GRM 2011: Practical application of markers for sorghum breeding
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GRM 2011: Practical application of markers for sorghum breeding
- 1. : ALTSORGHUM Project Practical Application of Markers Jurandir Magalhaes Maize and Sorghum - GCP General Research Meeting, Hyderabad, 21 – 25 September 2011 -
- 2. Physiological Mechanism Encoded by AltSB Al-induced organic acid release Al-citrate Citrate Citrate Citrate +Citrate Al3+ Citrate : Al3+ (Non-toxic) (phytotoxic) +Citrate Al3++Citrate Al3+ Citrate : Al3+ (Non-toxic) (phytotoxic) 0.0 1.0 2.0 3.0 4.0 0 50 100 150 RRG RRGRelativeExpression Al tolerance (RNRG) r=0.98 (P<0.001) 0.0 1.0 2.0 3.0 4.0 0 50 100 150 RRG RRGRelativeExpression Al tolerance (RNRG) r=0.98 (P<0.001) 24.6 Kb AltSB: ORF7 ATG TGA 1kb 8 9 AltSB: ORF7 ATG TGAATG TGA 1kb 8 9 Positonal Cloning/Comparative Genomics rice x sorghum AltSB: SbMATE
- 3. Molecular Breeding for Al Tolerance in Sorghum Weltzien et al. Sorghum diversity and adaptation to drought in West Africa Allele mining MABC
- 4. 1.3m 1.5m 1.4m 1.8m 2.0m 2.0m 1.3m 1.5m 1.4m 1.8m 2.0m 2.0m T A GA A C G GA A C G TA A T A TC G C G TA G T G GA G T A GA AT A GA A C G GA AC G GA A C G TA AC G TA A T A TC GT A TC G C G TA GC G TA G T G GA GT G GA G Association Mapping Linkage Mapping Allele MiningMABC Markers genetically linked to AltSB Functional loci or loci in LD with QTN(s) Nature Review Genetics 2:1-9 (2001)
- 5. G10-brazilian lines G9-Caudatum from Africa G7-Guinea from Western AfricaG7-Guinea from Western Africa G6- Guinea from Asia G5-Guinea from southern Africa G4-Dura from Asia andAfrica G3-Caudatum,bicolor from China G11-Kafir from southern Africa G8-transplanted sorghum from Chad and Cameron G1-Guine margaritiferum G2-USA lines G10-brazilian lines G9-Caudatum from Africa G7-Guinea from Western AfricaG7-Guinea from Western Africa G6- Guinea from Asia G5-Guinea from southern Africa G4-Dura from Asia andAfrica G3-Caudatum,bicolor from China G11-Kafir from southern Africa G8-transplanted sorghum from Chad and Cameron G1-Guine margaritiferum G2-USA lines Association Analysis of AltSB Fernanda Caniato
- 6. SbMATE_I2_6083pb Gene fragment 700pb C-specific allele 483pb A-specific allele 240pb (Gene Fragment) 700pb C-specific allele 483pb A C A-specific allele 240pb BR007 SC283 SC283 SC283 BR007 BR007 Het. Het. Gene fragment 700pb C-specific allele 483pb A-specific allele 240pb (Gene Fragment) 700pb C-specific allele 483pb A C A-specific allele 240pb BR007 SC283 SC283 SC283 BR007 BR007 Het. Het. Gene fragment 700pb C-specific allele 483pb A-specific allele 240pb (Gene Fragment) 700pb C-specific allele 483pb A C A-specific allele 240pb BR007 SC283 Gene fragment 700pb C-specific allele 483pb A-specific allele 240pb Gene fragment 700pbGene fragment 700pb C-specific allele 483pbC-specific allele 483pb A-specific allele 240pbA-specific allele 240pb (Gene Fragment) 700pb C-specific allele 483pb A C A-specific allele 240pb BR007 SC283 (Gene Fragment) 700pb C-specific allele 483pb A C A-specific allele 240pb (Gene Fragment) 700pb C-specific allele 483pb A C A C A-specific allele 240pb BR007 SC283 SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. independent amplicon (control) 700pb C G A-specific allele 254pb C-specific allele 254pb Gene fragment 700pb G-specific allele 254pb C-specific allele 254pb Gene fragment 700pb SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. BR007 SC283 independent amplicon (control) 700pb C G A-specific allele 254pb C-specific allele 254pb