc(TAM112) 4425 Cmc(TAM112)-7108-KASP Cmc(TAM112) SNP KASP CoDom
Insect damage resistance Wheat curl mite 6DS Cmc4 3884 CMC4 Cmc4 ? STS ABI Dom
Insect damage resistance Wheat curl mite 6DS Close Cmc4 2237 WMS0904 Cmc4 2 SSR ABI Mixed
Insect damage resistance Russian wheat aphid resistance 1RS Dn7 1129 IB267 Dn7 1 STS ABI Dom
Insect damage resistance Greenbug resistance 7DL Close Gb3 4424 GB3-15318-KASP Gb3 1 SNP KASP CoDom
Insect damage resistance Greenbug resistance 7DL Close Gb3 4422 GB3-18260-KASP Gb3 1 SNP KASP CoDom
Insect damage resistance Hessian fly resistance 1AS 0.3 H09 265 BAR0263 H09, Non-H09 ? SSR ABI CoDom
Insect damage resistance Hessian fly resistance 1AS 0.5 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 Sawfly resistance/Solid Stems 3DL Sawfly/Solid Stem 1113 GWM0645 Sawfly/Solid Stem 2 SSR ABI CoDom
Insect damage resistance Sawfly resistance/Solid Stems 3BL <2 Sawfly/Solid Stem 9767 Sawfly-SolidStem-BS73411-KASP Sawfly/Solid Stem 1 SNP KASP CoDom
Quality Grain length, grain weight 7AL Close GlGw 4430 GlGw-7AL-6693 GlGwLow, GlGwHigh STS ABI CoDom
Quality Grain length, grain weight 7AL Close GlGw 9733 GlGw-7AL-IWB13913-KASP GlGwHigh 1 SNP KASP CoDom
Quality Gluten strength 1AL 0 Glu-A1 9742 Glu-Ax1-x2*-KASP Glu-Ax1/Ax2*, Glu-A1-Ax-null 1 SNP KASP CoDom
Quality Gluten strength 1AL 0 Glu-A1 9743 Glu-Ax2-KASP Glu-A1-Ax2*, Glu-Ax1/Ax-null 1 Indel KASP CoDom
Quality Gluten strength 1AL Close Glu-A1 1388 UMN19 Glu-A1-Ax2* or Ax1/Ax-null 1 STS ABI CoDom
Quality Gluten strength 1BL Close Glu-B1 4429 Bx7oe-CSU-KASP Glu-B1al (Bx7oe) 1 Indel? KASP CoDom
Quality Gluten strength 1BL 0 Glu-B1 2281 Bx7oe(LJ) Glu-B1al (Bx7oe) 1 STS ABI Mixed
Quality Gluten strength 1BL 0 Glu-B1 568 BxMAR Glu-B1a (Bx7) & Glu-B1e (Bx20) 1 STS ABILong CoDom
Quality Gluten strength 1BL Glu-B1 9745 Glu-B1al-Bx7oe-866-KASP Glu-B1al(Bx7oe) 1 SNP KASP CoDom
Quality Gluten strength 1BL 0 Glu-B1 883 Glu-By8 Glu-By8 1 STS ABI Dom
Quality Gluten strength 1BL 0 Glu-B1 1126 HMWBx Glu-B1-Bx17 1 STS ABILong CoDom
Quality Gluten strength 1BL Glu-B1-1 9744 Glu-B1-1f-Bx13-1510-KASP Glu-B1-1f(Bx13) 1 SNP KASP CoDom
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 or Glu-D1-Dx5 1 STS ABI CoDom
Quality Gluten strength 1DL Close Glu-D1 1390 UMN26 Glu-D1-Dy12 or Glu-D1-Dy10 1 STS ABI CoDom
Quality Grain protein content 6BS Gpc-B1 9747 Gpc-B1-DUP-KASP HGPC/Yr36 1 SNP KASP CoDom
Quality Grain protein content 6BS .1 Gpc-B1, HGPC/Yr36 1386 UHW89 HGPC/Yr36 1 STS ABI CoDom
Quality TGW, yeild 7DS Gs-D1 9748 TGW-GS-D1-KASP TGW-GS-D1a(High TGW) 1 SNP KASP Mixed?
