GRM 2011: Practical application of markers for sorghum breeding

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GRM 2011: Practical application of markers for sorghum breeding

  1. 1. : ALTSORGHUM ProjectPractical Application of MarkersJurandir MagalhaesMaize and Sorghum- GCP General Research Meeting, Hyderabad, 21 – 25 September 2011 -
  2. 2. Physiological Mechanism Encoded by AltSB Al-induced organic acid releaseAl-citrateCitrateCitrateCitrate+Citrate Al3+Citrate : Al3+(Non-toxic)(phytotoxic)+Citrate Al3++Citrate Al3+Citrate : Al3+(Non-toxic)(phytotoxic)0.01.02.03.04.00 50 100 150RRGRRGRelativeExpressionAl tolerance (RNRG)r=0.98(P<0.001)0.01.02.03.04.00 50 100 150RRGRRGRelativeExpressionAl tolerance (RNRG)r=0.98(P<0.001)24.6 KbAltSB: ORF7ATG TGA 1kb8 9AltSB: ORF7ATG TGAATG TGA 1kb8 9Positonal Cloning/ComparativeGenomics rice x sorghumAltSB: SbMATE
  3. 3. Molecular Breeding for Al Tolerance in SorghumWeltzien et al. Sorghum diversity and adaptation to drought in West AfricaAllele mining MABC
  4. 4. 1.3m1.5m1.4m1.8m2.0m2.0m1.3m1.5m1.4m1.8m2.0m2.0mT A GA AC G GA AC G TA AT A TC GC G TA GT G GA GT A GA AT A GA AC G GA AC G GA AC G TA AC G TA AT A TC GT A TC GC G TA GC G TA GT G GA GT G GA GAssociation MappingLinkage MappingAllele MiningMABCMarkers genetically linked toAltSBFunctional loci orloci in LD with QTN(s)Nature Review Genetics2:1-9 (2001)
  5. 5. G10-brazilian linesG9-Caudatum from AfricaG7-Guinea from Western AfricaG7-Guinea from Western AfricaG6- Guinea from AsiaG5-Guinea from southern AfricaG4-Dura from Asia andAfricaG3-Caudatum,bicolor from ChinaG11-Kafir from southern AfricaG8-transplanted sorghum from Chad and CameronG1-Guine margaritiferumG2-USA linesG10-brazilian linesG9-Caudatum from AfricaG7-Guinea from Western AfricaG7-Guinea from Western AfricaG6- Guinea from AsiaG5-Guinea from southern AfricaG4-Dura from Asia andAfricaG3-Caudatum,bicolor from ChinaG11-Kafir from southern AfricaG8-transplanted sorghum from Chad and CameronG1-Guine margaritiferumG2-USA linesAssociation Analysis of AltSBFernanda Caniato
  6. 6. SbMATE_I2_6083pbGene fragment 700pbC-specific allele 483pbA-specific allele 240pb(Gene Fragment) 700pbC-specific allele 483pbACA-specific allele 240pbBR007SC283SC283SC283BR007BR007Het.Het.Gene fragment 700pbC-specific allele 483pbA-specific allele 240pb(Gene Fragment) 700pbC-specific allele 483pbACA-specific allele 240pbBR007SC283SC283SC283BR007BR007Het.Het.Gene fragment 700pbC-specific allele 483pbA-specific allele 240pb(Gene Fragment) 700pbC-specific allele 483pbACA-specific allele 240pbBR007SC283Gene fragment 700pbC-specific allele 483pbA-specific allele 240pbGene fragment 700pbGene fragment 700pbC-specific allele 483pbC-specific allele 483pbA-specific allele 240pbA-specific allele 240pb(Gene Fragment) 700pbC-specific allele 483pbACA-specific allele 240pbBR007SC283(Gene Fragment) 700pbC-specific allele 483pbACA-specific allele 240pb(Gene Fragment) 700pbC-specific allele 483pbACACA-specific allele 240pbBR007SC283SC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.independent amplicon (control) 700pbCGA-specific allele 254pbC-specific allele 254pbGene fragment 700pbG-specific allele 254pbC-specific allele 254pbGene fragment 