Gene fragment 700pb G-specific allele 254pb C-specific allele 254pb Gene fragment 700pb SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. BR007 SC283 independent amplicon (control) 700pb C G A-specific allele 254pb C-specific allele 254pb Gene fragment 700pb G-specific allele 254pb C-specific allele 254pb Gene fragment 700pb SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. independent amplicon (control) 700pb C G A-specific allele 254pb C-specific allele 254pb Gene fragment 700pb G-specific allele 254pb C-specific allele 254pb Gene fragment 700pb SC283 SC283 BR007 BR007 Het. Het. independent amplicon (control) 700pb C G A-specific allele 254pb C-specific allele 254pb Gene fragment 700pb G-specific allele 254pb C-specific allele 254pb Gene fragment 700pb independent amplicon (control) 700pb C G A-specific allele 254pb C-specific allele 254pb independent amplicon (control) 700pb C G A-specific allele 254pb C-specific allele 254pb independent amplicon (control) 700pb C G A-specific allele 254pb C-specific allele 254pb independent amplicon (control) 700pb C G C G A-specific allele 254pb C-specific allele 254pb Gene fragment 700pb G-specific allele 254pb C-specific allele 254pb Gene fragment 700pb Gene fragment 700pbGene fragment 700pb G-specific allele 254pbG-specific allele 254pb C-specific allele 254pbC-specific allele 254pb Gene fragment 700pbGene fragment 700pb SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. BR007 SC283 SBMATE_I2_6094pb independent amplicon (control) 700pb BR007 SC283 A G A-specific allele 361pb G-specific allele 361pb Gene fragment 700pb G-specific allele 361pb A-specific allele 361pb Gene fragment 700pb SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. independent amplicon (control) 700pb BR007 SC283 A G A-specific allele 361pb G-specific allele 361pb independent amplicon (control) 700pb BR007 SC283 A G A-specific allele 361pb G-specific allele 361pb BR007 SC283 A G A G A-specific allele 361pb G-specific allele 361pb Gene fragment 700pb G-specific allele 361pb A-specific allele 361pb Gene fragment 700pb SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. Gene fragment 700pbGene fragment 700pb G-specific allele 361pbG-specific allele 361pb A-specific allele 361pbA-specific allele 361pb Gene fragment 700pbGene fragment 700pb SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. SC283 SC283 BR007 BR007 Het. Het. SBMATE_I2_5985pb HETEROZIGOTES 0626050 HETEROZYGOTES BR007 0626050 Tag Markers for Allele Mining and MABC ARMS – PCR (Barbara Hufnagel) Gene fragment 615pb G-specific allele 496pb T-specific allele 166pb independent amplicon (control) 615pb G-specific allele 496pb T G T-specific allele 166pb BR007 SC283 SC283 SC283 BR007 BR007 Het. Het.
- 7. Q1: guineas WA Q2: caudatums (durras) Q3: Embrapa collection Q4: kafir from SA Q5: durras, bicolor/caudatums Q6: guineas SA and Asia RNRG5d(%) Subpopulations Al tolerance: RNRG (%) > 80% 30% < RNRG < 80% < 30% Freq. 0.05 0.15 0.80
- 8. 0 10000000 20000000 30000000 40000000 50000000 60000000 70000000 80000000 90000000 0 1 2 3 4 5 6 7 8 9 10 Physicalposition(bp) SorghumChromosomes Xcup010.0 Xtxp789.6 Xgap256 Xgap042 Xtxp20814.0 Xtxp32517.4 Xcup0619.6 Xtxp30225.0 SbAGF0829.3 Xcup7335.0 Xtxp35747.0 gpsb08953.8 Xtxp04365.8 Xtxp14967.8 Xtxp03277.0 Xtxp03792.4 mSbCIR28699.7 Xgap057109.0 Xtxp075116.0 Xtxp229120.0 Xgap036128.0 Xtxp522137.0 Xtxp61139.0 Xtxp319 Xcup62158.0 mSbCIR306176.1 Xtxp248179.6 Xcup53183.0 Xtxp46183.2 1 Xtxp960.0 Xtxp0634.3 Xtxp29719.0 mSbCIR22319.7 Xtxp5022.0 Xtxp30436.8 