Quality Grain width, grain weight 6AL Close GwGwd 9732 GwGwidth-6AL-738-KASP GwGwd(High) 1 SNP KASP CoDom
Quality Grain number 7A Moc-A1 9746 Gn-Moc-A1-2433-KASP High grain number 1 SNP KASP CoDom
Quality Grain texture 5DS 0 Pina-D1 9753 Pina-D1-KASP Pina-D1a(soft), Pina-D1b(hard) 1 SNP KASP CoDom
Quality Grain texture 5DS 0 Pina-D1 9754 Pinb-D1-KASP Pinb-D1a, Pinb-D1b New SNP KASP CoDom
Quality Grain texture 7BL 0 Pinb2-B2 9755 Pinb2-B2-v2-3-KASP Pinb-B2a(softer) 1 Indel KASP CoDom
Quality PPO activity 2AL 0 Ppo-A1 9762 Ppo-A1-KASP Ppo-A1a, b ? SNP KASP CoDom
Quality PPO activity 2AL 0 Ppo-A1 1242 PPO18 Ppo-A1a, b, or d/e 1 STS ABILong CoDom
Quality PPO activity 2DL 0 Ppo-D1 9763 Ppo-D1-KASP Ppo-D1a, b New SNP KASP CoDom
Quality Grain color 3A 0 R-A1 4307 Tamyb10-A1ab-KASP R-A1a, b 2 SNP KASP CoDom
Quality Grain color 3A 0 R-A1 4308 Tamyb10-A1aNor17-KASP R-A1aNor17 2 Indel KASP CoDom
Quality Grain color 3B 0 R-B1 4309 Tamyb10-B1ab-KASP R-B1a, b 2 Indel KASP CoDom
Quality Grain color 3D 0 R-D1 4310 Tamyb10-D1ab-KASP R-D1a, b ? Indel KASP Dom?
Quality TGW, yeild 2B Sus2-2B 9769 TGW-Sus2-2B-KASP High TGW 1 SNP KASP CoDom
Quality TGW, yeild 3AL Close TGW-3AL 9737 TGW6-A1-3AL-KASP HighTGW-3AL 1 SNP KASP CoDom
Quality TGW, yeild 6D? TGW6 9770 TGW6-KASP TGW6-A1a(High TGW) 1 SNP KASP CoDom
Quality Waxy type 7AS & 4AL 0 Wx-A1 & Wx-B1 1399 Waxy-A1 Wx-A1a or b, Wx-B1a or b 1 STS ABI Mixed
Quality Waxy type 4AL 0 Wx-B1 9780 Wx-B1-KASP Wx-B1a(Waxy), b 1 Indel KASP Dom
Quality Waxy type 7DS 0 Wx-D1 2241 Wx-D1-2 Wx-D1a or b 1 STS ABILong CoDom
Viral disease resistance BYDV resistance 7DL Alien Seg. Bdv2 569 BYAgi Bdv2 1 STS ABI Dom
Viral disease resistance BYDV resistance 7DL:7St Alien Seg. Bdv2&3 4294 Bdv2&3 Bdv2&3 SSR ABI Mixed
Viral disease resistance Soil-Borne Cereal Mosaic resistance 5DL Close Sbm1 4285 Sbm1-198467-KASP Sbm1 1 SNP KASP CoDom
Viral disease resistance WSMV resistance 4Ai:4DS Alien Seg. Wsm1 2238 WSMV1-BG263898 Wsm1 1 STS ABI Mixed
Viral disease resistance WSMV resistance 3BS 4.5 distal Wsm2 89 BAR0087 Wsm2 2 SSR ABI Mixed
Viral disease resistance WSMV resistance 3BS 1.6 proximal Wsm2 104 BAR0102 Wsm2 1 SSR ABI Mixed
Viral disease resistance WSMV resistance 3BS close Wsm2 4305 Wsm2-6660-KASP Wsm2 2 SNP KASP CoDom
Viral disease resistance WSMV resistance 3BS close Wsm2 4306 Wsm2-80940-KASP Wsm2 2 SNP KASP CoDom

Copyright (c) 2017 hwwgenotyping.ksu.edu. All rights reserved.