GRM 2011: Practical application of markers for sorghum breeding

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  • 1. : ALTSORGHUM ProjectPractical Application of MarkersJurandir MagalhaesMaize and Sorghum- GCP General Research Meeting, Hyderabad, 21 – 25 September 2011 -
  • 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. Molecular Breeding for Al Tolerance in SorghumWeltzien et al. Sorghum diversity and adaptation to drought in West AfricaAllele mining MABC
  • 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. 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. 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. 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. 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. Available ResourcesGene-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 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. 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