700pbSC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.BR007SC283independent amplicon (control) 700pbCGA-specific allele 254pbC-specific allele 254pbGene fragment 700pbG-specific allele 254pbC-specific allele 254pbGene fragment 700pbSC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.BR007SC283independent amplicon (control) 700pbCGA-specific allele 254pbC-specific allele 254pbGene fragment 700pbG-specific allele 254pbC-specific allele 254pbGene fragment 700pbSC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.independent amplicon (control) 700pbCGA-specific allele 254pbC-specific allele 254pbGene fragment 700pbG-specific allele 254pbC-specific allele 254pbGene fragment 700pbSC283SC283BR007BR007Het.Het.independent amplicon (control) 700pbCGA-specific allele 254pbC-specific allele 254pbGene fragment 700pbG-specific allele 254pbC-specific allele 254pbGene fragment 700pbindependent amplicon (control) 700pbCGA-specific allele 254pbC-specific allele 254pbindependent amplicon (control) 700pbCGA-specific allele 254pbC-specific allele 254pbindependent amplicon (control) 700pbCGA-specific allele 254pbC-specific allele 254pbindependent amplicon (control) 700pbCGCGA-specific allele 254pbC-specific allele 254pbGene fragment 700pbG-specific allele 254pbC-specific allele 254pbGene fragment 700pbGene fragment 700pbGene fragment 700pbG-specific allele 254pbG-specific allele 254pbC-specific allele 254pbC-specific allele 254pbGene fragment 700pbGene fragment 700pbSC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.BR007SC283SBMATE_I2_6094pbindependent amplicon (control) 700pbBR007SC283 AGA-specific allele 361pbG-specific allele 361pbGene fragment 700pbG-specific allele 361pbA-specific allele 361pbGene fragment 700pbSC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.independent amplicon (control) 700pbBR007SC283 AGA-specific allele 361pbG-specific allele 361pbindependent amplicon (control) 700pbBR007SC283 AGA-specific allele 361pbG-specific allele 361pbBR007SC283 AGAGA-specific allele 361pbG-specific allele 361pbGene fragment 700pbG-specific allele 361pbA-specific allele 361pbGene fragment 700pbSC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.Gene fragment 700pbGene fragment 700pbG-specific allele 361pbG-specific allele 361pbA-specific allele 361pbA-specific allele 361pbGene fragment 700pbGene fragment 700pbSC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.SC283SC283BR007BR007Het.Het.SBMATE_I2_5985pbHETEROZIGOTES0626050HETEROZYGOTESBR0070626050Tag Markers for Allele Mining and MABCARMS – PCR (Barbara Hufnagel)Gene fragment 615pbG-specific allele 496pbT-specific allele 166pbindependent amplicon (control) 615pbG-specific allele 496pbTGT-specific allele 166pbBR007SC283SC283SC283BR007BR007Het.Het.
  7. 7. Q1: guineas WAQ2: caudatums (durras)Q3: Embrapa collectionQ4: kafir from SAQ5: durras, bicolor/caudatumsQ6: guineas SA and AsiaRNRG5d(%)SubpopulationsAl tolerance: RNRG (%)> 80%30% < RNRG < 80%< 30%Freq.0.050.150.80