Xtxp00464.8 mSbCIR23866.3 Xtxp072 Xcup7474.0 Xtxp29892.9 SbAGB0397.7 Xcup63107.0 Xtxp445121.7 Xtxp056124.0 Xgap084140.7 Xtxp179143.0 Xtxp428153.2 Xtxp348157.0 Xtxp429158.7 Xcup26168.0 Xtxp296172.0 Xcup40190.0 Xtxp8193.8 ISEP0310199.5 2 Xtxp4560.0 Xcup112.0 Xcup616.0 Xtxp2666.1 ISEP01079.0 Xtxp49211.1 Xtxp49117.3 Xtxp48929.0 Xtxp21530.0 Xtxp48538.0 Xtxp50047.0 Xtxp46156.0 Xtxp03361.0 Xgap23662.8 Xtxp20568.0 Xtxp3171.1 mSbCIR27676.3 Xtxp12088.0 Xtxp231100.0 Xtxp218110.0 Xtxp114112.0 Xtxp439127.3 Xtxp441128.0 Xtxp446131.5 Xtxp442131.9 Xtxp447134.0 Xtxp038 Xtxp421138.0 Xtxp448138.7 Xtxp449140.0 Xtxp422141.0 Xtxp34147.8 Xtxp427158.0 Xcup14 Xtxp69160.0 Xtxp425160.1 Xtxp426164.2 3 Xtxp5060.0 Xtxp5046.1 Xgap12116.0 gpsb15120.0 Xcup0526.0 Xcup2336.0 mSbCIR32343.0 Xtxp343 Xtxp01273.0 Xgap01083.0 SbAGG0293.8 Xcup7196.0 Xtxp2598.8 Xtxp024107.0 Xtxp41108.0 Xtxp60120.7 Xtxp051128.5 Xtxp97150.0 Xtxp021153.0 Xcup20170.0 4 mSbCIR3293.0 Xtxp06514.4 Xtxp09423.0 mSbCIR24826.0 Xtxp03028.9 Xtxp30335.3 Xtxp22559.4 Xtxp01564.0 Xtxp02375.9 Xtxp26294.1 Xtxp13696.1 5 Xtxp5215.0 Xtxp00631.6 Xgap07248.3 Xcup3670.2 Xtxp14586.7 Xtxp26590.0 gpsb069104.7 Xtxp484116.0 Xtxp95125.7 Xtxp176134.1 Xtxp057141.0 Xtxp17149.3 Xcup37165.0 6 Xtxp0400.0 Xtxp364.0 gpsb14813.4 Xtxp41318.5 Xtxp48131.8 Xtxp15938.3 Xtxp31258.0 Xtxp22765.7 Xgap34272.0 Xtxp27874.1 Xcup5574.8 Xtxp09287.8 mSbCIR24689.8 Xcup7096.3 mSbCIR300101.8 Xcup19109.0 Xtxp295124.0 Xcup52126.2 SbAGB02130.8 Xtxp168132.0 7 Xtxp2730.0 Xtxp04732.1 Xtxp52050.0 mSbCIR24052.0 Xcup4753.4 gpsb06766.8 Xtxp29469.3 Xtxp35473.4 Xtxp01886.8 Xtxp32187.0 Xtxp10597.7 gpsb123100.0 Xgap34111.0 8 Xtxp28930.0 Xtxp35850.0 Xtxp45955.2 Xtxp41270.1 Xtxp28780.0 Xtxp41181.0 Xtxp23085.5 Xtxp06787.7 Xcup02104.0 Xtxp010108.4 Xtxp339135.0 Xgap032150.0 SbAGE03150.8 Xgap206160.0 Xgap015170.0 9 Xcup490.0 Xcup425.0 Xcup1310.0 Xtxp02053.0 Xtxp270 Xcup6755.0 mSbCIR28357.5 Xtxp217 Xtxp130(PepC)58.0 Xgap001*78.3 Xtxp320(phyB)82.5 mSbCIR26288.8 Xcup1693.6 Xcup43103.0 Xtxp141104.0 Xcup07115.2 10 Mbp 65 71 74 Kbp 300 - 400 100 - 200 400 - 500 100 - 200 400 - 500 700 - 800 800 - 900 600 - 700 800 - 900 900 - 1000 100 - 200 300 - 400 400 - 500 0 - 100 200 - 300 300 - 400 500 - 600 100 - 200 Xtxp38 STOP1 isu52 ctg29 S17 - AltSB - S73 - M181 Xcup14 DG1 EM1 - M96I2 M1762 - MBP Marker loci txp441 txp446 txp442 txp421 txp449 txp422 txp34 txp427 txp425 txp426 txp447 txp448 txp69 66 68 69 72 73 Marker Assisted Backross 1 – Foreground selection 2 – Flanking marker selection (linkage drag) 3 – Background selection
- 9. Available Resources Gene-specific markers (10) SNP markers: 1578 (Martha Hamblin) Illumina/KASPar
- 10. Products and Resources • Background SNP markers • Association pipeline for Al tolerance • Assessment of AltSB on acid soils (grain yield advantage)
- 11. Embrapa Maize and Sorghum Jurandir Magalhaes Robert E. Schaffert Fernanda Caniato Barbara Hufnagel Belkiss França Janaina Melo Claudia Guimarães Vera Alves Ubiraci Lana Moi Unversity Sam Gudu INRAN Soumana Souley ICRISAT – Mali: Eva Weltzien and Fred Rattunde, Willmar Leiser ICRISAT – Niamey: Bettina Haussmann and Tom Hash Cornell University/USDA-ARS Leon Kochian (USDA/CU) Jiping Liu (USDA/CU) Zhangjun Fei (USDA/CU) Stephen Kresovich (IGD/CU) Sharon Mitchell (IGD/CU) Martha Hamblin (IGD/CU) IRRI: Sigrid Heuer Sigrid Heuer (IRRI) Matthias Wissuwa (JIRCAS)
- 12. Funding The Generation Challenge Program The McKnight Foundation CCRP Project EMBRAPA USDA – NRI Competitive Grants Program U.S. National Science Foundation USDA-Agricultural Research Service