  8. 8. 01000000020000000300000004000000050000000600000007000000080000000900000000 1 2 3 4 5 6 7 8 9 10Physicalposition(bp) SorghumChromosomesXcup010.0Xtxp789.6Xgap256 Xgap042Xtxp20814.0Xtxp32517.4Xcup0619.6Xtxp30225.0SbAGF0829.3Xcup7335.0Xtxp35747.0gpsb08953.8Xtxp04365.8Xtxp14967.8Xtxp03277.0Xtxp03792.4mSbCIR28699.7Xgap057109.0Xtxp075116.0Xtxp229120.0Xgap036128.0Xtxp522137.0Xtxp61139.0Xtxp319 Xcup62158.0mSbCIR306176.1Xtxp248179.6Xcup53183.0Xtxp46183.21Xtxp960.0Xtxp0634.3Xtxp29719.0mSbCIR22319.7Xtxp5022.0Xtxp30436.8Xtxp00464.8mSbCIR23866.3Xtxp072 Xcup7474.0Xtxp29892.9SbAGB0397.7Xcup63107.0Xtxp445121.7Xtxp056124.0Xgap084140.7Xtxp179143.0Xtxp428153.2Xtxp348157.0Xtxp429158.7Xcup26168.0Xtxp296172.0Xcup40190.0Xtxp8193.8ISEP0310199.52Xtxp4560.0Xcup112.0Xcup616.0Xtxp2666.1ISEP01079.0Xtxp49211.1Xtxp49117.3Xtxp48929.0Xtxp21530.0Xtxp48538.0Xtxp50047.0Xtxp46156.0Xtxp03361.0Xgap23662.8Xtxp20568.0Xtxp3171.1mSbCIR27676.3Xtxp12088.0Xtxp231100.0Xtxp218110.0Xtxp114112.0Xtxp439127.3Xtxp441128.0Xtxp446131.5Xtxp442131.9Xtxp447134.0Xtxp038 Xtxp421138.0Xtxp448138.7Xtxp449140.0Xtxp422141.0Xtxp34147.8Xtxp427158.0Xcup14 Xtxp69160.0Xtxp425160.1Xtxp426164.23Xtxp5060.0Xtxp5046.1Xgap12116.0gpsb15120.0Xcup0526.0Xcup2336.0mSbCIR32343.0Xtxp343 Xtxp01273.0Xgap01083.0SbAGG0293.8Xcup7196.0Xtxp2598.8Xtxp024107.0Xtxp41108.0Xtxp60120.7Xtxp051128.5Xtxp97150.0Xtxp021153.0Xcup20170.04mSbCIR3293.0Xtxp06514.4Xtxp09423.0mSbCIR24826.0Xtxp03028.9Xtxp30335.3Xtxp22559.4Xtxp01564.0Xtxp02375.9Xtxp26294.1Xtxp13696.15Xtxp5215.0Xtxp00631.6Xgap07248.3Xcup3670.2Xtxp14586.7Xtxp26590.0gpsb069104.7Xtxp484116.0Xtxp95125.7Xtxp176134.1Xtxp057141.0Xtxp17149.3Xcup37165.06Xtxp0400.0Xtxp364.0gpsb14813.4Xtxp41318.5Xtxp48131.8Xtxp15938.3Xtxp31258.0Xtxp22765.7Xgap34272.0Xtxp27874.1Xcup5574.8Xtxp09287.8mSbCIR24689.8Xcup7096.3mSbCIR300101.8Xcup19109.0Xtxp295124.0Xcup52126.2SbAGB02130.8Xtxp168132.07Xtxp2730.0Xtxp04732.1Xtxp52050.0mSbCIR24052.0Xcup4753.4gpsb06766.8Xtxp29469.3Xtxp35473.4Xtxp01886.8Xtxp32187.0Xtxp10597.7gpsb123100.0Xgap34111.08Xtxp28930.0Xtxp35850.0Xtxp45955.2Xtxp41270.1Xtxp28780.0Xtxp41181.0Xtxp23085.5Xtxp06787.7Xcup02104.0Xtxp010108.4Xtxp339135.0Xgap032150.0SbAGE03150.8Xgap206160.0Xgap015170.09Xcup490.0Xcup425.0Xcup1310.0Xtxp02053.0Xtxp270 Xcup6755.0mSbCIR28357.5Xtxp217 Xtxp130(PepC)58.0Xgap001*78.3Xtxp320(phyB)82.5mSbCIR26288.8Xcup1693.6Xcup43103.0Xtxp141104.0Xcup07115.210Mbp 65 71 74Kbp 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 - 200Xtxp38 STOP1 isu52 ctg29 S17 - AltSB - S73 - M181 Xcup14 DG1 EM1 - M96I2 M1762 - MBPMarker loci txp441 txp446 txp442 txp421 txp449 txp422 txp34 txp427 txp425 txp426txp447 txp448 txp6966 68 69 72 73Marker Assisted Backross1 – Foreground selection2 – Flanking marker selection(linkage drag)3 – Background selection
  9. 9. Available ResourcesGene-specific markers (10)SNP markers: 1578(Martha Hamblin)Illumina/KASPar
  10. 10. Products and Resources• Background SNP markers• Association pipeline for Al tolerance• Assessment of AltSB on acid soils (grain yield advantage)
  11. 11. Embrapa Maize and SorghumJurandir MagalhaesRobert E. SchaffertFernanda CaniatoBarbara HufnagelBelkiss FrançaJanaina MeloClaudia GuimarãesVera AlvesUbiraci LanaMoi UnversitySam GuduINRANSoumana SouleyICRISAT – Mali: Eva Weltzien andFred Rattunde, Willmar LeiserICRISAT – Niamey: BettinaHaussmann and Tom HashCornell University/USDA-ARSLeon 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 HeuerSigrid Heuer (IRRI)Matthias Wissuwa (JIRCAS)
  12. 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

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